Search Results for author: Fabian Isensee

Found 32 papers, 16 papers with code

Continuous-Time Deep Glioma Growth Models

1 code implementation23 Jun 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

The ability to estimate how a tumor might evolve in the future could have tremendous clinical benefits, from improved treatment decisions to better dose distribution in radiation therapy.

Time Series Variational Inference

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

1 code implementation9 Jun 2021 Jens Petersen, Gregor Köhler, David Zimmerer, Fabian Isensee, Paul F. Jäger, Klaus H. Maier-Hein

Neural Processes (NPs) are a family of conditional generative models that are able to model a distribution over functions, in a way that allows them to perform predictions at test time conditioned on a number of context points.

Time Series

nnDetection: A Self-configuring Method for Medical Object Detection

1 code implementation1 Jun 2021 Michael Baumgartner, Paul F. Jaeger, Fabian Isensee, Klaus H. Maier-Hein

Simultaneous localisation and categorization of objects in medical images, also referred to as medical object detection, is of high clinical relevance because diagnostic decisions often depend on rating of objects rather than e. g. pixels.

Medical Object Detection Semantic Segmentation

Semantic segmentation of multispectral photoacoustic images using deep learning

no code implementations20 May 2021 Melanie Schellenberg, Kris Dreher, Niklas Holzwarth, Fabian Isensee, Annika Reinke, Nicholas Schreck, Alexander Seitel, Minu D. Tizabi, Lena Maier-Hein, Janek Gröhl

Due to the intuitive representation of high-dimensional information, such a preprocessing algorithm could be a valuable means to facilitate the clinical translation of photoacoustic imaging.

Semantic Segmentation Translation

Common Limitations of Image Processing Metrics: A Picture Story

1 code implementation12 Apr 2021 Annika Reinke, Minu D. Tizabi, Carole H. Sudre, Matthias Eisenmann, Tim Rädsch, Michael Baumgartner, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Peter Bankhead, Arriel Benis, M. Jorge Cardoso, Veronika Cheplygina, Beth Cimini, Gary S. Collins, Keyvan Farahani, Ben Glocker, Patrick Godau, Fred Hamprecht, Daniel A. Hashimoto, Doreen Heckmann-Nötzel, Michael M. Hoffmann, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Alexandros Karargyris, Alan Karthikesalingam, Bernhard Kainz, Emre Kavur, Hannes Kenngott, Jens Kleesiek, Thijs Kooi, Michal Kozubek, 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, Jens Petersen, Gorkem Polat, Nasir Rajpoot, Mauricio Reyes, Nicola Rieke, Michael Riegler, Hassan Rivaz, Julio Saez-Rodriguez, Clarisa Sanchez Gutierrez, Julien Schroeter, Anindo Saha, Shravya Shetty, Bram Stieltjes, Ronald M. Summers, Abdel A. Taha, Sotirios A. Tsaftaris, Bram van Ginneken, Gaël Varoquaux, Manuel Wiesenfarth, Ziv R. Yaniv, Annette Kopp-Schneider, Paul Jäger, Lena Maier-Hein

While the importance of automatic image analysis is continuously increasing, recent meta-research revealed major flaws with respect to algorithm validation.

Instance Segmentation Object Detection +1

Frequency Decomposition in Neural Processes

no code implementations1 Jan 2021 Jens Petersen, Paul F Jaeger, Gregor Koehler, David Zimmerer, Fabian Isensee, Klaus Maier-Hein

Neural Processes are a powerful tool for learning representations of function spaces purely from examples, in a way that allows them to perform predictions at test time conditioned on so-called context observations.

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

no code implementations27 Apr 2020 Fabian Isensee, Klaus H. Maier-Hein

Segmentation of endoscopic images is an essential processing step for computer and robotics-assisted interventions.

Data Augmentation Semantic Segmentation

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

1 code implementation17 Jan 2020 A. Emre Kavur, N. Sinem Gezer, Mustafa Barış, Sinem Aslan, 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, Debdoot Sheet, Gurbandurdy Dovletov, Oliver Speck, Andreas Nürnberger, Klaus H. Maier-Hein, Gözde BOZDAĞI AKAR, Gözde Ünal, Oğuz Dicle, M. Alper Selver

The analysis shows that the performance of DL models for single modality (CT / MR) can show reliable volumetric analysis performance (DICE: 0. 98 $\pm$ 0. 00 / 0. 95 $\pm$ 0. 01) but the best MSSD performance remain limited (21. 89 $\pm$ 13. 94 / 20. 85 $\pm$ 10. 63 mm).

