A user-friendly tool for cloud-based whole slide image segmentation with examples from renal histopathology
Authors: Lutnick Brendon , Manthey David , Becker Jan U. , Ginley Brandon , Moos Katharina , Zuckerman Jonathan E. , Rodrigues Luis , Gallan Alexander J. , Barisoni Laura , Alpers Charles E. , Wang Xiaoxin X. , Myakala Komuraiah , Jones Bryce A. , Levi Moshe , Kopp Jeffrey B. , Yoshida Teruhiko , Zee Jarcy , Han Seung Seok , Jain Sanjay , Rosenberg Avi Z. , Jen Kuang Yu. , Sarder Pinaki ,   the Kidney Precision Medicine Project, Lutnick Brendon , Ginley Brandon , Knight Richard , Lecker Stewart H. , Stillman Isaac , Bogen Steve , Amodu Afolarin A. , Ilori Titlayo , Schmidt Insa , Maikhor Shana , Beck Laurence H. , Verma Ashish , Henderson Joel M. , Onul Ingrid , Waikar Sushrut , McMahon Gearoid M. , Weins Astrid , Colona Mia R. , Valerius M. Todd , Hacohen Nir , Hoover Paul J. , Greka Anna , Marshall Jamie L. , Aulisio Mark , Chen Yijiang M. , Janowczyk Andrew , Jayapandian Catherine , Viswanathan Vidya S. , Bush William S. , Crawford Dana C. , Madabhushi Anant , O’toole John , Poggio Emilio , Sedor John , Cooperman Leslie , Jolly Stacey , Herlitz Leal , Nguyen Jane , Gonzalez-Vicente Agustin , Palmer Ellen , Sendrey Dianna , Taliercio Jonathan , Bush Lakeshia , Spates-Harden Kassandra , Vinovskis Carissa , Bjornstad Petter M. , Pyle Laura , Appelbaum Paul , Barasch Jonathan M. , Bomback Andrew S. , D’Agati Vivette D. , Kiryluk Krzysztof , Mehl Karla , Canetta Pietro A. , Shang Ning , Balderes Olivia , Kudose Satoru , Alexandrov Theodore , Rennke Helmut , El-Achkar Tarek M. , Cheng Yinghua , Dagher Pierre C. , Eadon Michael T. , Dunn Kenneth W. , Kelly Katherine J. , Sutton Timothy A. , Barwinska Daria , Ferkowicz Michael J. , Winfree Seth , Bledsoe Sharon , Rivera Marcelino , Williams James C. , Ferreira Ricardo Melo , Borner Katy , Bueckle Andreas , Herr Bruce W. , Quardokus Ellen M. , Record Elizabeth , Su Jing , Gisch Debora , Wofford Stephanie , Jain Yashvardhan , Parikh Chirag R. , Corona-Villalobos Celia P. , Menez Steven , Wen Yumeng , Johansen Camille , Rosas Sylvia E. , Roy Neil , Williams Mark , Sun Jennifer , Ardayfio Joseph , Bebiak Jack , Brown Keith , Campbell Catherine E. , Saul John , Shpigel Anna , Stutzke Christy , Koewler Robert , Campbell Taneisha , Hayashi Lynda , Jefferson Nichole , Roberts Glenda V. , Pinkeney Roy , Azeloglu Evren U. , He Cijang , Iyengar Ravi , Hansen Jens , Xiong Yuguang , Prasad Pottumarthi , Srivastava Anand , Rovin Brad , Parikh Samir , Shapiro John P. , Madhavan Sethu M. , Anderton Christopher R. , Pasa-Tolic Ljiljana , Velickovic Dusan , Lukowski Jessica , Oliver George Holt , Troyanskaya Olga , Sealfon Rachel , Wong Aaron , Tuttle Katherine R. , Pollack Ari , Goltsev Yury , Zhang Kun , Lake Blue B. , Laszik Zoltan G. , Nolan Garry , Boada Patrick , Sarwal Minnie , Anjani Kavya , Sigdel Tara , Mukatash Tariq , Lee Paul J. , Alloway Rita R. , Woodle E. Steve , Burg Ashley R. , Rike Adele , Shi Tiffany , Ascani Heather , Balis Ulysses G. J. , Hodgin Jeffrey B. , Kretzler Matthias , Lienczewski Chrysta , Mariani Laura H. , Menon Rajasree , Steck Becky , He Yougqun , Otto Edgar , Schaub Jennifer , Blanc Victoria M. , Eddy Sean , Conser Ninive C. , Luo Jinghui , Frey Renee , Palevsky Paul M. , Rosengart Matthew , Kellum John A. , Hall Daniel E. , Randhawa Parmjeet , Tublin Mitchell , Murugan Raghavan , Elder Michele M. , Winters James , Vita Tina , Bender Filitsa , Tan Roderick , Gilliam Matthew , Blank Kristina N. , Carson Jonas , De Boer Ian H. , Dighe Ashveena L. , Himmelfarb Jonathan , Mooney Sean D. , Shankland Stuart , Williams Kayleen , Park Christopher , Dowd Frederick , McClelland Robyn L. , Daniel Stephen , Hoofnagle Andrew N. , Wilcox Adam , Grewenow Stephanie M. , Berglund Ashley , Limonte Christine , Rezaei Kasra , Wang Ruikang , Snyder Jamie , Berry Brooke , Nam Yunbi , Sarkisova Natalya , Bansal Shweta , Sharma Kumar , Venkatachalam Manjeri , Zhang Guanshi , Pamreddy Annapurna , Ye Hongping , Montellano Richard , Toto Robert D. , Vazquez Miguel , Lee Simon C. , Miller R. Tyler , Moe Orson W. , Torrealba Jose , Wang Nancy , Kermani Asra , Sambandam Kamalanathan , Park Harold , Hedayati S. Susan , Lu Christopher Y. , Wen Natasha , Patel Jiten , Pillai Anil , Zhang Dianbo , Basit Mujeeb , Hendricks Allen H. , Caprioli Richard M. , Patterson Nathan , Sharman Kavya , Spraggins Jeffrey M. , Van de Plas Raf , Vijayan Anitha , Gaut Joseph P. , Basta Jeanine , Diettman Sabine M. , Rauchman Michael I. , Moledina Dennis , Wilson Francis P. , Ugwuowo Ugochukwu , Arora Tanima , Shaw Melissa M. , Cantley Lloyd G. , Kakade Vijaykumar R. , Victoria-Castro Angela 
Published: August 2022

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 developedHisto-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-Cloudis open source, accessible over the internet, and adaptable for segmentation of any histological structure regardless of stain.