HistoSegCap: Capsules for Weakly-Supervised Semantic Segmentation of Histological Tissue Type in Whole Slide Images (2402.10851v1)
Abstract: Digital pathology involves converting physical tissue slides into high-resolution Whole Slide Images (WSIs), which pathologists analyze for disease-affected tissues. However, large histology slides with numerous microscopic fields pose challenges for visual search. To aid pathologists, Computer Aided Diagnosis (CAD) systems offer visual assistance in efficiently examining WSIs and identifying diagnostically relevant regions. This paper presents a novel histopathological image analysis method employing Weakly Supervised Semantic Segmentation (WSSS) based on Capsule Networks, the first such application. The proposed model is evaluated using the Atlas of Digital Pathology (ADP) dataset and its performance is compared with other histopathological semantic segmentation methodologies. The findings underscore the potential of Capsule Networks in enhancing the precision and efficiency of histopathological image analysis. Experimental results show that the proposed model outperforms traditional methods in terms of accuracy and the mean Intersection-over-Union (mIoU) metric.
- Faherty, E. The role of digital pathology for histological diagnosis. \JournalTitleInternational Undergraduate Journal of Health Sciences 3, 5 (2023).
- Lu, C. et al. A prognostic model for overall survival of patients with early-stage non-small cell lung cancer: a multicentre, retrospective study. \JournalTitleThe Lancet Digital Health 2, e594–e606 (2020).
- Hyaline cell-rich chondroid syringoma: A potential pitfall on cytology. \JournalTitleDiagnostic Cytopathology (2023).
- Zhou, Y. et al. Cgc-net: Cell graph convolutional network for grading of colorectal cancer histology images. In Proceedings of the IEEE/CVF international conference on computer vision workshops, 0–0 (2019).
- Yu, K.-H. et al. Predicting non-small cell lung cancer prognosis by fully automated microscopic pathology image features. \JournalTitleNature communications 7, 12474 (2016).
- A survey on graph-based deep learning for computational histopathology. \JournalTitleComputerized Medical Imaging and Graphics 95, 102027 (2022).
- Elmore, J. G. et al. Diagnostic concordance among pathologists interpreting breast biopsy specimens. \JournalTitleJama 313, 1122–1132 (2015).
- Li, X. et al. A comprehensive review of computer-aided whole-slide image analysis: from datasets to feature extraction, segmentation, classification and detection approaches. \JournalTitleArtificial Intelligence Review 55, 4809–4878 (2022).
- Bokhorst, J.-M. et al. Deep learning for multi-class semantic segmentation enables colorectal cancer detection and classification in digital pathology images. \JournalTitleScientific Reports 13, 8398 (2023).
- Yacob, F. et al. Weakly supervised detection and classification of basal cell carcinoma using graph-transformer on whole slide images. \JournalTitleScientific Reports 13, 1–10 (2023).
- Histosegnet: Semantic segmentation of histological tissue type in whole slide images. In Proceedings of the IEEE/CVF International Conference on Computer Vision, 10662–10671 (2019).
- Lin, Y. et al. Clip is also an efficient segmenter: A text-driven approach for weakly supervised semantic segmentation. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 15305–15314 (2023).
- Deep contrastive learning based tissue clustering for annotation-free histopathology image analysis. \JournalTitleComputerized Medical Imaging and Graphics 97, 102053 (2022).
- Brain tumor type classification via capsule networks. In 2018 25th IEEE international conference on image processing (ICIP), 3129–3133 (IEEE, 2018).
- Bonheur, S. et al. Matwo-capsnet: a multi-label semantic segmentation capsules network. In Medical Image Computing and Computer Assisted Intervention–MICCAI 2019: 22nd International Conference, Shenzhen, China, October 13–17, 2019, Proceedings, Part V 22, 664–672 (Springer, 2019).
- Dynamic routing between capsules. \JournalTitleAdvances in neural information processing systems 30 (2017).
- Capsule networks for brain tumor classification based on mri images and coarse tumor boundaries. In ICASSP 2019-2019 IEEE international conference on acoustics, speech and signal processing (ICASSP), 1368–1372 (IEEE, 2019).
- Hosseini, M. S. et al. Atlas of digital pathology: A generalized hierarchical histological tissue type-annotated database for deep learning. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 11747–11756 (2019).
- Transforming auto-encoders. In Artificial Neural Networks and Machine Learning–ICANN 2011: 21st International Conference on Artificial Neural Networks, Espoo, Finland, June 14-17, 2011, Proceedings, Part I 21, 44–51 (Springer, 2011).
- Weakly-supervised semantic segmentation by iteratively mining common object features. In Proceedings of the IEEE conference on computer vision and pattern recognition, 1354–1362 (2018).
