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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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Diminishing Uncertainty within the Training Pool: Active Learning for Medical Image Segmentation


Jan 07, 2021
Vishwesh Nath, Dong Yang, Bennett A. Landman, Daguang Xu, Holger R. Roth

* IEEE Transactions on Medical Imaging, 2020 
* 19 pages, 13 figures, Transactions of Medical Imaging 

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Multi-Contrast Computed Tomography Healthy Kidney Atlas


Dec 24, 2020
Ho Hin Lee, Yucheng Tang, Kaiwen Xu, Shunxing Bao, Agnes B. Fogo, Raymond Harris, Mark P. de Caestecker, Mattias Heinrich, Jeffrey M. Spraggins, Yuankai Huo, Bennett A. Landman

* 8 pages, 5 figures 

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RAP-Net: Coarse-to-Fine Multi-Organ Segmentation with Single Random Anatomical Prior


Dec 24, 2020
Ho Hin Lee, Yucheng Tang, Shunxing Bao, Richard G. Abramson, Yuankai Huo, Bennett A. Landman

* 5 pages, 3 figures 

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Joint analysis of structural connectivity and cortical surface features: correlates with mild traumatic brain injury


Dec 15, 2020
Cailey I. Kerley, Leon Y. Cai, Chang Yu, Logan M. Crawford, Jason M. Elenberger, Eden S. Singh, Kurt G. Schilling, Katherine S. Aboud, Bennett A. Landman, Tonia S. Rex

* To be published in Proc SPIE Int Soc Opt Eng. 2021 Feb 

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Development and Characterization of a Chest CT Atlas


Dec 05, 2020
Kaiwen Xu, Riqiang Gao, Mirza S. Khan, Shunxing Bao, Yucheng Tang, Steve A. Deppen, Yuankai Huo, Kim L. Sandler, Pierre P. Massion, Mattias P. Heinrich, Bennett A. Landman

* Accepted by SPIE2021 Medical Imaging (oral) 

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Deep Multi-path Network Integrating Incomplete Biomarker and Chest CT Data for Evaluating Lung Cancer Risk


Oct 19, 2020
Riqiang Gao, Yucheng Tang, Kaiwen Xu, Michael N. Kammer, Sanja L. Antic, Steve Deppen, Kim L. Sandler, Pierre P. Massion, Yuankai Huo, Bennett A. Landman

* Accepted by SPIE2021 Medical Imaging, oral 

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Faster Mean-shift: GPU-accelerated Embedding-clustering for Cell Segmentation and Tracking


Jul 28, 2020
Mengyang Zhao, Aadarsh Jha, Quan Liu, Bryan A. Millis, Anita Mahadevan-Jansen, Le Lu, Bennett A. Landman, Matthew J. Tyskac, Yuankai Huo


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Harvesting, Detecting, and Characterizing Liver Lesions from Large-scale Multi-phase CT Data via Deep Dynamic Texture Learning


Jun 28, 2020
Yuankai Huo, Jinzheng Cai, Chi-Tung Cheng, Ashwin Raju, Ke Yan, Bennett A. Landman, Jing Xiao, Le Lu, Chien-Hung Liao, Adam Harrison


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CircleNet: Anchor-free Detection with Circle Representation


Jun 03, 2020
Haichun Yang, Ruining Deng, Yuzhe Lu, Zheyu Zhu, Ye Chen, Joseph T. Roland, Le Lu, Bennett A. Landman, Agnes B. Fogo, Yuankai Huo


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The Value of Nullspace Tuning Using Partial Label Information


Mar 17, 2020
Colin B. Hansen, Vishwesh Nath, Diego A. Mesa, Yuankai Huo, Bennett A. Landman, Thomas A. Lasko


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Deep Learning Estimation of Multi-Tissue Constrained Spherical Deconvolution with Limited Single Shell DW-MRI


Feb 20, 2020
Vishwesh Nath, Sudhir K. Pathak, Kurt G. Schilling, Walt Schneider, Bennett A. Landman

* 10 pages, 7 figures 

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Validation and Optimization of Multi-Organ Segmentation on Clinical Imaging Archives


Feb 10, 2020
Yuchen Xu, Olivia Tang, Yucheng Tang, Ho Hin Lee, Yunqiang Chen, Dashan Gao, Shizhong Han, Riqiang Gao, Michael R. Savona, Richard G. Abramson, Yuankai Huo, Bennett A. Landman

* SPIE2020 Medical Imaging 

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Outlier Guided Optimization of Abdominal Segmentation


Feb 10, 2020
Yuchen Xu, Olivia Tang, Yucheng Tang, Ho Hin Lee, Yunqiang Chen, Dashan Gao, Shizhong Han, Riqiang Gao, Michael R. Savona, Richard G. Abramson, Yuankai Huo, Bennett A. Landman

* SPIE2020 Medical Imaging 

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Internal-transfer Weighting of Multi-task Learning for Lung Cancer Detection


Dec 16, 2019
Yiyuan Yang, Riqiang Gao, Yucheng Tang, Sanja L. Antic, Steve Deppen, Yuankai Huo, Kim L. Sandler, Pierre P. Massion, Bennett A. Landman

* Accepted by Medical Imaging, SPIE2020 

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MRI correlates of chronic symptoms in mild traumatic brain injury


Dec 06, 2019
Cailey I. Kerley, Kurt G. Schilling, Justin Blaber, Beth Miller, Allen Newton, Adam W. Anderson, Bennett A. Landman, Tonia S. Rex

