TorchIO: A Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning

9 March 2020

Fernando Pérez-García

Sébastien Ourselin

Papers citing "TorchIO: A Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning"

34 / 34 papers shown

Title
DeepThalamus: A novel deep learning method for automatic segmentation of brain thalamic nuclei from multimodal ultra-high resolution MRI Marina Ruiz-Perez Sergio Morell-Ortega Marien Gadea Roberto Vivó Hernando Gregorio Rubio F. Aparici-Robles M. Iglesia-Vayá T. Tourdias Pierrick Coupé J. V. Manjón 96 0 0 15 Jan 2024
Guided Reconstruction with Conditioned Diffusion Models for Unsupervised Anomaly Detection in Brain MRIs F. Behrendt Debayan Bhattacharya R. Mieling Lennart Maack Julia Kruger R. Opfer Alexander Schlaefer DiffM MedIm 69 10 0 07 Dec 2023
MONAIfbs: MONAI-based fetal brain MRI deep learning segmentation M. Ranzini Lucas Fidon Sébastien Ourselin Marc Modat Tom Vercauteren 23 24 0 21 Mar 2021
Are we using appropriate segmentation metrics? Identifying correlates of human expert perception for CNN training beyond rolling the DICE coefficient Florian Kofler Ivan Ezhov Fabian Isensee F. Balsiger Christoph Berger ... C. Zimmer D. Ankerst Jan Kirschke Benedikt Wiestler Bjoern Menze 48 51 0 10 Mar 2021
Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical MRI exams with scans of different orientation, resolution and contrast Juan Eugenio Iglesias Benjamin Billot Yael Balbastre A. Tabari J. Conklin Daniel C. Alexander Polina Golland B. Edlow Bruce Fischl 111 102 0 24 Dec 2020
pymia: A Python package for data handling and evaluation in deep learning-based medical image analysis Alain Jungo Olivier Scheidegger Mauricio Reyes F. Balsiger 31 39 0 07 Oct 2020
Simulation of Brain Resection for Cavity Segmentation Using Self-Supervised and Semi-Supervised Learning Fernando Pérez-García R. Rodionov Ali Alim-Marvasti Rachel Sparks J. Duncan Sébastien Ourselin 31 10 0 28 Jun 2020
Partial Volume Segmentation of Brain MRI Scans of any Resolution and Contrast Benjamin Billot Eleanor D. Robinson Adrian Dalca Juan Eugenio Iglesias 40 36 0 21 Apr 2020
Eisen: a python package for solid deep learning Frank Mancolo 26 3 0 18 Mar 2020
A Learning Strategy for Contrast-agnostic MRI Segmentation Benjamin Billot Douglas N. Greve Koen van Leemput Bruce Fischl Juan Eugenio Iglesias Adrian Dalca 53 77 0 04 Mar 2020
A Simple Framework for Contrastive Learning of Visual Representations Ting-Li Chen Simon Kornblith Mohammad Norouzi Geoffrey E. Hinton SSL 335 18,721 0 13 Feb 2020
A Heteroscedastic Uncertainty Model for Decoupling Sources of MRI Image Quality Richard Shaw Carole H. Sudre Sebastien Ourselin M. Jorge Cardoso UQCV 58 13 0 31 Jan 2020
PyTorch: An Imperative Style, High-Performance Deep Learning Library Adam Paszke Sam Gross Francisco Massa Adam Lerer James Bradbury ... Sasank Chilamkurthy Benoit Steiner Lu Fang Junjie Bai Soumith Chintala ODL 391 42,299 0 03 Dec 2019
Kornia: an Open Source Differentiable Computer Vision Library for PyTorch F. Mokhayeri Dmytro Mishkin Daniel Ponsa Ethan Rublee Gary R. Bradski VLM AI4TS 128 355 0 05 Oct 2019
Image-and-Spatial Transformer Networks for Structure-Guided Image Registration Matthew C. H. Lee Ozan Oktay A. Schuh M. Schaap Ben Glocker MedIm ViT 55 77 0 22 Jul 2019
