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A user-friendly tool for cloud-based whole slide image segmentation with examples from renal histopathology

2022; Nature Portfolio; Volume: 2; Issue: 1 Linguagem: Inglês

10.1038/s43856-022-00138-z

2730-664X

Brendon Lutnick, David Manthey, Jan U. Becker, Brandon Ginley, Katharina Moos, Jonathan E. Zuckerman, Luís Rodrigues, Alexander J. Gallan, Laura Barisoni, Charles E. Alpers, Xiaoxin X. Wang, Komuraiah Myakala, Bryce A. Jones, Moshe Levi, Jeffrey B. Kopp, Teruhiko Yoshida, Jarcy Zee, Seung Seok Han, Sanjay Jain, Avi Z. Rosenberg, Kuang‐Yu Jen, Pinaki Sarder, Brendon Lutnick, Brandon Ginley, Richard Knight, Stewart H. Lecker, Isaac E. Stillman, Steve Bogen, Afolarin Amodu, Titlayo Ilori, Insa M. Schmidt, Shana Maikhor, Laurence H. Beck, Ashish Verma, Joel Henderson, Ingrid Onul, Sushrut S. Waikar, Gearoid M. McMahon, Astrid Weins, Mia R. Colona, M. Todd Valerius, Nir Hacohen, Paul Hoover, Anna Greka, Jamie L. Marshall, Mark P. Aulisio, Yijiang M. Chen, Andrew Janowczyk, Catherine Jayapandian, Vidya Sankar Viswanathan, William S. Bush, Dana C. Crawford, Anant Madabhushi, John O’Toole, Emilio D. Poggio, John R. Sedor, Leslie Cooperman, Stacey E. Jolly, Leal Herlitz, Jane Nguyen, Agustin Gonzalez‐Vicente, Ellen L. Palmer, Dianna Sendrey, Jonathan J. Taliercio, Lakeshia Bush, Kassandra Spates-Harden, Carissa Vinovskis, P. M. Bjørnstad, Laura Pyle, Paul S. Appelbaum, Jonathan Barasch, Andrew S. Bomback, Vivette D. D’Agati, Krzysztof Kiryluk, Karla Mehl, Pietro A. Canetta, Ning Shang, Olivia Balderes, Satoru Kudose, Theodore Alexandrov, Helmut G. Rennke, Tarek M. El‐Achkar, Ying‐Hua Cheng, Pierre C. Dagher, Michael T. Eadon, Kenneth W. Dunn, Katherine J. Kelly, Timothy A. Sutton, Daria Barwinska, Michael J. Ferkowicz, Seth Winfree, Sharon B. Bledsoe, Marcelino Rivera, James C. Williams, Ricardo Melo Ferreira, Katy Börner, Andreas Bueckle, Bruce Herr, Ellen M. Quardokus, Éric Record, Jing Su, Debora Gisch, Stephanie Wofford, Yashvardhan Jain, Chirag R. Parikh, Celia P. Corona-Villalobos, Steven Menez, Yumeng Wen, Camille Johansen, Sylvia E. Rosas, Neil Roy, Mark V. Williams, Jennifer K. Sun, Joseph Ardayfio, Jack Bebiak, Keith Brown, Catherine E. Campbell, John Saul, Anna Shpigel, Christy Stutzke, Robert Koewler, Taneisha Campbell, Lynda Hayashi, Nichole Jefferson, Glenda V. Roberts, Roy Pinkeney, Evren U. Azeloglu, Cijang He, Ravi Iyengar, Jens Hansen, Yuguang Xiong, Pottumarthi Prasad, Anand Srivastava, Brad H. Rovin, Samir V. Parikh, John P. Shapiro, Sethu M. Madhavan, Christopher Anderton, Ljiljana Paša‐Tolić, Dušan Veličković, Jessica Lukowski, George Oliver, Olga G. Troyanskaya, Rachel Sealfon, Aaron K. Wong, Katherine R. Tuttle, Ari H. Pollack, Yury Goltsev, Kun Zhang, Blue B. Lake, Zoltán Lászik, Garry P. Nolan, Patrick Boada, Minnie Sarwal, Kavya Anjani, Tara K. Sigdel, Tariq Mukatash, Paul J. Lee, Rita R. Alloway, E. Steve Woodle, Ashley R. Burg, Adele Rike, Tiffany Shi, Heather Ascani, Ulysses J. Balis, Jeffrey B. Hodgin, Matthias Kretzler, Chrysta Lienczewski, Laura H. Mariani, Rajasree Menon, Becky Steck, Yougqun He, Edgar A. Otto, Jennifer A. Schaub, Victoria M. Blanc, Sean Eddy, Ninive C. Conser, Jinghui Luo, Renee Frey, Paul M. Palevsky, Matthew R. Rosengart, John A. Kellum, Daniel E. Hall, Parmjeet Randhawa, Xiaogang Li, Raghavan Murugan, Michele Elder, James Winters, Tina Vita, Filitsa Bender, Roderick J. Tan, Matthew Gilliam, Kristina N. Blank, Jonas Carson, Ian H. de Boer, Ashveena Dighe, Jonathan Himmelfarb, Sean D. Mooney, Stuart J. Shankland, Kayleen Williams, Chris Park, Frederick Dowd, Robyn L. McClelland, Stephen Daniel, Andrew N. Hoofnagle, Adam B. Wilcox, Stephanie M. Grewenow, Ashley Berglund, Christine P. Limonte, Kasra A. Rezaei, Ruikang K. Wang, Jamie A. Snyder, Brooke Berry, Yunbi Nam, Natalya Sarkisova, Shweta Bansal, Kumar Sharma, Manjeri A. Venkatachalam, Guanshi Zhang, Annapurna Pamreddy, Hongping Ye, Richard Montellano, Robert D. Toto, Miguel A. Vazquez, Simon J. Craddock Lee, R. Tyler Miller, Orson W. Moe, José Torrealba, Nancy Wang, Asra Kermani, Kamalanathan K. Sambandam, Harold S. Park, S. Susan Hedayati, Christopher Y. Lu, Natasha Wen, Jiten Patel, Anil K. Pillai, Dianbo Zhang, Mujeeb Basit, Allen H. Hendricks, Richard M. Caprioli, Nathan Heath Patterson, Kavya Sharman, Jeffrey M. Spraggins, Raf Van de Plas, Anitha Vijayan, Joseph P. Gaut, Jeanine Basta, Sabine M. Diettman, Michael Rauchman, Dennis G. Moledina, F. Perry Wilson, Ugochukwu Ugwuowo, Tanima Arora, Melissa Shaw, Lloyd G. Cantley, Vijaykumar R. Kakade, Angela Victoria-Castro,

Digital Imaging for Blood Diseases

Abstract Background Image-based machine learning tools hold great promise for clinical applications in pathology research. However, the ideal end-users of these computational tools (e.g., pathologists and biological scientists) often lack the programming experience required for the setup and use of these tools which often rely on the use of command line interfaces. Methods We have developed Histo-Cloud , a tool for segmentation of whole slide images (WSIs) that has an easy-to-use graphical user interface. This tool runs a state-of-the-art convolutional neural network (CNN) for segmentation of WSIs in the cloud and allows the extraction of features from segmented regions for further analysis. Results By segmenting glomeruli, interstitial fibrosis and tubular atrophy, and vascular structures from renal and non-renal WSIs, we demonstrate the scalability, best practices for transfer learning, and effects of dataset variability. Finally, we demonstrate an application for animal model research, analyzing glomerular features in three murine models. Conclusions Histo-Cloud is open source, accessible over the internet, and adaptable for segmentation of any histological structure regardless of stain.