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

the Kidney Precision Medicine Project; Brendon Lutnick; David Manthey; Jan U. Becker; Brandon Ginley; Katharina Moos; Jonathan E. Zuckerman; Luis 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 Stillman; Steve Bogen; Afolarin A. Amodu; Titlayo Ilori; Insa Schmidt; Shana Maikhor; Laurence H. Beck; Ashish Verma; Joel M. Henderson; Ingrid Onul; Sushrut Waikar; Gearoid M. McMahon; Astrid Weins; Mia R. Colona; M. Todd Valerius; Nir Hacohen; Paul J. Hoover; Anna Greka; Jamie L. Marshall; Mark Aulisio; Yijiang M. Chen; Andrew Janowczyk; Catherine Jayapandian; Vidya S. Viswanathan; William S. Bush; Dana C. Crawford; Anant Madabhushi; John O’toole; Emilio Poggio; John Sedor; Leslie Cooperman; Stacey Jolly; Leal Herlitz; Jane Nguyen; Agustin Gonzalez-Vicente; Ellen Palmer; Dianna Sendrey; Jonathan Taliercio; Lakeshia Bush; Kassandra Spates-Harden; Carissa Vinovskis; Petter M. Bjornstad; Laura Pyle; Paul Appelbaum; Jonathan M. Barasch; Andrew S. Bomback; Vivette D. D’Agati; Krzysztof Kiryluk; Karla Mehl; Pietro A. Canetta; Ning Shang; Olivia Balderes; Satoru Kudose; Theodore Alexandrov; Helmut Rennke; Tarek M. El-Achkar; Yinghua Cheng; Pierre C. Dagher; Michael T. Eadon; Kenneth W. Dunn; Katherine J. Kelly; Timothy A. Sutton; Daria Barwinska; Michael J. Ferkowicz; Seth Winfree; Sharon Bledsoe; Marcelino Rivera; James C. Williams; Ricardo Melo Ferreira; Katy Borner; Andreas Bueckle; Bruce W. Herr; Ellen M. Quardokus; Elizabeth 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 Williams; Jennifer 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 Rovin; Samir Parikh; John P. Shapiro; Sethu M. Madhavan; Christopher R. Anderton; Ljiljana Pasa-Tolic; Dusan Velickovic; Jessica Lukowski; George Holt Oliver; Olga Troyanskaya; Rachel Sealfon; Aaron Wong; Katherine R. Tuttle; Ari Pollack; Yury Goltsev; Kun Zhang; Blue B. Lake; Zoltan G. Laszik; Garry Nolan; Patrick Boada; Minnie Sarwal; Kavya Anjani; Tara Sigdel; Tariq Mukatash; Paul J. Lee; Rita R. Alloway; E. Steve Woodle; Ashley R. Burg; Adele Rike; Tiffany Shi; Heather Ascani; Ulysses G.J. Balis; Jeffrey B. Hodgin; Matthias Kretzler; Chrysta Lienczewski; Laura H. Mariani; Rajasree Menon; Becky Steck; Yougqun He; Edgar Otto; Jennifer Schaub; Victoria M. Blanc; Sean Eddy; Ninive C. Conser; Jinghui Luo; Renee Frey; Paul M. Palevsky; Matthew Rosengart; John A. Kellum; Daniel E. Hall; Parmjeet Randhawa; Mitchell Tublin; Raghavan Murugan; Michele M. Elder; James Winters; Tina Vita; Filitsa Bender; Roderick Tan; Matthew Gilliam; Kristina N. Blank; Jonas Carson; Ian H. De Boer; Ashveena L. Dighe; Stuart Shankland; Anitha Vijayan; Joseph P. Gaut; Michael I. Rauchman

