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The University of California San Francisco Preoperative Diffuse Glioma (UCSF-PDGM) MRI Dataset


Aug 30, 2021
Evan Calabrese, Javier Villanueva-Meyer, Jeffrey Rudie, Andreas Rauschecker, Ujjwal Baid, Spyridon Bakas, John Mongan, Christopher Hess, Soonmee Cha

* 6 pages, 1 figure, 2 tables 

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The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification


Jul 05, 2021
Ujjwal Baid, Satyam Ghodasara, Michel Bilello, Suyash Mohan, Evan Calabrese, Errol Colak, Keyvan Farahani, Jayashree Kalpathy-Cramer, Felipe C. Kitamura, Sarthak Pati, Luciano M. Prevedello, Jeffrey D. Rudie, Chiharu Sako, Russell T. Shinohara, Timothy Bergquist, Rong Chai, James Eddy, Julia Elliott, Walter Reade, Thomas Schaffter, Thomas Yu, Jiaxin Zheng, BraTS Annotators, Christos Davatzikos, John Mongan, Christopher Hess, Soonmee Cha, Javier Villanueva-Meyer, John B. Freymann, Justin S. Kirby, Benedikt Wiestler, Priscila Crivellaro, Rivka R. Colen, Aikaterini Kotrotsou, Daniel Marcus, Mikhail Milchenko, Arash Nazeri, Hassan Fathallah-Shaykh, Roland Wiest, Andras Jakab, Marc-Andre Weber, Abhishek Mahajan, Bjoern Menze, Adam E. Flanders, Spyridon Bakas

* 17 pages, 2 figures, 1 table 

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The Medical Segmentation Decathlon


Jun 10, 2021
Michela Antonelli, Annika Reinke, Spyridon Bakas, Keyvan Farahani, AnnetteKopp-Schneider, Bennett A. Landman, Geert Litjens, Bjoern Menze, Olaf Ronneberger, Ronald M. Summers, Bram van Ginneken, Michel Bilello, Patrick Bilic, Patrick F. Christ, Richard K. G. Do, Marc J. Gollub, Stephan H. Heckers, Henkjan Huisman, William R. Jarnagin, Maureen K. McHugo, Sandy Napel, Jennifer S. Goli Pernicka, Kawal Rhode, Catalina Tobon-Gomez, Eugene Vorontsov, Henkjan Huisman, James A. Meakin, Sebastien Ourselin, Manuel Wiesenfarth, Pablo Arbelaez, Byeonguk Bae, Sihong Chen, Laura Daza, Jianjiang Feng, Baochun He, Fabian Isensee, Yuanfeng Ji, Fucang Jia, Namkug Kim, Ildoo Kim, Dorit Merhof, Akshay Pai, Beomhee Park, Mathias Perslev, Ramin Rezaiifar, Oliver Rippel, Ignacio Sarasua, Wei Shen, Jaemin Son, Christian Wachinger, Liansheng Wang, Yan Wang, Yingda Xia, Daguang Xu, Zhanwei Xu, Yefeng Zheng, Amber L. Simpson, Lena Maier-Hein, M. Jorge Cardoso


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The Federated Tumor Segmentation (FeTS) Challenge


May 14, 2021
Sarthak Pati, Ujjwal Baid, Maximilian Zenk, Brandon Edwards, Micah Sheller, G. Anthony Reina, Patrick Foley, Alexey Gruzdev, Jason Martin, Shadi Albarqouni, Yong Chen, Russell Taki Shinohara, Annika Reinke, David Zimmerer, John B. Freymann, Justin S. Kirby, Christos Davatzikos, Rivka R. Colen, Aikaterini Kotrotsou, Daniel Marcus, Mikhail Milchenko, Arash Nazeri, Hassan Fathallah-Shaykh, Roland Wiest, Andras Jakab, Marc-Andre Weber, Abhishek Mahajan, Lena Maier-Hein, Jens Kleesiek, Bjoern Menze, Klaus Maier-Hein, Spyridon Bakas


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OpenFL: An open-source framework for Federated Learning


