Unified Brain MR-Ultrasound Synthesis using Multi-Modal Hierarchical Representations

1 code implementation • 15 Sep 2023 • Reuben Dorent, Nazim Haouchine, Fryderyk Kögl, Samuel Joutard, Parikshit Juvekar, Erickson Torio, Alexandra Golby, Sebastien Ourselin, Sarah Frisken, Tom Vercauteren, Tina Kapur, William M. Wells

We introduce MHVAE, a deep hierarchical variational auto-encoder (VAE) that synthesizes missing images from various modalities.

Driving Points Prediction For Abdominal Probabilistic Registration

1 code implementation • 5 Aug 2022 • Samuel Joutard, Reuben Dorent, Sebastien Ourselin, Tom Vercauteren, Marc Modat

Among the various registration methods proposed for this task, probabilistic displacement registration models estimate displacement distribution for a subset of points by comparing feature vectors of points from the two images.

Anatomy

A multi-organ point cloud registration algorithm for abdominal CT registration

no code implementations • 15 Mar 2022 • Samuel Joutard, Thomas Pheiffer, Chloe Audigier, Patrick Wohlfahrt, Reuben Dorent, Sebastien Piat, Tom Vercauteren, Marc Modat, Tommaso Mansi

Registering CT images of the chest is a crucial step for several tasks such as disease progression tracking or surgical planning.

Point Cloud Registration Segmentation

CrossMoDA 2021 challenge: Benchmark of Cross-Modality Domain Adaptation techniques for Vestibular Schwannoma and Cochlea Segmentation

3 code implementations • 8 Jan 2022 • Reuben Dorent, Aaron Kujawa, Marina Ivory, Spyridon Bakas, Nicola Rieke, Samuel Joutard, Ben Glocker, Jorge Cardoso, Marc Modat, Kayhan Batmanghelich, Arseniy Belkov, Maria Baldeon Calisto, Jae Won Choi, Benoit M. Dawant, Hexin Dong, Sergio Escalera, Yubo Fan, Lasse Hansen, Mattias P. Heinrich, Smriti Joshi, Victoriya Kashtanova, Hyeon Gyu Kim, Satoshi Kondo, Christian N. Kruse, Susana K. Lai-Yuen, Hao Li, Han Liu, Buntheng Ly, Ipek Oguz, Hyungseob Shin, Boris Shirokikh, Zixian Su, Guotai Wang, Jianghao Wu, Yanwu Xu, Kai Yao, Li Zhang, Sebastien Ourselin, Jonathan Shapey, Tom Vercauteren

The aim was to automatically perform unilateral VS and bilateral cochlea segmentation on hrT2 as provided in the testing set (N=137).

Brain Segmentation Domain Adaptation +4

Learn2Reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning

no code implementations • 8 Dec 2021 • Alessa Hering, Lasse Hansen, Tony C. W. Mok, Albert C. S. Chung, Hanna Siebert, Stephanie Häger, Annkristin Lange, Sven Kuckertz, Stefan Heldmann, Wei Shao, Sulaiman Vesal, Mirabela Rusu, Geoffrey Sonn, Théo Estienne, Maria Vakalopoulou, Luyi Han, Yunzhi Huang, Pew-Thian Yap, Mikael Brudfors, Yaël Balbastre, Samuel Joutard, Marc Modat, Gal Lifshitz, Dan Raviv, Jinxin Lv, Qiang Li, Vincent Jaouen, Dimitris Visvikis, Constance Fourcade, Mathieu Rubeaux, Wentao Pan, Zhe Xu, Bailiang Jian, Francesca De Benetti, Marek Wodzinski, Niklas Gunnarsson, Jens Sjölund, Daniel Grzech, Huaqi Qiu, Zeju Li, Alexander Thorley, Jinming Duan, Christoph Großbröhmer, Andrew Hoopes, Ingerid Reinertsen, Yiming Xiao, Bennett Landman, Yuankai Huo, Keelin Murphy, Nikolas Lessmann, Bram van Ginneken, Adrian V. Dalca, Mattias P. Heinrich

Image registration is a fundamental medical image analysis task, and a wide variety of approaches have been proposed.

Image Registration Medical Image Registration

Inter Extreme Points Geodesics for End-to-End Weakly Supervised Image Segmentation

1 code implementation • 1 Jul 2021 • Reuben Dorent, Samuel Joutard, Jonathan Shapey, Aaron Kujawa, Marc Modat, Sebastien Ourselin, Tom Vercauteren

We introduce $\textit{InExtremIS}$, a weakly supervised 3D approach to train a deep image segmentation network using particularly weak train-time annotations: only 6 extreme clicks at the boundary of the objects of interest.

Image Segmentation Segmentation +2

Scribble-based Domain Adaptation via Co-segmentation

1 code implementation • 7 Jul 2020 • Reuben Dorent, Samuel Joutard, Jonathan Shapey, Sotirios Bisdas, Neil Kitchen, Robert Bradford, Shakeel Saeed, Marc Modat, Sebastien Ourselin, Tom Vercauteren

Instead of requiring detailed but time-consuming annotations, scribbles on the target domain are used to perform domain adaptation.

Domain Adaptation Image Segmentation +3

Hetero-Modal Variational Encoder-Decoder for Joint Modality Completion and Segmentation

1 code implementation • 25 Jul 2019 • Reuben Dorent, Samuel Joutard, Marc Modat, Sébastien Ourselin, Tom Vercauteren

We propose a new deep learning method for tumour segmentation when dealing with missing imaging modalities.

Segmentation

Permutohedral Attention Module for Efficient Non-Local Neural Networks

1 code implementation • 1 Jul 2019 • Samuel Joutard, Reuben Dorent, Amanda Isaac, Sebastien Ourselin, Tom Vercauteren, Marc Modat

Medical image processing tasks such as segmentation often require capturing non-local information.

Segmentation