Unmixing Optical Signals from Undersampled Volumetric Measurements by Filtering the Pixel Latent Variables (2312.05357v3)
Abstract: The development of signal unmixing algorithms is essential for leveraging multimodal datasets acquired through a wide array of scientific imaging technologies, including hyperspectral or time-resolved acquisitions. In experimental physics, enhancing the spatio-temporal resolution or expanding the number of detection channels often leads to diminished sampling rate and signal-to-noise ratio (SNR), significantly affecting the efficacy of signal unmixing algorithms. We propose Latent Unmixing, a new approach which applies band-pass filters to the latent space of a multi-dimensional convolutional neural network to disentangle overlapping signal components. It enables better isolation and quantification of individual signal contributions, especially in the context of undersampled distributions. Using multi-dimensional convolution kernels to process all dimensions simultaneously enhances the network's ability to extract information from adjacent pixels, and time- or spectral-bins. This approach enables more effective separation of components in cases where individual pixels do not provide clear, well-resolved information. We showcase the method's practical use in experimental physics through two test cases that highlight the versatility of our approach: fluorescence lifetime microscopy and mode decomposition in optical fibers. The latent unmixing method extracts valuable information from complex signals that cannot be resolved by standard methods. It opens new possibilities in optics and photonics for multichannel separations at an increased sampling rate.
- Deep learning-based real-time mode decomposition for multimode fibers. IEEE Journal of Selected Topics in Quantum Electronics, 26(4):1–6, 2020.
- Comparing 3d, 2.5 d, and 2d approaches to brain image auto-segmentation. Bioengineering, 10(2):181, 2023.
- Maximum likelihood method for the analysis of time-resolved fluorescence decay curves. European biophysics journal, 20:247–262, 1991.
- Wolfgang Becker. Fluorescence lifetime imaging–techniques and applications. Journal of microscopy, 247(2):119–136, 2012.
- Fluorescence lifetime measurements and biological imaging. Chemical reviews, 110(5):2641–2684, 2010.
- Fluorescence lifetime tracking and imaging of single moving particles assisted by a low-photon-count analysis algorithm. Biomedical Optics Express, 14(4):1718, Apr. 2023.
- A maximum likelihood method for lifetime estimation in photon counting-based fluorescence lifetime imaging microscopy. In 21st European Signal Processing Conference (EUSIPCO 2013), pages 1–5. IEEE, 2013.
- The phasor approach to fluorescence lifetime imaging analysis. Biophysical journal, 94(2):L14–L16, 2008.
- Vector finite difference modesolver for anisotropic dielectric waveguides. J. Lightwave Technol., 26(11):1423–1431, Jun 2008.
- High speed multispectral fluorescence lifetime imaging. Optics express, 21(10):11769–11782, 2013.
- Detlef Gloge. Optical power flow in multimode fibers. Bell System Technical Journal, 51(8):1767–1783, 1972.
- RP Haugland. Fluorophores and their amine-reactive derivatives. Handbook of fluorescent probes and research products, 9:7–78, 1996.
- Real-time mode decomposition for few-mode fiber based on numerical method. Opt. Express, 23(4):4620–4629, Feb 2015.
- 3d convolutional neural networks for human action recognition. IEEE transactions on pattern analysis and machine intelligence, 35(1):221–231, 2012.
- A 2.5 d cascaded convolutional neural network with temporal information for automatic mitotic cell detection in 4d microscopic images. In 2018 14th International Conference on Natural Computation, Fuzzy Systems and Knowledge Discovery (ICNC-FSKD), pages 202–205. IEEE, 2018.
- Mnist handwritten digit database, 2010.
- Latent space cartography: Visual analysis of vector space embeddings. Computer graphics forum, 38(3):67–78, 2019.
- Fast mode decomposition in few-mode fibers. Nature Communications, 11(5507), 2020.
- Robust blind spectral unmixing for fluorescence microscopy using unsupervised learning. PloS one, 14(12):e0225410, 2019.
- Modal decomposition technique for multimode fibers. Appl. Opt., 51(4):450–456, Feb 2012.
- Spatially and spectrally resolved imaging of modal content in large-mode-area fibers. Optics express, 16(10):7233–7243, 2008.
- Spatially and spectrally resolved imaging of modal content in large-mode-area fibers. Opt. Express, 16(10):7233–7243, May 2008.
- Lambdaunet: 2.5 d stroke lesion segmentation of diffusion-weighted mr images. In Medical Image Computing and Computer Assisted Intervention–MICCAI 2021: 24th International Conference, Strasbourg, France, September 27–October 1, 2021, Proceedings, Part I 24, pages 731–741. Springer, 2021.
- Mode recovery by s2 imaging without a fourier transform. J. Lightwave Technol., 39(13):4453–4461, Jul 2021.
- Bayesian analysis of fluorescence lifetime imaging data. In Ammasi Periasamy, Karsten K”onig, and Peter T. C. So, editors, SPIE BiOS, page 790325, San Francisco, California, USA, Feb. 2011.
- Advanced s22{}^{2}start_FLOATSUPERSCRIPT 2 end_FLOATSUPERSCRIPT imaging: Application of multivariate statistical analysis to spatially and spectrally resolved datasets. Journal of Lightwave Technology, 32(23):4606–4612, 2014.
- 3d convolutional neural network for object recognition: a review. Multimedia Tools and Applications, 78:15951–15995, 2019.
- 3d deep learning on medical images: a review. Sensors, 20(18):5097, 2020.
- Unmix-me: spectral and lifetime fluorescence unmixing via deep learning. Biomedical Optics Express, 11(7):3857–3874, 2020.
- Fast fit-free analysis of fluorescence lifetime imaging via deep learning. Proceedings of the National Academy of Sciences, 116(48):24019–24030, 2019.
- Investigating protein-protein interactions in living cells using fluorescence lifetime imaging microscopy. Nature protocols, 6(9):1324–1340, 2011.
- Chuqi Wang. A review on 3d convolutional neural network. In 2023 IEEE 3rd International Conference on Power, Electronics and Computer Applications (ICPECA), pages 1204–1208, 2023.
- Compact and robust deep learning architecture for fluorescence lifetime imaging and fpga implementation. Methods and Applications in Fluorescence, 11(2):025002, 2023.