doi:10.1038/s43856-022-00138-z

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

the Kidney Precision Medicine Project, Brendon Lutnick, David Manthey, Jan U. Becker, Brandon Ginley, Katharina Moos, Jonathan E. Zuckerman, Luis 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 JainAvi Z. Rosenberg, Kuang Yu Jen, Pinaki Sarder, Brendon Lutnick, Brandon Ginley, Richard Knight, Stewart H. Lecker, Isaac Stillman, Steve Bogen, Afolarin A. Amodu, Titlayo Ilori, Insa Schmidt, Shana Maikhor, Laurence H. Beck, Ashish Verma, Joel M. Henderson, Ingrid Onul, Sushrut Waikar, Gearoid M. McMahon, Astrid Weins, Mia R. Colona, M. Todd Valerius, Nir Hacohen, Paul J. Hoover, Anna Greka, Jamie L. Marshall, Mark Aulisio, Yijiang M. Chen, Andrew Janowczyk, Catherine Jayapandian, Vidya S. Viswanathan, William S. Bush, Dana C. Crawford, Anant Madabhushi, John O’toole, Emilio Poggio, John Sedor, Leslie Cooperman, Stacey Jolly, Leal Herlitz, Jane Nguyen, Agustin Gonzalez-Vicente, Ellen Palmer, Dianna Sendrey, Jonathan Taliercio, Lakeshia Bush, Kassandra Spates-Harden, Carissa Vinovskis, Petter M. Bjornstad, Laura Pyle, Paul Appelbaum, Jonathan M. Barasch, Andrew S. Bomback, Vivette D. D’Agati, Krzysztof Kiryluk, Karla Mehl, Pietro A. Canetta, Ning Shang, Olivia Balderes, Satoru Kudose, Theodore Alexandrov, Helmut Rennke, Tarek M. El-Achkar, Yinghua Cheng, Pierre C. Dagher, Michael T. Eadon, Kenneth W. Dunn, Katherine J. Kelly, Timothy A. Sutton, Daria Barwinska, Michael J. Ferkowicz, Seth Winfree, Sharon Bledsoe, Marcelino Rivera, James C. Williams, Ricardo Melo Ferreira, Katy Borner, Andreas Bueckle, Bruce W. Herr, Ellen M. Quardokus, Elizabeth 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 Williams, Jennifer 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 Rovin, Samir Parikh, John P. Shapiro, Sethu M. Madhavan, Christopher R. Anderton, Ljiljana Pasa-Tolic, Dusan Velickovic, Jessica Lukowski, George Holt Oliver, Olga Troyanskaya, Rachel Sealfon, Aaron Wong, Katherine R. Tuttle, Ari Pollack, Yury Goltsev, Kun Zhang, Blue B. Lake, Zoltan G. Laszik, Garry Nolan, Patrick Boada, Minnie Sarwal, Kavya Anjani, Tara Sigdel, Tariq Mukatash, Paul J. Lee, Rita R. Alloway, E. Steve Woodle, Ashley R. Burg, Adele Rike, Tiffany Shi, Heather Ascani, Ulysses G.J. Balis, Jeffrey B. Hodgin, Matthias Kretzler, Chrysta Lienczewski, Laura H. Mariani, Rajasree Menon, Becky Steck, Yougqun He, Edgar Otto, Jennifer Schaub, Victoria M. Blanc, Sean Eddy, Ninive C. Conser, Jinghui Luo, Renee Frey, Paul M. Palevsky, Matthew Rosengart, John A. Kellum, Daniel E. Hall, Parmjeet Randhawa, Mitchell Tublin, Raghavan Murugan, Michele M. Elder, James Winters, Tina Vita, Filitsa Bender, Roderick Tan, Matthew Gilliam, Kristina N. Blank, Jonas Carson, Ian H. De Boer, Ashveena L. Dighe, Stuart Shankland, Anitha Vijayan, Joseph P. Gaut, Michael I. Rauchman

Research output: Contribution to journal › Article › peer-review

18 Scopus citations

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.

Original language	English
Article number	105
Journal	Communications Medicine
Volume	2
Issue number	1
DOIs	https://doi.org/10.1038/s43856-022-00138-z
State	Published - Dec 2022

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10.1038/s43856-022-00138-z

Cite this

the Kidney Precision Medicine Project, Lutnick, B., Manthey, D., Becker, J. U., Ginley, B., Moos, K., Zuckerman, J. E., Rodrigues, L., Gallan, A. J., Barisoni, L., Alpers, C. E., Wang, X. X., Myakala, K., Jones, B. A., Levi, M., Kopp, J. B., Yoshida, T., Zee, J., Han, S. S., ... Rauchman, M. I. (2022). A user-friendly tool for cloud-based whole slide image segmentation with examples from renal histopathology. Communications Medicine, 2(1), Article 105. https://doi.org/10.1038/s43856-022-00138-z

