ConIFSeg - Confocal Immunofluorescence Segmentation with Deep Learning


Abstract:

In this project we consider automatic multi-class segmentations using deep learning models for lung immunofluorescent (IF) confocal images, along with synthetic image generation of lung images for training these models.

Web-based Annotation Tool [1]

Automatic Segmentation Results [2]

Augmentation using GAN [3]

Reference:

1. S. Isaka, H. Kawanaka, V. B. S. Prasath, B. J. Aronow, S. Tsuruoka. Development of a web based image annotation tool for lung immunofluorescent confocal images. 4th International Symposium on Affective Science and Engineering, and the 29th Modern Artificial Intelligence and Cognitive Science Conference (ISASE-MAICS), Spokane, WA, USA, June 2018. doi:10.5057/isase.2018-C000036

2. S. Isaka, H. Kawanaka, B. Aronow, V. B. S. Prasath. Multi-class segmentation of lung immunofluorescence confocal images using deep learning. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), International Workshop on Deep Learning in Bioinformatics, Biomedicine, and Healthcare Informatics (DLB2H), San Diego, CA, USA. Proc. IEEE, 2362-2368, November 2019. doi:10.1109/BIBM47256.2019.8983146

3. D. Katsuma, H. Kawanaka, V. B. S. Prasath, B. J. Aronow. Data augmentation using generative adversarial networks for multi-class segmentation of lung confocal IF images. Journal of Advanced Computational Intelligence and Intelligent Informatics, 26(2), 138-146, March 2022. doi:10.20965/jaciii.2022.p0138

4. B. Iyer et al. ConIFSeg - Confocal immunofluorescence segmentation with deep learning. In preparation, 2022. Preliminary version at arXiv:22xx.abcde.


See also our LungMAP DCC reference:

Nathan Gaddis, Joshua Fortriede, Minzhe Guo, Eric E. Bardes, Michal Kouril, Scott Tabar, Kevin Burns, Maryanne E. Ardini-Poleske, Stephanie Loos, Daniel Schnell, Kang Jin, Balaji Iyer, Yina Du, Bing-Xing Huo, Anukana Bhattacharjee, Jeff Korte, Ruchi Munshi, Victoria Smith, Andrew Herbst, Joseph A. Kitzmiller, Geremy C. Clair, James P. Carson, Joshua Adkins, Edward E. Morrisey, Gloria S. Pryhuber, Ravi Misra, Jeffrey A. Whitsett, Xin Sun, Trevor Heathorn, Benedict Paten, V. B. S. Prasath, Yan Xu, Tim Tickle, Bruce J. Aronow, Nathan Salomonis. LungMAP portal ecosystem: Systems-level exploration of the lung. American Journal of Respiratory Cell and Molecular Biology, 2022. doi: 10.1165/rcmb.2022-0165OC

Biorxiv version doi:10.1101/2021.12.05.471312


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