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Corneal Endothelial Cell Segmentation with Multiple Long-range Dependencies

Published:28 February 2024Publication History

ABSTRACT

Corneal endothelial cell segmentation is an important task in ophthalmology, but it is challenging due to variations in image characteristics across different datasets. Existing deep learning methods have limitations in capturing long-range dependencies that are critical for accurate segmentation. To address this issue, we propose a novel multiple long-range dependencies network (MLD-Net) that effectively incorporates different types of long-range dependency information to achieve robust segmentation across datasets. The network employs dilated convolutions and attention gates to capture spatial and layer-level dependencies, respectively. The entire network is densely connected, facilitating the sharing of long-range dependency information across multiple scales. We demonstrate the effectiveness of MLD-Net on four different corneal endothelium microscope image datasets: SREP, BiolmLab, Rodrep, and TM-EM3000. Our experimental results show that MLD-Net outperforms existing state-of-the-art methods, achieving robustness and high accuracy in corneal endothelial cell segmentation.

References

  1. Oluwatobi Afolabi, Fulufhelo Nelwamondo, and Gugulethu Mabuza. 2020. Blood Vessel Segmentation from Fundus Images Using Modified U-net Convolutional Neural Network. Journal of Image and Graphics 8 (01 2020), 21–25. https://doi.org/10.18178/joig.8.1.21-25Google ScholarGoogle ScholarCross RefCross Ref
  2. Shumoos Al-Fahdawi, Rami Qahwaji, Alaa S. Al-Waisy, Stanley Ipson, Maryam Ferdousi, Rayaz A. Malik, and Arun Brahma. 2018. A fully automated cell segmentation and morphometric parameter system for quantifying corneal endothelial cell morphology. Computer Methods and Programs in Biomedicine 160 (2018), 11–23. https://doi.org/10.1016/j.cmpb.2018.03.015Google ScholarGoogle ScholarCross RefCross Ref
  3. Yousef Al-Kofahi, Wiem Lassoued, William Lee, and Badrinath Roysam. 2010. Improved Automatic Detection and Segmentation of Cell Nuclei in Histopathology Images. IEEE Transactions on Biomedical Engineering 57, 4 (2010), 841–852. https://doi.org/10.1109/TBME.2009.2035102Google ScholarGoogle ScholarCross RefCross Ref
  4. A. Almustofa, A. Handayani, and T. Mengko. 2022. Optic Disc and Optic Cup Segmentation on Retinal Image Based on Multimap Localization and U-Net Convolutional Neural Network. Journal of Image and Graphics 10 (01 2022). https://doi.org/10.18178/joig.10.3.109-115Google ScholarGoogle ScholarCross RefCross Ref
  5. Abhishek Chaurasia and Eugenio Culurciello. 2017. LinkNet: Exploiting encoder representations for efficient semantic segmentation. In 2017 IEEE Visual Communications and Image Processing (VCIP). 1–4. https://doi.org/10.1109/VCIP.2017.8305148Google ScholarGoogle ScholarCross RefCross Ref
  6. Jieneng Chen, Yongyi Lu, Qihang Yu, Xiangde Luo, Ehsan Adeli, Yan Wang, Le Lu, Alan Loddon Yuille, and Yuyin Zhou. 2021. TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation. ArXiv abs/2102.04306 (2021). https://api.semanticscholar.org/CorpusID:231847326Google ScholarGoogle Scholar
  7. Leyza Baldo Dorini, Rodrigo Minetto, and Neucimar Jeronimo Leite. 2007. White blood cell segmentation using morphological operators and scale-space analysis. In XX Brazilian Symposium on Computer Graphics and Image Processing (SIBGRAPI 2007). 294–304. https://doi.org/10.1109/SIBGRAPI.2007.33Google ScholarGoogle ScholarDigital LibraryDigital Library