@article{90ab6ec4ba424d0092b75875537cddc6,

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

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.",

author = "{the Kidney Precision Medicine Project} and Brendon Lutnick and David Manthey and Becker, {Jan U.} and Brandon Ginley and Katharina Moos and Zuckerman, {Jonathan E.} and Luis Rodrigues and Gallan, {Alexander J.} and Laura Barisoni and Alpers, {Charles E.} and Wang, {Xiaoxin X.} and Komuraiah Myakala and Jones, {Bryce A.} and Moshe Levi and Kopp, {Jeffrey B.} and Teruhiko Yoshida and Jarcy Zee and Han, {Seung Seok} and Sanjay Jain and Rosenberg, {Avi Z.} and Jen, {Kuang Yu} and Pinaki Sarder and Brendon Lutnick and Brandon Ginley and Richard Knight and Lecker, {Stewart H.} and Isaac Stillman and Steve Bogen and Amodu, {Afolarin A.} and Titlayo Ilori and Insa Schmidt and Shana Maikhor and Beck, {Laurence H.} and Ashish Verma and Henderson, {Joel M.} and Ingrid Onul and Sushrut Waikar and McMahon, {Gearoid M.} and Astrid Weins and Colona, {Mia R.} and Valerius, {M. Todd} and Nir Hacohen and Hoover, {Paul J.} and Anna Greka and Marshall, {Jamie L.} and Mark Aulisio and Chen, {Yijiang M.} and Andrew Janowczyk and Catherine Jayapandian and Viswanathan, {Vidya S.} and Bush, {William S.} and Crawford, {Dana C.} and Anant Madabhushi and John O{\textquoteright}toole and Emilio Poggio and John Sedor and Leslie Cooperman and Stacey Jolly and Leal Herlitz and Jane Nguyen and Agustin Gonzalez-Vicente and Ellen Palmer and Dianna Sendrey and Jonathan Taliercio and Lakeshia Bush and Kassandra Spates-Harden and Carissa Vinovskis and Bjornstad, {Petter M.} and Laura Pyle and Paul Appelbaum and Barasch, {Jonathan M.} and Bomback, {Andrew S.} and D{\textquoteright}Agati, {Vivette D.} and Krzysztof Kiryluk and Karla Mehl and Canetta, {Pietro A.} and Ning Shang and Olivia Balderes and Satoru Kudose and Theodore Alexandrov and Helmut Rennke and El-Achkar, {Tarek M.} and Yinghua Cheng and Dagher, {Pierre C.} and Eadon, {Michael T.} and Dunn, {Kenneth W.} and Kelly, {Katherine J.} and Sutton, {Timothy A.} and Daria Barwinska and Ferkowicz, {Michael J.} and Seth Winfree and Sharon Bledsoe and Marcelino Rivera and Williams, {James C.} and Ferreira, {Ricardo Melo} and Katy Borner and Andreas Bueckle and Herr, {Bruce W.} and Quardokus, {Ellen M.} and Elizabeth Record and Jing Su and Debora Gisch and Stephanie Wofford and Yashvardhan Jain and Parikh, {Chirag R.} and Corona-Villalobos, {Celia P.} and Steven Menez and Yumeng Wen and Camille Johansen and Rosas, {Sylvia E.} and Neil Roy and Mark Williams and Jennifer Sun and Joseph Ardayfio and Jack Bebiak and Keith Brown and Campbell, {Catherine E.} and John Saul and Anna Shpigel and Christy Stutzke and Robert Koewler and Taneisha Campbell and Lynda Hayashi and Nichole Jefferson and Roberts, {Glenda V.} and Roy Pinkeney and Azeloglu, {Evren U.} and Cijang He and Ravi Iyengar and Jens Hansen and Yuguang Xiong and Pottumarthi Prasad and Anand Srivastava and Brad Rovin and Samir Parikh and Shapiro, {John P.} and Madhavan, {Sethu M.} and Anderton, {Christopher R.} and Ljiljana Pasa-Tolic and Dusan Velickovic and Jessica Lukowski and Oliver, {George Holt} and Olga Troyanskaya and Rachel Sealfon and Aaron Wong and Tuttle, {Katherine R.} and Ari Pollack and Yury Goltsev and Kun Zhang and Lake, {Blue B.} and Laszik, {Zoltan G.} and Garry Nolan and Patrick Boada and Minnie Sarwal and Kavya Anjani and Tara Sigdel and Tariq Mukatash and Lee, {Paul J.} and Alloway, {Rita R.} and Woodle, {E. Steve} and Burg, {Ashley R.} and Adele Rike and Tiffany Shi and Heather Ascani and Balis, {Ulysses G.J.} and Hodgin, {Jeffrey B.} and Matthias Kretzler and Chrysta Lienczewski and Mariani, {Laura H.} and Rajasree Menon and Becky Steck and Yougqun He and Edgar Otto and Jennifer Schaub and Blanc, {Victoria M.} and Sean Eddy and Conser, {Ninive C.} and Jinghui Luo and Renee Frey and Palevsky, {Paul M.} and Matthew Rosengart and Kellum, {John A.} and Hall, {Daniel E.} and Parmjeet Randhawa and Mitchell Tublin and Raghavan Murugan and Elder, {Michele M.} and James Winters and Tina Vita and Filitsa Bender and Roderick Tan and Matthew Gilliam and Blank, {Kristina N.} and Jonas Carson and {De Boer}, {Ian H.} and Dighe, {Ashveena L.} and Stuart Shankland and Anitha Vijayan and Gaut, {Joseph P.} and Rauchman, {Michael I.}",