ModelHub.AI: Dissemination Platform for Deep Learning Models

no code implementations26 Nov 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

Recent advances in artificial intelligence research have led to a profusion of studies that apply deep learning to problems in image analysis and natural language processing among others.

An attempt at beating the 3D U-Net

1 code implementation6 Aug 2019 Fabian Isensee, Klaus H. Maier-Hein

The U-Net is arguably the most successful segmentation architecture in the medical domain.

Tumor Segmentation

Deep Probabilistic Modeling of Glioma Growth

1 code implementation9 Jul 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

Existing approaches to modeling the dynamics of brain tumor growth, specifically glioma, employ biologically inspired models of cell diffusion, using image data to estimate the associated parameters.

Representation Learning

Unsupervised Anomaly Localization using Variational Auto-Encoders

1 code implementation4 Jul 2019 David Zimmerer, Fabian Isensee, Jens Petersen, Simon Kohl, Klaus Maier-Hein

An assumption-free automatic check of medical images for potentially overseen anomalies would be a valuable assistance for a radiologist.

Automated Design of Deep Learning Methods for Biomedical Image Segmentation

4 code implementations17 Apr 2019 Fabian Isensee, Paul F. Jäger, Simon A. A. Kohl, Jens Petersen, Klaus H. Maier-Hein

Biomedical imaging is a driver of scientific discovery and core component of medical care, currently stimulated by the field of deep learning.

Medical Image Segmentation Semantic Segmentation

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

5 code implementations21 Nov 2018 Paul F. Jaeger, Simon A. A. Kohl, Sebastian Bickelhaupt, Fabian Isensee, Tristan Anselm Kuder, Heinz-Peter Schlemmer, Klaus H. Maier-Hein

The proposed architecture recaptures discarded supervision signals by complementing object detection with an auxiliary task in the form of semantic segmentation without introducing the additional complexity of previously proposed two-stage detectors.