* SPIE Medical Imaging 2020 

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Stochastic tissue window normalization of deep learning on computed tomography


Dec 01, 2019
Yuankai Huo, Yucheng Tang, Yunqiang Chen, Dashan Gao, Shizhong Han, Shunxing Bao, Smita De, James G. Terry, Jeffrey J. Carr, Richard G. Abramson, Bennett A. Landman

* Journal of Medical Imaging 6.4 (2019): 044005 

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Contrast Phase Classification with a Generative Adversarial Network


Nov 14, 2019
Yucheng Tang, Ho Hin Lee, Yuchen Xu, Olivia Tang, Yunqiang Chen, Dashan Gao, Shizhong Han, Riqiang Gao, Camilo Bermudez, Michael R. Savona, Richard G. Abramson, Yuankai Huo, Bennett A. Landman

* SPIE2020 
* 8 pages, 4 figures 

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Extracting 2D weak labels from volume labels using multiple instance learning in CT hemorrhage detection


Nov 13, 2019
Samuel W. Remedios, Zihao Wu, Camilo Bermudez, Cailey I. Kerley, Snehashis Roy, Mayur B. Patel, John A. Butman, Bennett A. Landman, Dzung L. Pham


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Deep Learning Captures More Accurate Diffusion Fiber Orientations Distributions than Constrained Spherical Deconvolution


Nov 13, 2019
Vishwesh Nath, Kurt G. Schilling, Colin B. Hansen, Prasanna Parvathaneni, Allison E. Hainline, Camilo Bermudez, Andrew J. Plassard, Vaibhav Janve, Yurui Gao, Justin A. Blaber, Iwona Stępniewska, Adam W. Anderson, Bennett A. Landman

* 2 pages, 4 figures. This work was accepted and published as an abstract at ISMRM 2018 held in Paris, France 

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Deep Multi-task Prediction of Lung Cancer and Cancer-free Progression from Censored Heterogenous Clinical Imaging


Nov 12, 2019
Riqiang Gao, Lingfeng Li, Yucheng Tang, Sanja L. Antic, Alexis B. Paulson, Yuankai Huo, Kim L. Sandler, Pierre P. Massion, Bennett A. Landman

* 8 pages, 5 figures, SPIE 2020 Medical Imaging, oral presentation 

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Semi-Supervised Multi-Organ Segmentation through Quality Assurance Supervision


Nov 12, 2019
Ho Hin Lee, Yucheng Tang, Olivia Tang, Yuchen Xu, Yunqiang Chen, Dashan Gao, Shizhong Han, Riqiang Gao, Michael R. Savona, Richard G. Abramson, Yuankai Huo, Bennett A. Landman

* 7 pages, 5 figures, Accepted by SPIE 2020: Medical Imaging 

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Methods and open-source toolkit for analyzing and visualizing challenge results


Oct 11, 2019
Manuel Wiesenfarth, Annika Reinke, Bennett A. Landman, Manuel Jorge Cardoso, Lena Maier-Hein, Annette Kopp-Schneider


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Distanced LSTM: Time-Distanced Gates in Long Short-Term Memory Models for Lung Cancer Detection


Sep 11, 2019
Riqiang Gao, Yuankai Huo, Shunxing Bao, Yucheng Tang, Sanja L. Antic, Emily S. Epstein, Aneri B. Balar, Steve Deppen, Alexis B. Paulson, Kim L. Sandler, Pierre P. Massion, Bennett A. Landman

* This paper is accepted by MLMI (oral), MICCAI workshop 

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Generalizing Deep Whole Brain Segmentation for Pediatric and Post-Contrast MRI with Augmented Transfer Learning


Aug 13, 2019
Camilo Bermudez, Justin Blaber, Samuel W. Remedios, Jess E. Reynolds, Catherine Lebel, Maureen McHugo, Stephan Heckers, Yuankai Huo, Bennett A. Landman


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Enabling Multi-Shell b-Value Generalizability of Data-Driven Diffusion Models with Deep SHORE


Jul 15, 2019
Vishwesh Nath, Ilwoo Lyu, Kurt G. Schilling, Prasanna Parvathaneni, Colin B. Hansen, Yucheng Tang, Yuankai Huo, Vaibhav A. Janve, Yurui Gao, Iwona Stepniewska, Adam W. Anderson, Bennett A. Landman


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Fully Automatic Liver Attenuation Estimation Combing CNN Segmentation and Morphological Operations


Jun 29, 2019
Yuankai Huo, James G. Terry, Jiachen Wang, Sangeeta Nair, Thomas A. Lasko, Barry I. Freedman, J. Jeffery Carr, Bennett A. Landman

* Medical Physics 

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3D Whole Brain Segmentation using Spatially Localized Atlas Network Tiles


Mar 28, 2019
Yuankai Huo, Zhoubing Xu, Yunxi Xiong, Katherine Aboud, Prasanna Parvathaneni, Shunxing Bao, Camilo Bermudez, Susan M. Resnick, Laurie E. Cutting, Bennett A. Landman


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Distributed deep learning for robust multi-site segmentation of CT imaging after traumatic brain injury


Mar 11, 2019
Samuel Remedios, Snehashis Roy, Justin Blaber, Camilo Bermudez, Vishwesh Nath, Mayur B. Patel, John A. Butman, Bennett A. Landman, Dzung L. Pham


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