note = "Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = dec,

doi = "10.1038/s43856-022-00138-z",

language = "English",

volume = "2",

journal = "Communications Medicine",

issn = "2730-664X",

number = "1",

}

the Kidney Precision Medicine Project, Lutnick, B, Manthey, D, Becker, JU, Ginley, B, Moos, K, Zuckerman, JE, Rodrigues, L, Gallan, AJ, Barisoni, L, Alpers, CE, Wang, XX, Myakala, K, Jones, BA, Levi, M, Kopp, JB, Yoshida, T, Zee, J, Han, SS, Jain, S, Rosenberg, AZ, Jen, KY, Sarder, P, Lutnick, B, Ginley, B, Knight, R, Lecker, SH, Stillman, I, Bogen, S, Amodu, AA, Ilori, T, Schmidt, I, Maikhor, S, Beck, LH, Verma, A, Henderson, JM, Onul, I, Waikar, S, McMahon, GM, Weins, A, Colona, MR, Valerius, MT, Hacohen, N, Hoover, PJ, Greka, A, Marshall, JL, Aulisio, M, Chen, YM, Janowczyk, A, Jayapandian, C, Viswanathan, VS, Bush, WS, Crawford, DC, Madabhushi, A, O’toole, J, Poggio, E, Sedor, J, Cooperman, L, Jolly, S, Herlitz, L, Nguyen, J, Gonzalez-Vicente, A, Palmer, E, Sendrey, D, Taliercio, J, Bush, L, Spates-Harden, K, Vinovskis, C, Bjornstad, PM, Pyle, L, Appelbaum, P, Barasch, JM, Bomback, AS, D’Agati, VD, Kiryluk, K, Mehl, K, Canetta, PA, Shang, N, Balderes, O, Kudose, S, Alexandrov, T, Rennke, H, El-Achkar, TM, Cheng, Y, Dagher, PC, Eadon, MT, Dunn, KW, Kelly, KJ, Sutton, TA, Barwinska, D, Ferkowicz, MJ, Winfree, S, Bledsoe, S, Rivera, M, Williams, JC, Ferreira, RM, Borner, K, Bueckle, A, Herr, BW, Quardokus, EM, Record, E, Su, J, Gisch, D, Wofford, S, Jain, Y, Parikh, CR, Corona-Villalobos, CP, Menez, S, Wen, Y, Johansen, C, Rosas, SE, Roy, N, Williams, M, Sun, J, Ardayfio, J, Bebiak, J, Brown, K, Campbell, CE, Saul, J, Shpigel, A, Stutzke, C, Koewler, R, Campbell, T, Hayashi, L, Jefferson, N, Roberts, GV, Pinkeney, R, Azeloglu, EU, He, C, Iyengar, R, Hansen, J, Xiong, Y, Prasad, P, Srivastava, A, Rovin, B, Parikh, S, Shapiro, JP, Madhavan, SM, Anderton, CR, Pasa-Tolic, L, Velickovic, D, Lukowski, J, Oliver, GH, Troyanskaya, O, Sealfon, R, Wong, A, Tuttle, KR, Pollack, A, Goltsev, Y, Zhang, K, Lake, BB, Laszik, ZG, Nolan, G, Boada, P, Sarwal, M, Anjani, K, Sigdel, T, Mukatash, T, Lee, PJ, Alloway, RR, Woodle, ES, Burg, AR, Rike, A, Shi, T, Ascani, H, Balis, UGJ, Hodgin, JB, Kretzler, M, Lienczewski, C, Mariani, LH, Menon, R, Steck, B, He, Y, Otto, E, Schaub, J, Blanc, VM, Eddy, S, Conser, NC, Luo, J, Frey, R, Palevsky, PM, Rosengart, M, Kellum, JA, Hall, DE, Randhawa, P, Tublin, M, Murugan, R, Elder, MM, Winters, J, Vita, T, Bender, F, Tan, R, Gilliam, M, Blank, KN, Carson, J, De Boer, IH, Dighe, AL, Shankland, S, Vijayan, A, Gaut, JP & Rauchman, MI 2022, 'A user-friendly tool for cloud-based whole slide image segmentation with examples from renal histopathology', Communications Medicine, vol. 2, no. 1, 105. https://doi.org/10.1038/s43856-022-00138-z