  8. Charles Duyckaerts and Gilles Godefroy. 2000. Voronoi tessellation to study the numerical density and the spatial distribution of neurones. Journal of Chemical Neuroanatomy 20, 1 (2000), 83–92. https://doi.org/10.1016/S0891-0618(00)00064-8Google ScholarGoogle ScholarCross RefCross Ref
  9. Huimin Huang, Lanfen Lin, Ruofeng Tong, Hongjie Hu, Qiaowei Zhang, Yutaro Iwamoto, Xianhua Han, Yen-Wei Chen, and Jian Wu. 2020. UNet 3+: A Full-Scale Connected UNet for Medical Image Segmentation. In ICASSP 2020 - 2020 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP). 1055–1059. https://doi.org/10.1109/ICASSP40776.2020.9053405Google ScholarGoogle ScholarCross RefCross Ref
  10. Yuanfeng Ji, Ruimao Zhang, Huijie Wang, Zhen Li, Lingyun Wu, Shaoting Zhang, and Ping Luo. 2021. Multi-compound Transformer for Accurate Biomedical Image Segmentation. In Medical Image Computing and Computer Assisted Intervention – MICCAI 2021, Marleen de Bruijne, Philippe C. Cattin, Stéphane Cotin, Nicolas Padoy, Stefanie Speidel, Yefeng Zheng, and Caroline Essert (Eds.). Springer International Publishing, Cham, 326–336.Google ScholarGoogle ScholarDigital LibraryDigital Library
  11. Ozan Oktay, Jo Schlemper, Loïc Le Folgoc, M. J. Lee, Mattias P. Heinrich, Kazunari Misawa, Kensaku Mori, Steven G. McDonagh, Nils Y. Hammerla, Bernhard Kainz, Ben Glocker, and Daniel Rueckert. 2018. Attention U-Net: Learning Where to Look for the Pancreas. ArXiv abs/1804.03999 (2018). https://api.semanticscholar.org/CorpusID:4861068Google ScholarGoogle Scholar
  12. Kenji Ono, Yutaro Iwamoto, Yen-Wei Chen, and Masahiro Nonaka. 2020. Automatic Segmentation of Infant Brain Ventricles with Hydrocephalus in MRI Based on 2.5D U-Net and Transfer Learning. Journal of Image and Graphics (01 2020), 42–46. https://doi.org/10.18178/joig.8.2.42-46Google ScholarGoogle ScholarCross RefCross Ref
  13. Stanley Osher and Ronald P. Fedkiw. 2001. Level Set Methods: An Overview and Some Recent Results. J. Comput. Phys. 169, 2 (2001), 463–502. https://doi.org/10.1006/jcph.2000.6636Google ScholarGoogle ScholarDigital LibraryDigital Library
  14. Kazuki Otsuki, Yutaro Iwamoto, Yen-Wei Chen, Akira Furukawa, and Shuzo Kanasaki. 2019. Cine-MR Image Segmentation for Assessment of Small Bowel Motility Function Using 3D U-Net. Journal of Image and Graphics 7 (01 2019), 134–139. https://doi.org/10.18178/joig.7.4.134-139Google ScholarGoogle ScholarCross RefCross Ref
  15. Olivier Petit, Nicolas Thome, Clement Rambour, Loic Themyr, Toby Collins, and Luc Soler. 2021. U-Net Transformer: Self and Cross Attention for Medical Image Segmentation. In Machine Learning in Medical Imaging, Chunfeng Lian, Xiaohuan Cao, Islem Rekik, Xuanang Xu, and Pingkun Yan (Eds.). Springer International Publishing, Cham, 267–276.Google ScholarGoogle Scholar
  16. Olaf Ronneberger, Philipp Fischer, and Thomas Brox. 2015. U-Net: Convolutional Networks for Biomedical Image Segmentation. In Medical Image Computing and Computer-Assisted Intervention – MICCAI 2015, Nassir Navab, Joachim Hornegger, William M. Wells, and Alejandro F. Frangi (Eds.). Springer International Publishing, Cham, 234–241.Google ScholarGoogle ScholarCross RefCross Ref
