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Patch-based medical image segmentation using Quantum Tensor Networks


Sep 15, 2021
Raghavendra Selvan, Erik B Dam, S├Şren Alexander Flensborg, Jens Petersen

* Possible journal extension of our preliminary conference work "Segmenting two-dimensional structures with strided tensor networks", Selvan et al. 2021, available at arXiv:2102.06900. 22 pages, 12 figures 

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Continuous-Time Deep Glioma Growth Models


Jul 02, 2021
Jens Petersen, Fabian Isensee, Gregor K├Âhler, Paul F. J├Ąger, David Zimmerer, Ulf Neuberger, Wolfgang Wick, J├╝rgen Debus, Sabine Heiland, Martin Bendszus, Philipp Vollmuth, Klaus H. Maier-Hein

* MICCAI 2021 

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RootPainter3D: Interactive-machine-learning enables rapid and accurate contouring for radiotherapy


Jun 22, 2021
Abraham George Smith, Jens Petersen, Cynthia Terrones-Campos, Anne Kiil Berthelsen, Nora Jarrett Forbes, Sune Darkner, Lena Specht, Ivan Richter Vogelius


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


Jun 11, 2021
Jens Petersen, Gregor K├Âhler, David Zimmerer, Fabian Isensee, Paul F. J├Ąger, Klaus H. Maier-Hein

* UAI 2021 

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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 R├Ądsch, Michela Antonelli, Tal Arbel, Spyridon Bakas, M. Jorge Cardoso, Veronika Cheplygina, Keyvan Farahani, Ben Glocker, Doreen Heckmann-N├Âtzel, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Jens Kleesiek, Tahsin Kurc, Michal Kozubek, Bennett A. Landman, Geert Litjens, Klaus Maier-Hein, Bjoern Menze, Henning M├╝ller, Jens Petersen, Mauricio Reyes, Nicola Rieke, Bram Stieltjes, Ronald M. Summers, Sotirios A. Tsaftaris, Bram van Ginneken, Annette Kopp-Schneider, Paul J├Ąger, 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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Segmenting two-dimensional structures with strided tensor networks


Feb 13, 2021
Raghavendra Selvan, Erik B Dam, Jens Petersen

* Accepted to be presented at the 27th international conference on Information Processing in Medical Imaging (IPMI-2021), Bornholm, Denmark. Source code at https://github.com/raghavian/strided-tenet 

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A Case for the Score: Identifying Image Anomalies using Variational Autoencoder Gradients


Nov 28, 2019
David Zimmerer, Jens Petersen, Simon A. A. Kohl, Klaus H. Maier-Hein


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High- and Low-level image component decomposition using VAEs for improved reconstruction and anomaly detection


Nov 27, 2019
David Zimmerer, Jens Petersen, Klaus 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. J├Ąger, Fabian Isensee, Simon A. A. Kohl, Ulf Neuberger, Wolfgang Wick, J├╝rgen 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. J├Ąger, Klaus H. Maier-Hein


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Segmentation of Roots in Soil with U-Net


Mar 18, 2019
Abraham George Smith, Jens Petersen, Raghavendra Selvan, Camilla Ru├Ş Rasmussen


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A cross-center smoothness prior for variational Bayesian brain tissue segmentation


Mar 11, 2019
Wouter M. Kouw, Silas N. ├śrting, Jens Petersen, Kim S. Pedersen, Marleen de Bruijne

* 12 pages, 2 figures, 1 table. Accepted to the International Conference on Information Processing in Medical Imaging (2019) 

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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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Graph Refinement based Tree Extraction using Mean-Field Networks and Graph Neural Networks


Nov 21, 2018
Raghavendra Selvan, Thomas Kipf, Max Welling, Jesper H Pedersen, Jens Petersen, Marleen de Bruijne

* 10 pages. Journal preprint 

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Learning to quantify emphysema extent: What labels do we need?


Oct 17, 2018
Silas Nyboe ├śrting, Jens Petersen, Laura H. Thomsen, Mathilde M. W. Wille, Marleen de Bruijne


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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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Extracting Tree-structures in CT data by Tracking Multiple Statistically Ranked Hypotheses


Jun 23, 2018
Raghavendra Selvan, Jens Petersen, Jesper H Pedersen, Marleen de Bruijne

* 8 pages 

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Feature learning based on visual similarity triplets in medical image analysis: A case study of emphysema in chest CT scans


Jun 19, 2018
Silas Nyboe ├śrting, Jens Petersen, Veronika Cheplygina, Laura H. Thomsen, Mathilde M W Wille, Marleen de Bruijne

* 10 pages. Submitted to LABELS2018 - MICCAI Workshop on Large-scale Annotation of Biomedical data and Expert Label Synthesis 

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Extraction of Airways using Graph Neural Networks


Apr 12, 2018
Raghavendra Selvan, Thomas Kipf, Max Welling, Jesper H. Pedersen, Jens Petersen, Marleen de Bruijne

* Extended Abstract submitted to MIDL, 2018. 3 pages 

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Mean Field Network based Graph Refinement with application to Airway Tree Extraction


Apr 10, 2018
Raghavendra Selvan, Max Welling, Jesper H. Pedersen, Jens Petersen, Marleen de Bruijne

* 10 pages. Preprint 

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Extraction of Airways with Probabilistic State-space Models and Bayesian Smoothing


Aug 07, 2017
Raghavendra Selvan, Jens Petersen, Jesper H. Pedersen, Marleen de Bruijne

* 10 pages. Pre-print of the paper accepted at Workshop on Graphs in Biomedical Image Analysis. MICCAI 2017. Quebec City 

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Extraction of airway trees using multiple hypothesis tracking and template matching


Nov 24, 2016
Raghavendra Selvan, Jens Petersen, Jesper H. Pedersen, Marleen de Bruijne

* 12 pages. Presented at the MICCAI Pulmonary Image Analysis Workshop, Athens, Greece, 2016 

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Geometric tree kernels: Classification of COPD from airway tree geometry


Apr 08, 2013
Aasa Feragen, Jens Petersen, Dominik Grimm, Asger Dirksen, Jesper Holst Pedersen, Karsten Borgwardt, Marleen de Bruijne

* 12 pages 

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