TY - JOUR

T1 - A user-friendly tool for cloud-based whole slide image segmentation with examples from renal histopathology

AU - the Kidney Precision Medicine Project

AU - Lutnick, Brendon

AU - Manthey, David

AU - Becker, Jan U.

AU - Ginley, Brandon

AU - Moos, Katharina

AU - Zuckerman, Jonathan E.

AU - Rodrigues, Luis

AU - Gallan, Alexander J.

AU - Barisoni, Laura

AU - Alpers, Charles E.

AU - Wang, Xiaoxin X.

AU - Myakala, Komuraiah

AU - Jones, Bryce A.

AU - Levi, Moshe

AU - Kopp, Jeffrey B.

AU - Yoshida, Teruhiko

AU - Zee, Jarcy

AU - Han, Seung Seok

AU - Jain, Sanjay

AU - Rosenberg, Avi Z.

AU - Jen, Kuang Yu

AU - Sarder, Pinaki

AU - Lutnick, Brendon

AU - Ginley, Brandon

AU - Knight, Richard

AU - Lecker, Stewart H.

AU - Stillman, Isaac

AU - Bogen, Steve

AU - Amodu, Afolarin A.

AU - Ilori, Titlayo

AU - Schmidt, Insa

AU - Maikhor, Shana

AU - Beck, Laurence H.

AU - Verma, Ashish

AU - Henderson, Joel M.

AU - Onul, Ingrid

AU - Waikar, Sushrut

AU - McMahon, Gearoid M.

AU - Weins, Astrid

AU - Colona, Mia R.

AU - Valerius, M. Todd

AU - Hacohen, Nir

AU - Hoover, Paul J.

AU - Greka, Anna

AU - Marshall, Jamie L.

AU - Aulisio, Mark

AU - Chen, Yijiang M.

AU - Janowczyk, Andrew

AU - Jayapandian, Catherine

AU - Viswanathan, Vidya S.

AU - Bush, William S.

AU - Crawford, Dana C.

AU - Madabhushi, Anant

AU - O’toole, John

AU - Poggio, Emilio

AU - Sedor, John

AU - Cooperman, Leslie

AU - Jolly, Stacey

AU - Herlitz, Leal

AU - Nguyen, Jane

AU - Gonzalez-Vicente, Agustin

AU - Palmer, Ellen

AU - Sendrey, Dianna

AU - Taliercio, Jonathan

AU - Bush, Lakeshia

AU - Spates-Harden, Kassandra

AU - Vinovskis, Carissa

AU - Bjornstad, Petter M.

AU - Pyle, Laura

AU - Appelbaum, Paul

AU - Barasch, Jonathan M.

AU - Bomback, Andrew S.

AU - D’Agati, Vivette D.

AU - Kiryluk, Krzysztof

AU - Mehl, Karla

AU - Canetta, Pietro A.

AU - Shang, Ning

AU - Balderes, Olivia

AU - Kudose, Satoru

AU - Alexandrov, Theodore

AU - Rennke, Helmut

AU - El-Achkar, Tarek M.

AU - Cheng, Yinghua

AU - Dagher, Pierre C.

AU - Eadon, Michael T.

