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Learning Topological Interactions for Multi-Class Medical Image Segmentation


Jul 20, 2022
Saumya Gupta, Xiaoling Hu, James Kaan, Michael Jin, Mutshipay Mpoy, Katherine Chung, Gagandeep Singh, Mary Saltz, Tahsin Kurc, Joel Saltz, Apostolos Tassiopoulos, Prateek Prasanna, Chao Chen

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* Accepted to ECCV 2022 (Oral); 32 pages, 19 figures 

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AI and Pathology: Steering Treatment and Predicting Outcomes


Jun 15, 2022
Rajarsi Gupta, Jakub Kaczmarzyk, Soma Kobayashi, Tahsin Kurc, Joel Saltz

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Metrics reloaded: Pitfalls and recommendations for image analysis validation


Jun 03, 2022
Lena Maier-Hein, Annika Reinke, Evangelia Christodoulou, Ben Glocker, Patrick Godau, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A. Riegler, Manuel Wiesenfarth, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A. Emre Kavur, Tim Rädsch, Minu D. Tizabi, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Peter Bankhead, Arriel Benis, M. Jorge Cardoso, Veronika Cheplygina, Beth Cimini, Gary S. Collins, Keyvan Farahani, Bram van Ginneken, Daniel A. Hashimoto, Michael M. Hoffman, Merel Huisman, Pierre Jannin, Charles E. Kahn, Alexandros Karargyris, Alan Karthikesalingam, Hannes Kenngott, Annette Kopp-Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L. Martel, Peter Mattson, Erik Meijering, Bjoern Menze, David Moher, Karel G. M. Moons, Henning Müller, Felix Nickel, Brennan Nichyporuk, Jens Petersen, Nasir Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clarisa Sánchez Gutiérrez, Shravya Shetty, Maarten van Smeden, Carole H. Sudre, Ronald M. Summers, Abdel A. Taha, Sotirios A. Tsaftaris, Ben Van Calster, Gaël Varoquaux, Paul F. Jäger

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* Shared first authors: Lena Maier-Hein, Annika Reinke. arXiv admin note: substantial text overlap with arXiv:2104.05642 

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A Novel Framework for Characterization of Tumor-Immune Spatial Relationships in Tumor Microenvironment


May 01, 2022
Mahmudul Hasan, Jakub R. Kaczmarzyk, David Paredes, Lyanne Oblein, Jaymie Oentoro, Shahira Abousamra, Michael Horowitz, Dimitris Samaras, Chao Chen, Tahsin Kurc, Kenneth R. Shroyer, Joel Saltz

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Federated Learning Enables Big Data for Rare Cancer Boundary Detection


