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Continuous-Time Deep Glioma Growth Models


Jul 02, 2021
Jens Petersen, Fabian Isensee, Gregor Köhler, Paul F. Jäger, David Zimmerer, Ulf Neuberger, Wolfgang Wick, Jürgen Debus, Sabine Heiland, Martin Bendszus, Philipp Vollmuth, Klaus H. Maier-Hein

* MICCAI 2021 

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How can we learn (more) from challenges? A statistical approach to driving future algorithm development


Jun 17, 2021
Tobias Roß, Pierangela Bruno, Annika Reinke, Manuel Wiesenfarth, Lisa Koeppel, Peter M. Full, Bünyamin Pekdemir, Patrick Godau, Darya Trofimova, Fabian Isensee, Sara Moccia, Francesco Calimeri, Beat P. Müller-Stich, Annette Kopp-Schneider, Lena Maier-Hein


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GP-ConvCNP: Better Generalization for Convolutional Conditional Neural Processes on Time Series Data


Jun 11, 2021
Jens Petersen, Gregor Köhler, David Zimmerer, Fabian Isensee, Paul F. Jäger, Klaus H. Maier-Hein

* UAI 2021 

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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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nnDetection: A Self-configuring Method for Medical Object Detection


Jun 01, 2021
Michael Baumgartner, Paul F. Jaeger, Fabian Isensee, Klaus H. Maier-Hein

* *Michael Baumgartner and Paul F. J\"ager contributed equally 

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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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Studying Robustness of Semantic Segmentation under Domain Shift in cardiac MRI


Nov 15, 2020
Peter M. Full, Fabian Isensee, Paul F. Jäger, Klaus Maier-Hein

* 12 pages, 3 Figures, Contribution to the STACOM Workshop at MICCAI 2020 

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nnU-Net for Brain Tumor Segmentation


Nov 02, 2020
Fabian Isensee, Paul F. Jaeger, Peter M. Full, Philipp Vollmuth, Klaus H. Maier-Hein


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OR-UNet: an Optimized Robust Residual U-Net for Instrument Segmentation in Endoscopic Images


Apr 27, 2020
Fabian Isensee, Klaus H. Maier-Hein


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Robust Medical Instrument Segmentation Challenge 2019


Mar 23, 2020
Tobias Ross, Annika Reinke, Peter M. Full, Martin Wagner, Hannes Kenngott, Martin Apitz, Hellena Hempe, Diana Mindroc Filimon, Patrick Scholz, Thuy Nuong Tran, Pierangela Bruno, Pablo Arbeláez, Gui-Bin Bian, Sebastian Bodenstedt, Jon Lindström Bolmgren, Laura Bravo-Sánchez, Hua-Bin Chen, Cristina González, Dong Guo, Pål Halvorsen, Pheng-Ann Heng, Enes Hosgor, Zeng-Guang Hou, Fabian Isensee, Debesh Jha, Tingting Jiang, Yueming Jin, Kadir Kirtac, Sabrina Kletz, Stefan Leger, Zhixuan Li, Klaus H. Maier-Hein, Zhen-Liang Ni, Michael A. Riegler, Klaus Schoeffmann, Ruohua Shi, Stefanie Speidel, Michael Stenzel, Isabell Twick, Gutai Wang, Jiacheng Wang, Liansheng Wang, Lu Wang, Yujie Zhang, Yan-Jie Zhou, Lei Zhu, Manuel Wiesenfarth, Annette Kopp-Schneider, Beat P. Müller-Stich, Lena Maier-Hein

* A pre-print 

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CHAOS Challenge -- Combined (CT-MR) Healthy Abdominal Organ Segmentation


Jan 17, 2020
A. Emre Kavur, N. Sinem Gezer, Mustafa Barış, Pierre-Henri Conze, Vladimir Groza, Duc Duy Pham, Soumick Chatterjee, Philipp Ernst, Savaş Özkan, Bora Baydar, Dmitry Lachinov, Shuo Han, Josef Pauli, Fabian Isensee, Matthias Perkonigg, Rachana Sathish, Ronnie Rajan, Sinem Aslan, Debdoot Sheet, Gurbandurdy Dovletov, Oliver Speck, Andreas Nürnberger, Klaus H. Maier-Hein, Gözde Bozdağı Akar, Gözde Ünal, Oğuz Dicle, M. Alper Selver

* 10 pages, 2 figures 

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The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 Challenge