AU - Dunn, Kenneth W.

AU - Kelly, Katherine J.

AU - Sutton, Timothy A.

AU - Barwinska, Daria

AU - Ferkowicz, Michael J.

AU - Winfree, Seth

AU - Bledsoe, Sharon

AU - Rivera, Marcelino

AU - Williams, James C.

AU - Ferreira, Ricardo Melo

AU - Borner, Katy

AU - Bueckle, Andreas

AU - Herr, Bruce W.

AU - Quardokus, Ellen M.

AU - Record, Elizabeth

AU - Su, Jing

AU - Gisch, Debora

AU - Wofford, Stephanie

AU - Jain, Yashvardhan

AU - Parikh, Chirag R.

AU - Corona-Villalobos, Celia P.

AU - Menez, Steven

AU - Wen, Yumeng

AU - Johansen, Camille

AU - Rosas, Sylvia E.

AU - Roy, Neil

AU - Williams, Mark

AU - Sun, Jennifer

AU - Ardayfio, Joseph

AU - Bebiak, Jack

AU - Brown, Keith

AU - Campbell, Catherine E.

AU - Saul, John

AU - Shpigel, Anna

AU - Stutzke, Christy

AU - Koewler, Robert

AU - Campbell, Taneisha

AU - Hayashi, Lynda

AU - Jefferson, Nichole

AU - Roberts, Glenda V.

AU - Pinkeney, Roy

AU - Azeloglu, Evren U.

AU - He, Cijang

AU - Iyengar, Ravi

AU - Hansen, Jens

AU - Xiong, Yuguang

AU - Prasad, Pottumarthi

AU - Srivastava, Anand

AU - Rovin, Brad

AU - Parikh, Samir

AU - Shapiro, John P.

AU - Madhavan, Sethu M.

AU - Anderton, Christopher R.

AU - Pasa-Tolic, Ljiljana

AU - Velickovic, Dusan

AU - Lukowski, Jessica

AU - Oliver, George Holt

AU - Troyanskaya, Olga

AU - Sealfon, Rachel

AU - Wong, Aaron

AU - Tuttle, Katherine R.

AU - Pollack, Ari

AU - Goltsev, Yury

AU - Zhang, Kun

AU - Lake, Blue B.

AU - Laszik, Zoltan G.

AU - Nolan, Garry

AU - Boada, Patrick

AU - Sarwal, Minnie

AU - Anjani, Kavya

AU - Sigdel, Tara

AU - Mukatash, Tariq

AU - Lee, Paul J.

AU - Alloway, Rita R.

AU - Woodle, E. Steve

AU - Burg, Ashley R.

AU - Rike, Adele

AU - Shi, Tiffany

AU - Ascani, Heather

AU - Balis, Ulysses G.J.

AU - Hodgin, Jeffrey B.

AU - Kretzler, Matthias

AU - Lienczewski, Chrysta

AU - Mariani, Laura H.

AU - Menon, Rajasree

AU - Steck, Becky

AU - He, Yougqun

AU - Otto, Edgar

AU - Schaub, Jennifer

AU - Blanc, Victoria M.

AU - Eddy, Sean

AU - Conser, Ninive C.

AU - Luo, Jinghui

AU - Frey, Renee

AU - Palevsky, Paul M.

AU - Rosengart, Matthew

AU - Kellum, John A.

AU - Hall, Daniel E.

AU - Randhawa, Parmjeet

AU - Tublin, Mitchell

AU - Murugan, Raghavan

AU - Elder, Michele M.

AU - Winters, James

AU - Vita, Tina

AU - Bender, Filitsa

AU - Tan, Roderick

AU - Gilliam, Matthew

AU - Blank, Kristina N.

AU - Carson, Jonas

AU - De Boer, Ian H.

AU - Dighe, Ashveena L.

AU - Shankland, Stuart

AU - Vijayan, Anitha

AU - Gaut, Joseph P.

AU - Rauchman, Michael I.

PY - 2022/12

Y1 - 2022/12

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85148639650&partnerID=8YFLogxK

U2 - 10.1038/s43856-022-00138-z

DO - 10.1038/s43856-022-00138-z

M3 - Article

AN - SCOPUS:85148639650

SN - 2730-664X

VL - 2

JO - Communications Medicine

JF - Communications Medicine

IS - 1

M1 - 105

ER -

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

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