May 13, 2021
G Anthony Reina, Alexey Gruzdev, Patrick Foley, Olga Perepelkina, Mansi Sharma, Igor Davidyuk, Ilya Trushkin, Maksim Radionov, Aleksandr Mokrov, Dmitry Agapov, Jason Martin, Brandon Edwards, Micah J. Sheller, Sarthak Pati, Prakash Narayana Moorthy, Shih-han Wang, Prashant Shah, Spyridon Bakas


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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

* 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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Are we using appropriate segmentation metrics? Identifying correlates of human expert perception for CNN training beyond rolling the DICE coefficient


Mar 10, 2021
Florian Kofler, Ivan Ezhov, Fabian Isensee, Fabian Balsiger, Christoph Berger, Maximilian Koerner, Johannes Paetzold, Hongwei Li, Suprosanna Shit, Richard McKinley, Spyridon Bakas, Claus Zimmer, Donna Ankerst, Jan Kirschke, Benedikt Wiestler, Bjoern H. Menze


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GaNDLF: A Generally Nuanced Deep Learning Framework for Scalable End-to-End Clinical Workflows in Medical Imaging


Feb 26, 2021
Sarthak Pati, Siddhesh P. Thakur, Megh Bhalerao, Ujjwal Baid, Caleb Grenko, Brandon Edwards, Micah Sheller, Jose Agraz, Bhakti Baheti, Vishnu Bashyam, Parth Sharma, Babak Haghighi, Aimilia Gastounioti, Mark Bergman, Bjoern Menze, Despina Kontos, Christos Davatzikos, Spyridon Bakas


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A Deep Network for Joint Registration and Reconstruction of Images with Pathologies


Aug 17, 2020
Xu Han, Zhengyang Shen, Zhenlin Xu, Spyridon Bakas, Hamed Akbari, Michel Bilello, Christos Davatzikos, Marc Niethammer


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The Future of Digital Health with Federated Learning


Mar 18, 2020
Nicola Rieke, Jonny Hancox, Wenqi Li, Fausto Milletari, Holger Roth, Shadi Albarqouni, Spyridon Bakas, Mathieu N. Galtier, Bennett Landman, Klaus Maier-Hein, Sebastien Ourselin, Micah Sheller, Ronald M. Summers, Andrew Trask, Daguang Xu, Maximilian Baust, M. Jorge Cardoso


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ModelHub.AI: Dissemination Platform for Deep Learning Models


Nov 26, 2019
Ahmed Hosny, Michael Schwier, Christoph Berger, Evin P Örnek, Mehmet Turan, Phi V Tran, Leon Weninger, Fabian Isensee, Klaus H Maier-Hein, Richard McKinley, Michael T Lu, Udo Hoffmann, Bjoern Menze, Spyridon Bakas, Andriy Fedorov, Hugo JWL Aerts


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Accurate and Robust Alignment of Variable-stained Histologic Images Using a General-purpose Greedy Diffeomorphic Registration Tool


Apr 26, 2019
Ludovic Venet, Sarthak Pati, Paul Yushkevich, Spyridon Bakas


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A large annotated medical image dataset for the development and evaluation of segmentation algorithms


Feb 25, 2019
Amber L. Simpson, Michela Antonelli, Spyridon Bakas, Michel Bilello, Keyvan Farahani, Bram van Ginneken, Annette Kopp-Schneider, Bennett A. Landman, Geert Litjens, Bjoern Menze, Olaf Ronneberger, Ronald M. Summers, Patrick Bilic, Patrick F. Christ, Richard K. G. Do, Marc Gollub, Jennifer Golia-Pernicka, Stephan H. Heckers, William R. Jarnagin, Maureen K. McHugo, Sandy Napel, Eugene Vorontsov, Lena Maier-Hein, M. Jorge Cardoso


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Multi-Institutional Deep Learning Modeling Without Sharing Patient Data: A Feasibility Study on Brain Tumor Segmentation


Oct 22, 2018
Micah J Sheller, G Anthony Reina, Brandon Edwards, Jason Martin, Spyridon Bakas

* MICCAI, Brain Lesion (BrainLes) workshop, September 16, 2018, Granada, Spain 

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Brain Extraction from Normal and Pathological Images: A Joint PCA/Image-Reconstruction Approach


Apr 30, 2018
Xu Han, Roland Kwitt, Stephen Aylward, Spyridon Bakas, Bjoern Menze, Alexander Asturias, Paul Vespa, John Van Horn, Marc Niethammer


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