Apr 25, 2022
Sarthak Pati, Ujjwal Baid, Brandon Edwards, Micah Sheller, Shih-Han Wang, G Anthony Reina, Patrick Foley, Alexey Gruzdev, Deepthi Karkada, Christos Davatzikos, Chiharu Sako, Satyam Ghodasara, Michel Bilello, Suyash Mohan, Philipp Vollmuth, Gianluca Brugnara, Chandrakanth J Preetha, Felix Sahm, Klaus Maier-Hein, Maximilian Zenk, Martin Bendszus, Wolfgang Wick, Evan Calabrese, Jeffrey Rudie, Javier Villanueva-Meyer, Soonmee Cha, Madhura Ingalhalikar, Manali Jadhav, Umang Pandey, Jitender Saini, John Garrett, Matthew Larson, Robert Jeraj, Stuart Currie, Russell Frood, Kavi Fatania, Raymond Y Huang, Ken Chang, Carmen Balana, Jaume Capellades, Josep Puig, Johannes Trenkler, Josef Pichler, Georg Necker, Andreas Haunschmidt, Stephan Meckel, Gaurav Shukla, Spencer Liem, Gregory S Alexander, Joseph Lombardo, Joshua D Palmer, Adam E Flanders, Adam P Dicker, Haris I Sair, Craig K Jones, Archana Venkataraman, Meirui Jiang, Tiffany Y So, Cheng Chen, Pheng Ann Heng, Qi Dou, Michal Kozubek, Filip Lux, Jan Michálek, Petr Matula, Miloš Keřkovský, Tereza Kopřivová, Marek Dostál, Václav Vybíhal, Michael A Vogelbaum, J Ross Mitchell, Joaquim Farinhas, Joseph A Maldjian, Chandan Ganesh Bangalore Yogananda, Marco C Pinho, Divya Reddy, James Holcomb, Benjamin C Wagner, Benjamin M Ellingson, Timothy F Cloughesy, Catalina Raymond, Talia Oughourlian, Akifumi Hagiwara, Chencai Wang, Minh-Son To, Sargam Bhardwaj, Chee Chong, Marc Agzarian, Alexandre Xavier Falcão, Samuel B Martins, Bernardo C A Teixeira, Flávia Sprenger, David Menotti, Diego R Lucio, Pamela LaMontagne, Daniel Marcus, Benedikt Wiestler, Florian Kofler, Ivan Ezhov, Marie Metz, Rajan Jain, Matthew Lee, Yvonne W Lui, Richard McKinley, Johannes Slotboom, Piotr Radojewski, Raphael Meier, Roland Wiest, Derrick Murcia, Eric Fu, Rourke Haas, John Thompson, David Ryan Ormond, Chaitra Badve, Andrew E Sloan, Vachan Vadmal, Kristin Waite, Rivka R Colen, Linmin Pei, Murat Ak, Ashok Srinivasan, J Rajiv Bapuraj, Arvind Rao, Nicholas Wang, Ota Yoshiaki, Toshio Moritani, Sevcan Turk, Joonsang Lee, Snehal Prabhudesai, Fanny Morón, Jacob Mandel, Konstantinos Kamnitsas, Ben Glocker, Luke V M Dixon, Matthew Williams, Peter Zampakis, Vasileios Panagiotopoulos, Panagiotis Tsiganos, Sotiris Alexiou, Ilias Haliassos, Evangelia I Zacharaki, Konstantinos Moustakas, Christina Kalogeropoulou, Dimitrios M Kardamakis, Yoon Seong Choi, Seung-Koo Lee, Jong Hee Chang, Sung Soo Ahn, Bing Luo, Laila Poisson, Ning Wen, Pallavi Tiwari, Ruchika Verma, Rohan Bareja, Ipsa Yadav, Jonathan Chen, Neeraj Kumar, Marion Smits, Sebastian R van der Voort, Ahmed Alafandi, Fatih Incekara, Maarten MJ Wijnenga, Georgios Kapsas, Renske Gahrmann, Joost W Schouten, Hendrikus J Dubbink, Arnaud JPE Vincent, Martin J van den Bent, Pim J French, Stefan Klein, Yading Yuan, Sonam Sharma, Tzu-Chi Tseng, Saba Adabi, Simone P Niclou, Olivier Keunen, Ann-Christin Hau, Martin Vallières, David Fortin, Martin Lepage, Bennett Landman, Karthik Ramadass, Kaiwen Xu, Silky Chotai, Lola B Chambless, Akshitkumar Mistry, Reid C Thompson, Yuriy Gusev, Krithika Bhuvaneshwar, Anousheh Sayah, Camelia Bencheqroun, Anas Belouali, Subha Madhavan, Thomas C Booth, Alysha Chelliah, Marc Modat, Haris Shuaib, Carmen Dragos, Aly Abayazeed, Kenneth Kolodziej, Michael Hill, Ahmed Abbassy, Shady Gamal, Mahmoud Mekhaimar, Mohamed Qayati, Mauricio Reyes, Ji Eun Park, Jihye Yun, Ho Sung Kim, Abhishek Mahajan, Mark Muzi, Sean Benson, Regina G H Beets-Tan, Jonas Teuwen, Alejandro Herrera-Trujillo, Maria Trujillo, William Escobar, Ana Abello, Jose Bernal, Jhon Gómez, Joseph Choi, Stephen Baek, Yusung Kim, Heba Ismael, Bryan Allen, John M Buatti, Aikaterini Kotrotsou, Hongwei Li, Tobias Weiss, Michael Weller, Andrea Bink, Bertrand Pouymayou, Hassan F Shaykh, Joel Saltz, Prateek Prasanna, Sampurna Shrestha, Kartik M Mani, David Payne, Tahsin Kurc, Enrique Pelaez, Heydy Franco-Maldonado, Francis Loayza, Sebastian Quevedo, Pamela Guevara, Esteban Torche, Cristobal Mendoza, Franco Vera, Elvis Ríos, Eduardo López, Sergio A Velastin, Godwin Ogbole, Dotun Oyekunle, Olubunmi Odafe-Oyibotha, Babatunde Osobu, Mustapha Shu'aibu, Adeleye Dorcas, Mayowa Soneye, Farouk Dako, Amber L Simpson, Mohammad Hamghalam, Jacob J Peoples, Ricky Hu, Anh Tran, Danielle Cutler, Fabio Y Moraes, Michael A Boss, James Gimpel, Deepak Kattil Veettil, Kendall Schmidt, Brian Bialecki, Sailaja Marella, Cynthia Price, Lisa Cimino, Charles Apgar, Prashant Shah, Bjoern Menze, Jill S Barnholtz-Sloan, Jason Martin, Spyridon Bakas

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* federated learning, deep learning, convolutional neural network, segmentation, brain tumor, glioma, glioblastoma, FeTS, BraTS 

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Multi-Class Cell Detection Using Spatial Context Representation


Oct 10, 2021
Shahira Abousamra, David Belinsky, John Van Arnam, Felicia Allard, Eric Yee, Rajarsi Gupta, Tahsin Kurc, Dimitris Samaras, Joel Saltz, Chao Chen

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Common Limitations of Image Processing Metrics: A Picture Story


Apr 13, 2021
Annika Reinke, Matthias Eisenmann, Minu D. Tizabi, Carole H. Sudre, Tim Rädsch, Michela Antonelli, Tal Arbel, Spyridon Bakas, M. Jorge Cardoso, Veronika Cheplygina, Keyvan Farahani, Ben Glocker, Doreen Heckmann-Nötzel, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Jens Kleesiek, Tahsin Kurc, Michal Kozubek, Bennett A. Landman, Geert Litjens, Klaus Maier-Hein, Bjoern Menze, Henning Müller, Jens Petersen, Mauricio Reyes, Nicola Rieke, Bram Stieltjes, Ronald M. Summers, Sotirios A. Tsaftaris, Bram van Ginneken, Annette Kopp-Schneider, Paul Jäger, Lena Maier-Hein

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* This is a dynamic paper on limitations of commonly used metrics. The current version discusses segmentation metrics only, while future versions will also include metrics for classification and detection. For missing use cases, comments or questions, please contact [email protected] or [email protected]. Substantial contributions to this document will be acknowledged with a co-authorship 

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Learning from Thresholds: Fully Automated Classification of Tumor Infiltrating Lymphocytes for Multiple Cancer Types


Jul 09, 2019
Shahira Abousamra, Le Hou, Rajarsi Gupta, Chao Chen, Dimitris Samaras, Tahsin Kurc, Rebecca Batiste, Tianhao Zhao, Shroyer Kenneth, Joel Saltz

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