  17. L. Shafarenko, M. Petrou, and J. Kittler. 1997. Automatic watershed segmentation of randomly textured color images. IEEE Transactions on Image Processing 6, 11 (1997), 1530–1544. https://doi.org/10.1109/83.641413Google ScholarGoogle ScholarDigital LibraryDigital Library
  18. Naofumi Shigeta, Mikoto Kamata, and Masayuki Kikuchi. 2019. Effectiveness of Pseudo 3D Feature Learning for Spinal Segmentation by CNN with U-Net Architecture. Journal of Image and Graphics 7 (01 2019), 107–111. https://doi.org/10.18178/joig.7.3.107-111Google ScholarGoogle ScholarCross RefCross Ref
  19. Jeya Maria Jose Valanarasu, Vishwanath A. Sindagi, Ilker Hacihaliloglu, and Vishal M. Patel. 2022. KiU-Net: Overcomplete Convolutional Architectures for Biomedical Image and Volumetric Segmentation. IEEE Transactions on Medical Imaging 41, 4 (2022), 965–976. https://doi.org/10.1109/TMI.2021.3130469Google ScholarGoogle ScholarCross RefCross Ref
  20. Juan P. Vigueras-Guillén, Eleni-Rosalina Andrinopoulou, Angela Engel, Hans G. Lemij, Jeroen van Rooij, Koenraad A. Vermeer, and Lucas J. van Vliet. 2018. Corneal Endothelial Cell Segmentation by Classifier-Driven Merging of Oversegmented Images. IEEE Transactions on Medical Imaging 37, 10 (2018), 2278–2289. https://doi.org/10.1109/TMI.2018.2841910Google ScholarGoogle ScholarCross RefCross Ref
  21. Carolina Wählby, Joakim Lindblad, Mikael Vondrus, Ewert Bengtsson, and Lennart Björkesten. 2002. Algorithms for Cytoplasm Segmentation of Fluorescence Labelled Cells. Analytical Cellular Pathology : the Journal of the European Society for Analytical Cellular Pathology 24 (2002), 101 – 111. https://api.semanticscholar.org/CorpusID:279231Google ScholarGoogle Scholar
  22. Haonan Wang, Peng Cao, Jiaqi Wang, and Osmar R Zaiane. 2021. UCTransNet: Rethinking the Skip Connections in U-Net from a Channel-wise Perspective with Transformer. In AAAI Conference on Artificial Intelligence. https://api.semanticscholar.org/CorpusID:237453471Google ScholarGoogle Scholar
  23. Lichen Zhou, Chuang Zhang, and Ming Wu. 2018. D-LinkNet: LinkNet with Pretrained Encoder and Dilated Convolution for High Resolution Satellite Imagery Road Extraction. In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW). 192–1924. https://doi.org/10.1109/CVPRW.2018.00034Google ScholarGoogle ScholarCross RefCross Ref
  24. Zongwei Zhou, Md Mahfuzur Rahman Siddiquee, Nima Tajbakhsh, and Jianming Liang. 2018. UNet++: A Nested U-Net Architecture for Medical Image Segmentation. In Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support, Danail Stoyanov, Zeike Taylor, Gustavo Carneiro, Tanveer Syeda-Mahmood, Anne Martel, Lena Maier-Hein, João Manuel R.S. Tavares, Andrew Bradley, João Paulo Papa, Vasileios Belagiannis, Jacinto C. Nascimento, Zhi Lu, Sailesh Conjeti, Mehdi Moradi, Hayit Greenspan, and Anant Madabhushi (Eds.). Springer International Publishing, Cham, 3–11.Google ScholarGoogle Scholar

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    • Published in

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      ICBBE '23: Proceedings of the 2023 10th International Conference on Biomedical and Bioinformatics Engineering
      November 2023
      295 pages
      ISBN:9798400708343
      DOI:10.1145/3637732

      Copyright © 2023 ACM

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      Publication History

      • Published: 28 February 2024

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