Search Results for author: Colin Jacobs

Found 14 papers, 5 papers with code

Transfer learning from a sparsely annotated dataset of 3D medical images

1 code implementation8 Nov 2023 Gabriel Efrain Humpire-Mamani, Colin Jacobs, Mathias Prokop, Bram van Ginneken, Nikolas Lessmann

A base segmentation model (3D U-Net) was trained on a large and sparsely annotated dataset; its weights were used for transfer learning on four new down-stream segmentation tasks for which a fully annotated dataset was available.

Organ Segmentation Segmentation +1

Kidney abnormality segmentation in thorax-abdomen CT scans

no code implementations6 Sep 2023 Gabriel Efrain Humpire Mamani, Nikolas Lessmann, Ernst Th. Scholten, Mathias Prokop, Colin Jacobs, Bram van Ginneken

Our end-to-end segmentation method was trained on 215 contrast-enhanced thoracic-abdominal CT scans, with half of these scans containing one or more abnormalities.

Segmentation

Structure and position-aware graph neural network for airway labeling

1 code implementation12 Jan 2022 Weiyi Xie, Colin Jacobs, Jean-Paul Charbonnier, Bram van Ginneken

The proposed method formulates airway labeling as a branch classification problem in the airway tree graph, where branch features are extracted using convolutional neural networks (CNN) and enriched using graph neural networks.

Position

Deep Clustering Activation Maps for Emphysema Subtyping

no code implementations1 Jun 2021 Weiyi Xie, Colin Jacobs, Bram van Ginneken

We propose a deep learning clustering method that exploits dense features from a segmentation network for emphysema subtyping from computed tomography (CT) scans.

Clustering Computed Tomography (CT) +1

Relational Modeling for Robust and Efficient Pulmonary Lobe Segmentation in CT Scans

no code implementations16 Apr 2020 Weiyi Xie, Colin Jacobs, Jean-Paul Charbonnier, Bram van Ginneken

We argue that such structural relationships play a critical role in the accurate delineation of pulmonary lobes when the lungs are affected by diseases such as COVID-19 or COPD.

Transfer Learning

The Liver Tumor Segmentation Benchmark (LiTS)

6 code implementations13 Jan 2019 Patrick Bilic, Patrick Christ, Hongwei Bran Li, Eugene Vorontsov, Avi Ben-Cohen, Georgios Kaissis, Adi Szeskin, Colin Jacobs, Gabriel Efrain Humpire Mamani, Gabriel Chartrand, Fabian Lohöfer, Julian Walter Holch, Wieland Sommer, Felix Hofmann, Alexandre Hostettler, Naama Lev-Cohain, Michal Drozdzal, Michal Marianne Amitai, Refael Vivantik, Jacob Sosna, Ivan Ezhov, Anjany Sekuboyina, Fernando Navarro, Florian Kofler, Johannes C. Paetzold, Suprosanna Shit, Xiaobin Hu, Jana Lipková, Markus Rempfler, Marie Piraud, Jan Kirschke, Benedikt Wiestler, Zhiheng Zhang, Christian Hülsemeyer, Marcel Beetz, Florian Ettlinger, Michela Antonelli, Woong Bae, Míriam Bellver, Lei Bi, Hao Chen, Grzegorz Chlebus, Erik B. Dam, Qi Dou, Chi-Wing Fu, Bogdan Georgescu, Xavier Giró-i-Nieto, Felix Gruen, Xu Han, Pheng-Ann Heng, Jürgen Hesser, Jan Hendrik Moltz, Christian Igel, Fabian Isensee, Paul Jäger, Fucang Jia, Krishna Chaitanya Kaluva, Mahendra Khened, Ildoo Kim, Jae-Hun Kim, Sungwoong Kim, Simon Kohl, Tomasz Konopczynski, Avinash Kori, Ganapathy Krishnamurthi, Fan Li, Hongchao Li, Junbo Li, Xiaomeng Li, John Lowengrub, Jun Ma, Klaus Maier-Hein, Kevis-Kokitsi Maninis, Hans Meine, Dorit Merhof, Akshay Pai, Mathias Perslev, Jens Petersen, Jordi Pont-Tuset, Jin Qi, Xiaojuan Qi, Oliver Rippel, Karsten Roth, Ignacio Sarasua, Andrea Schenk, Zengming Shen, Jordi Torres, Christian Wachinger, Chunliang Wang, Leon Weninger, Jianrong Wu, Daguang Xu, Xiaoping Yang, Simon Chun-Ho Yu, Yading Yuan, Miao Yu, Liping Zhang, Jorge Cardoso, Spyridon Bakas, Rickmer Braren, Volker Heinemann, Christopher Pal, An Tang, Samuel Kadoury, Luc Soler, Bram van Ginneken, Hayit Greenspan, Leo Joskowicz, Bjoern Menze

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018.

Benchmarking Computed Tomography (CT) +3

Finding strong lenses in CFHTLS using convolutional neural networks

no code implementations10 Apr 2017 Colin Jacobs, Karl Glazebrook, Thomas Collett, Anupreeta More, Christopher McCarthy

An ensemble of trained networks was applied to all of the 171 square degrees of the CFHTLS wide field image data, identifying 18, 861 candidates including 63 known and 139 other potential lens candidates.

Instrumentation and Methods for Astrophysics Astrophysics of Galaxies

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