- A deep convolutional neural network for segmenting and classifying epithelial and stromal regions in histopathological images. \JournalTitleNeurocomputing 191, 214–223 (2016).
- Antibody-supervised deep learning for quantification of tumor-infiltrating immune cells in hematoxylin and eosin stained breast cancer samples. \JournalTitleJournal of pathology informatics 7, 38 (2016).
- Detection of brain tumors from mri images base on deep learning using hybrid model cnn and nade. \JournalTitlebiocybernetics and biomedical engineering 40, 1225–1232 (2020).
- Nogueira-Rodríguez, A. et al. Deep neural networks approaches for detecting and classifying colorectal polyps. \JournalTitleNeurocomputing 423, 721–734 (2021).
- Scribblesup: Scribble-supervised convolutional networks for semantic segmentation. In Proceedings of the IEEE conference on computer vision and pattern recognition, 3159–3167 (2016).
- Zhang, L. et al. Representative discovery of structure cues for weakly-supervised image segmentation. \JournalTitleIEEE transactions on multimedia 16, 470–479 (2013).
- Robust roi localization based on image segmentation and outlier detection in finger vein recognition. \JournalTitleMultimedia Tools and Applications 79, 20039–20059 (2020).
- Selvaraju, R. R. et al. Grad-cam: Visual explanations from deep networks via gradient-based localization. In Proceedings of the IEEE international conference on computer vision, 618–626 (2017).
- Deep inside convolutional networks: Visualising image classification models and saliency maps. \JournalTitlearXiv preprint arXiv:1312.6034 (2013).
- Axiomatic attribution for deep networks. In International conference on machine learning, 3319–3328 (PMLR, 2017).
- Smoothgrad: removing noise by adding noise. \JournalTitlearXiv preprint arXiv:1706.03825 (2017).
- Cao, H. et al. Dual-branch residual network for lung nodule segmentation. \JournalTitleApplied Soft Computing 86, 105934 (2020).
- Chlebus, G. et al. Automatic liver tumor segmentation in ct with fully convolutional neural networks and object-based postprocessing. \JournalTitleScientific reports 8, 15497 (2018).
- Grad-cam++: Generalized gradient-based visual explanations for deep convolutional networks. In 2018 IEEE winter conference on applications of computer vision (WACV), 839–847 (IEEE, 2018).
- Wang, H. et al. Score-cam: Score-weighted visual explanations for convolutional neural networks. In Proceedings of the IEEE/CVF conference on computer vision and pattern recognition workshops, 24–25 (2020).
- Ss-cam: Smoothed score-cam for sharper visual feature localization. \JournalTitlearXiv preprint arXiv:2006.14255 (2020).
- Full-gradient representation for neural network visualization. \JournalTitleAdvances in neural information processing systems 32 (2019).
- Semantic segmentation of colon glands with deep convolutional neural networks and total variation segmentation. \JournalTitlearXiv preprint arXiv:1511.06919 (2015).
- Automatic detection of cell divisions (mitosis) in live-imaging microscopy images using convolutional neural networks. In 2015 37th annual international conference of the IEEE engineering in medicine and biology society (EMBC), 743–746 (IEEE, 2015).
- Classification of mitotic figures with convolutional neural networks and seeded blob features. \JournalTitleJournal of pathology informatics 4, 9 (2013).
- Xu, Y. et al. Weakly supervised histopathology cancer image segmentation and classification. \JournalTitleMedical image analysis 18, 591–604 (2014).
- Seed, expand and constrain: Three principles for weakly-supervised image segmentation. In Computer Vision–ECCV 2016: 14th European Conference, Amsterdam, The Netherlands, October 11–14, 2016, Proceedings, Part IV 14, 695–711 (Springer, 2016).
- Weakly-supervised semantic segmentation network with deep seeded region growing. In Proceedings of the IEEE conference on computer vision and pattern recognition, 7014–7023 (2018).
- Self-supervised equivariant attention mechanism for weakly supervised semantic segmentation. In Proceedings of the IEEE/CVF conference on computer vision and pattern recognition, 12275–12284 (2020).
- Han, C. et al. Multi-layer pseudo-supervision for histopathology tissue semantic segmentation using patch-level classification labels. \JournalTitleMedical Image Analysis 80, 102487 (2022).
- A histo-puzzle network for weakly supervised semantic segmentation of histological tissue type. In Proceedings of the 2023 2nd Asia Conference on Algorithms, Computing and Machine Learning, 504–509 (2023).
- Sirinukunwattana, K. et al. Gland segmentation in colon histology images: The glas challenge contest. \JournalTitleMedical image analysis 35, 489–502 (2017).
- Mobina Mansoori (5 papers)
- Sajjad Shahabodini (5 papers)
- Jamshid Abouei (22 papers)
- Arash Mohammadi (69 papers)
- Konstantinos N. Plataniotis (109 papers)