Dec 02, 2019
Nicholas Heller, Fabian Isensee, Klaus H. Maier-Hein, Xiaoshuai Hou, Chunmei Xie, Fengyi Li, Yang Nan, Guangrui Mu, Zhiyong Lin, Miofei Han, Guang Yao, Yaozong Gao, Yao Zhang, Yixin Wang, Feng Hou, Jiawei Yang, Guangwei Xiong, Jiang Tian, Cheng Zhong, Jun Ma, Jack Rickman, Joshua Dean, Bethany Stai, Resha Tejpaul, Makinna Oestreich, Paul Blake, Heather Kaluzniak, Shaneabbas Raza, Joel Rosenberg, Keenan Moore, Edward Walczak, Zachary Rengel, Zach Edgerton, Ranveer Vasdev, Matthew Peterson, Sean McSweeney, Sarah Peterson, Arveen Kalapara, Niranjan Sathianathen, Christopher Weight, Nikolaos Papanikolopoulos

* 18 pages, 7 figures 

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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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An attempt at beating the 3D U-Net


Aug 06, 2019
Fabian Isensee, Klaus H. Maier-Hein


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Unsupervised Anomaly Localization using Variational Auto-Encoders


Jul 11, 2019
David Zimmerer, Fabian Isensee, Jens Petersen, Simon Kohl, Klaus Maier-Hein


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Deep Probabilistic Modeling of Glioma Growth


Jul 09, 2019
Jens Petersen, Paul F. Jäger, Fabian Isensee, Simon A. A. Kohl, Ulf Neuberger, Wolfgang Wick, Jürgen Debus, Sabine Heiland, Martin Bendszus, Philipp Kickingereder, Klaus H. Maier-Hein

* MICCAI 2019 

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nnU-Net: Breaking the Spell on Successful Medical Image Segmentation


Apr 17, 2019
Fabian Isensee, Jens Petersen, Simon A. A. Kohl, Paul F. Jäger, Klaus H. Maier-Hein


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Automated brain extraction of multi-sequence MRI using artificial neural networks


Jan 31, 2019
Fabian Isensee, Marianne Schell, Irada Tursunova, Gianluca Brugnara, David Bonekamp, Ulf Neuberger, Antje Wick, Heinz-Peter Schlemmer, Sabine Heiland, Wolfgang Wick, Martin Bendszus, Klaus Hermann Maier-Hein, Philipp Kickingereder


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Context-encoding Variational Autoencoder for Unsupervised Anomaly Detection


Dec 14, 2018
David Zimmerer, Simon A. A. Kohl, Jens Petersen, Fabian Isensee, Klaus H. Maier-Hein


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Retina U-Net: Embarrassingly Simple Exploitation of Segmentation Supervision for Medical Object Detection


Nov 21, 2018
Paul F. Jaeger, Simon A. A. Kohl, Sebastian Bickelhaupt, Fabian Isensee, Tristan Anselm Kuder, Heinz-Peter Schlemmer, Klaus H. Maier-Hein


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nnU-Net: Self-adapting Framework for U-Net-Based Medical Image Segmentation


Sep 27, 2018
Fabian Isensee, Jens Petersen, Andre Klein, David Zimmerer, Paul F. Jaeger, Simon Kohl, Jakob Wasserthal, Gregor Koehler, Tobias Norajitra, Sebastian Wirkert, Klaus H. Maier-Hein


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No New-Net


Sep 27, 2018
Fabian Isensee, Philipp Kickingereder, Wolfgang Wick, Martin Bendszus, Klaus H. Maier-Hein


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Brain Tumor Segmentation and Radiomics Survival Prediction: Contribution to the BRATS 2017 Challenge


Feb 28, 2018
Fabian Isensee, Philipp Kickingereder, Wolfgang Wick, Martin Bendszus, Klaus H. Maier-Hein


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Exploiting the potential of unlabeled endoscopic video data with self-supervised learning


Jan 31, 2018
Tobias Ross, David Zimmerer, Anant Vemuri, Fabian Isensee, Manuel Wiesenfarth, Sebastian Bodenstedt, Fabian Both, Philip Kessler, Martin Wagner, Beat Müller, Hannes Kenngott, Stefanie Speidel, Annette Kopp-Schneider, Klaus Maier-Hein, Lena Maier-Hein


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Automatic Cardiac Disease Assessment on cine-MRI via Time-Series Segmentation and Domain Specific Features


Jan 25, 2018
Fabian Isensee, Paul Jaeger, Peter M. Full, Ivo Wolf, Sandy Engelhardt, Klaus H. Maier-Hein

* To appear in the STACOM 2017 proceedings 

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Clickstream analysis for crowd-based object segmentation with confidence


Nov 29, 2017
Eric Heim, Alexander Seitel, Jonas Andrulis, Fabian Isensee, Christian Stock, Tobias Ross, Lena Maier-Hein

* to appear in IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI) 

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