Medical Object Detection Semantic Segmentation +1

Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge

1 code implementation5 Nov 2018 Spyridon Bakas, Mauricio Reyes, Andras Jakab, Stefan Bauer, Markus Rempfler, Alessandro Crimi, Russell Takeshi Shinohara, Christoph Berger, Sung Min Ha, Martin Rozycki, Marcel Prastawa, Esther Alberts, Jana Lipkova, John Freymann, Justin Kirby, Michel Bilello, Hassan Fathallah-Shaykh, Roland Wiest, Jan Kirschke, Benedikt Wiestler, Rivka Colen, Aikaterini Kotrotsou, Pamela Lamontagne, Daniel Marcus, Mikhail Milchenko, Arash Nazeri, Marc-Andre Weber, Abhishek Mahajan, Ujjwal Baid, Elizabeth Gerstner, Dongjin Kwon, Gagan Acharya, Manu Agarwal, Mahbubul Alam, Alberto Albiol, Antonio Albiol, Francisco J. Albiol, Varghese Alex, Nigel Allinson, Pedro H. A. Amorim, Abhijit Amrutkar, Ganesh Anand, Simon Andermatt, Tal Arbel, Pablo Arbelaez, Aaron Avery, Muneeza Azmat, Pranjal B., W Bai, Subhashis Banerjee, Bill Barth, Thomas Batchelder, Kayhan Batmanghelich, Enzo Battistella, Andrew Beers, Mikhail Belyaev, Martin Bendszus, Eze Benson, Jose Bernal, Halandur Nagaraja Bharath, George Biros, Sotirios Bisdas, James Brown, Mariano Cabezas, Shilei Cao, Jorge M. Cardoso, Eric N Carver, Adrià Casamitjana, Laura Silvana Castillo, Marcel Catà, Philippe Cattin, Albert Cerigues, Vinicius S. Chagas, Siddhartha Chandra, Yi-Ju Chang, Shiyu Chang, Ken Chang, Joseph Chazalon, Shengcong Chen, Wei Chen, Jefferson W. Chen, Zhaolin Chen, Kun Cheng, Ahana Roy Choudhury, Roger Chylla, Albert Clérigues, Steven Colleman, Ramiro German Rodriguez Colmeiro, Marc Combalia, Anthony Costa, Xiaomeng Cui, Zhenzhen Dai, Lutao Dai, Laura Alexandra Daza, Eric Deutsch, Changxing Ding, Chao Dong, Shidu Dong, Wojciech Dudzik, Zach Eaton-Rosen, Gary Egan, Guilherme Escudero, Théo Estienne, Richard Everson, Jonathan Fabrizio, Yong Fan, Longwei Fang, Xue Feng, Enzo Ferrante, Lucas Fidon, Martin Fischer, Andrew P. French, Naomi Fridman, Huan Fu, David Fuentes, Yaozong Gao, Evan Gates, David Gering, Amir Gholami, Willi Gierke, Ben Glocker, Mingming Gong, Sandra González-Villá, T. Grosges, Yuanfang Guan, Sheng Guo, Sudeep Gupta, Woo-Sup Han, Il Song Han, Konstantin Harmuth, Huiguang He, Aura Hernández-Sabaté, Evelyn Herrmann, Naveen Himthani, Winston Hsu, Cheyu Hsu, Xiaojun Hu, Xiaobin Hu, Yan Hu, Yifan Hu, Rui Hua, Teng-Yi Huang, Weilin Huang, Sabine Van Huffel, Quan Huo, Vivek HV, Khan M. Iftekharuddin, Fabian Isensee, Mobarakol Islam, Aaron S. Jackson, Sachin R. Jambawalikar, Andrew Jesson, Weijian Jian, Peter Jin, V Jeya Maria Jose, Alain Jungo, B Kainz, Konstantinos Kamnitsas, Po-Yu Kao, Ayush Karnawat, Thomas Kellermeier, Adel Kermi, Kurt Keutzer, Mohamed Tarek Khadir, Mahendra Khened, Philipp Kickingereder, Geena Kim, Nik King, Haley Knapp, Urspeter Knecht, Lisa Kohli, Deren Kong, Xiangmao Kong, Simon Koppers, Avinash Kori, Ganapathy Krishnamurthi, Egor Krivov, Piyush Kumar, Kaisar Kushibar, Dmitrii Lachinov, Tryphon Lambrou, Joon Lee, Chengen Lee, Yuehchou Lee, M Lee, Szidonia Lefkovits, Laszlo Lefkovits, James Levitt, Tengfei Li, Hongwei Li, Hongyang Li, Xiaochuan Li, Yuexiang Li, Heng Li, Zhenye Li, Xiaoyu Li, Zeju Li, Xiaogang Li, Wenqi Li, Zheng-Shen Lin, Fengming Lin, Pietro Lio, Chang Liu, Boqiang Liu, Xiang Liu, Mingyuan Liu, Ju Liu, Luyan Liu, Xavier Llado, Marc Moreno Lopez, Pablo Ribalta Lorenzo, Zhentai Lu, Lin Luo, Zhigang Luo, Jun Ma, Kai Ma, Thomas Mackie, Anant Madabushi, Issam Mahmoudi, Klaus H. Maier-Hein, Pradipta Maji, CP Mammen, Andreas Mang, B. S. Manjunath, Michal Marcinkiewicz, S McDonagh, Stephen McKenna, Richard McKinley, Miriam Mehl, Sachin Mehta, Raghav Mehta, Raphael Meier, Christoph Meinel, Dorit Merhof, Craig Meyer, Robert Miller, Sushmita Mitra, Aliasgar Moiyadi, David Molina-Garcia, Miguel A. B. Monteiro, Grzegorz Mrukwa, Andriy Myronenko, Jakub Nalepa, Thuyen Ngo, Dong Nie, Holly Ning, Chen Niu, Nicholas K Nuechterlein, Eric Oermann, Arlindo Oliveira, Diego D. C. Oliveira, Arnau Oliver, Alexander F. I. Osman, Yu-Nian Ou, Sebastien Ourselin, Nikos Paragios, Moo Sung Park, Brad Paschke, J. Gregory Pauloski, Kamlesh Pawar, Nick Pawlowski, Linmin Pei, Suting Peng, Silvio M. Pereira, Julian Perez-Beteta, Victor M. Perez-Garcia, Simon Pezold, Bao Pham, Ashish Phophalia, Gemma Piella, G. N. Pillai, Marie Piraud, Maxim Pisov, Anmol Popli, Michael P. Pound, Reza Pourreza, Prateek Prasanna, Vesna Prkovska, Tony P. Pridmore, Santi Puch, Élodie Puybareau, Buyue Qian, Xu Qiao, Martin Rajchl, Swapnil Rane, Michael Rebsamen, Hongliang Ren, Xuhua Ren, Karthik Revanuru, Mina Rezaei, Oliver Rippel, Luis Carlos Rivera, Charlotte Robert, Bruce Rosen, Daniel Rueckert, Mohammed Safwan, Mostafa Salem, Joaquim Salvi, Irina Sanchez, Irina Sánchez, Heitor M. Santos, Emmett Sartor, Dawid Schellingerhout, Klaudius Scheufele, Matthew R. Scott, Artur A. Scussel, Sara Sedlar, Juan Pablo Serrano-Rubio, N. Jon Shah, Nameetha Shah, Mazhar Shaikh, B. Uma Shankar, Zeina Shboul, Haipeng Shen, Dinggang Shen, Linlin Shen, Haocheng Shen, Varun Shenoy, Feng Shi, Hyung Eun Shin, Hai Shu, Diana Sima, M Sinclair, Orjan Smedby, James M. Snyder, Mohammadreza Soltaninejad, Guidong Song, Mehul Soni, Jean Stawiaski, Shashank Subramanian, Li Sun, Roger Sun, Jiawei Sun, Kay Sun, Yu Sun, Guoxia Sun, Shuang Sun, Yannick R Suter, Laszlo Szilagyi, Sanjay Talbar, DaCheng Tao, Zhongzhao Teng, Siddhesh Thakur, Meenakshi H Thakur, Sameer Tharakan, Pallavi Tiwari, Guillaume Tochon, Tuan Tran, Yuhsiang M. Tsai, Kuan-Lun Tseng, Tran Anh Tuan, Vadim Turlapov, Nicholas Tustison, Maria Vakalopoulou, Sergi Valverde, Rami Vanguri, Evgeny Vasiliev, Jonathan Ventura, Luis Vera, Tom Vercauteren, C. A. Verrastro, Lasitha Vidyaratne, Veronica Vilaplana, Ajeet Vivekanandan, Qian Wang, Chiatse J. Wang, Wei-Chung Wang, Duo Wang, Ruixuan Wang, Yuanyuan Wang, Chunliang Wang, Guotai Wang, Ning Wen, Xin Wen, Leon Weninger, Wolfgang Wick, Shaocheng Wu, Qiang Wu, Yihong Wu, Yong Xia, Yanwu Xu, Xiaowen Xu, Peiyuan Xu, Tsai-Ling Yang, Xiaoping Yang, Hao-Yu Yang, Junlin Yang, Haojin Yang, Guang Yang, Hongdou Yao, Xujiong Ye, Changchang Yin, Brett Young-Moxon, Jinhua Yu, Xiangyu Yue, Songtao Zhang, Angela Zhang, Kun Zhang, Xue-jie Zhang, Lichi Zhang, Xiaoyue Zhang, Yazhuo Zhang, Lei Zhang, Jian-Guo Zhang, Xiang Zhang, Tianhao Zhang, Sicheng Zhao, Yu Zhao, Xiaomei Zhao, Liang Zhao, Yefeng Zheng, Liming Zhong, Chenhong Zhou, Xiaobing Zhou, Fan Zhou, Hongtu Zhu, Jin Zhu, Ying Zhuge, Weiwei Zong, Jayashree Kalpathy-Cramer, Keyvan Farahani, Christos Davatzikos, Koen van Leemput, Bjoern Menze

This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i. e., 2012-2018.

Brain Tumor Segmentation Survival Prediction +1

No New-Net

no code implementations27 Sep 2018 Fabian Isensee, Philipp Kickingereder, Wolfgang Wick, Martin Bendszus, Klaus H. Maier-Hein

By incorporating additional measures such as region based training, additional training data, a simple postprocessing technique and a combination of loss functions, we obtain Dice scores of 77. 88, 87. 81 and 80. 62, and Hausdorff Distances (95th percentile) of 2. 90, 6. 03 and 5. 08 for the enhancing tumor, whole tumor and tumor core, respectively on the test data.

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

1 code implementation3 Jul 2017 Fabian Isensee, Paul Jaeger, Peter M. Full, Ivo Wolf, Sandy Engelhardt, Klaus H. Maier-Hein

We evaluated our method on the ACDC dataset (4 pathology groups, 1 healthy group) and achieve dice scores of 0. 945 (LVC), 0. 908 (RVC) and 0. 905 (LVM) in a cross-validation over the training set (100 cases) and 0. 950 (LVC), 0. 923 (RVC) and 0. 911 (LVM) on the test set (50 cases).

General Classification Time Series

Direct White Matter Bundle Segmentation using Stacked U-Nets

no code implementations6 Mar 2017 Jakob Wasserthal, Peter F. Neher, Fabian Isensee, Klaus H. Maier-Hein

We present a novel supervised approach for direct tract segmentation that shows major performance gains.

Semantic Segmentation

Clickstream analysis for crowd-based object segmentation with confidence

no code implementations25 Nov 2016 Eric Heim, Alexander Seitel, Jonas Andrulis, Fabian Isensee, Christian Stock, Tobias Ross, Lena Maier-Hein

Using a total of 29, 000 crowd annotations performed on publicly available data of different object classes, we show that (1) our method is highly accurate in estimating the segmentation quality based on clickstream data, (2) outperforms state-of-the-art methods for merging multiple annotations.

Semantic Segmentation

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