A Partially Reversible U-Net for Memory-Efficient Volumetric Image Segmentation Robin Brügger Christian F. Baumgartner E. Konukoglu SSeg 51 74 0 14 Jun 2019
Transfusion: Understanding Transfer Learning for Medical Imaging M. Raghu Chiyuan Zhang Jon M. Kleinberg Samy Bengio MedIm 75 983 0 14 Feb 2019
Cats or CAT scans: transfer learning from natural or medical image source datasets? Veronika Cheplygina OOD MedIm 57 58 0 12 Oct 2018
Albumentations: fast and flexible image augmentations A. Buslaev Alex Parinov Eugene Khvedchenya V. Iglovikov Alexandr A Kalinin 136 1,966 0 18 Sep 2018
Deep learning to achieve clinically applicable segmentation of head and neck anatomy for radiotherapy Stanislav Nikolov Sam Blackwell Alexei Zverovitch R. Mendes Michelle Livne ... Mustafa Suleyman T. Back Ricky A. Sharma J. Ledsam Olaf Ronneberger 116 297 0 12 Sep 2018
Aleatoric uncertainty estimation with test-time augmentation for medical image segmentation with convolutional neural networks Guotai Wang Wenqi Li Michael Aertsen Jan Deprest Sebastien Ourselin Tom Vercauteren UQCV MedIm OOD 143 591 0 19 Jul 2018
Unsupervised End-to-end Learning for Deformable Medical Image Registration Siyuan Shan Wen Yan Xiaoqing Guo E. Chang Yubo Fan Yan Xu MedIm 59 49 0 23 Nov 2017
DLTK: State of the Art Reference Implementations for Deep Learning on Medical Images Nick Pawlowski S. Ktena M. J. Lee Bernhard Kainz Daniel Rueckert Ben Glocker Martin Rajchl LM&MA MedIm 44 82 0 18 Nov 2017
Multimodal and Multiscale Deep Neural Networks for the Early Diagnosis of Alzheimer's Disease using structural MR and FDG-PET images Donghuan Lu K. Popuri G. Ding R. Balachandar M. Beg MedIm 43 316 0 13 Oct 2017
Mixed Precision Training Paulius Micikevicius Sharan Narang Jonah Alben G. Diamos Erich Elsen ... Boris Ginsburg Michael Houston Oleksii Kuchaiev Ganesh Venkatesh Hao Wu 149 1,792 0 10 Oct 2017
NiftyNet: a deep-learning platform for medical imaging Eli Gibson Wenqi Li Carole Sudre Lucas Fidon D. I. Shakir ... Marc Modat D. Barratt Sébastien Ourselin M. Jorge Cardoso Tom Vercauteren 76 549 0 11 Sep 2017
An Adaptive Sampling Scheme to Efficiently Train Fully Convolutional Networks for Semantic Segmentation L. Berger E. Hyde M. Jorge Cardoso Sebastien Ourselin SSeg 48 40 0 08 Sep 2017
On the Compactness, Efficiency, and Representation of 3D Convolutional Networks: Brain Parcellation as a Pretext Task Wenqi Li Guotai Wang Lucas Fidon Sebastien Ourselin M. Jorge Cardoso Tom Vercauteren 3DV 93 339 0 06 Jul 2017
3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation Özgün Çiçek Ahmed Abdulkadir S. Lienkamp Thomas Brox Olaf Ronneberger 3DV 3DPC SSeg 3DH 148 6,516 0 21 Jun 2016
V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation Fausto Milletari Nassir Navab Seyed-Ahmad Ahmadi 204 8,660 0 15 Jun 2016
TensorFlow: A system for large-scale machine learning Martín Abadi P. Barham Jianmin Chen Zhiwen Chen Andy Davis ... Vijay Vasudevan Pete Warden Martin Wicke Yuan Yu Xiaoqiang Zhang GNN AI4CE 417 18,334 0 27 May 2016
Training Deep Nets with Sublinear Memory Cost Tianqi Chen Bing Xu Chiyuan Zhang Carlos Guestrin 98 1,165 0 21 Apr 2016
TensorFlow: Large-Scale Machine Learning on Heterogeneous Distributed Systems Martín Abadi Ashish Agarwal P. Barham E. Brevdo Zhiwen Chen ... Pete Warden Martin Wattenberg Martin Wicke Yuan Yu Xiaoqiang Zheng 257 11,145 0 14 Mar 2016
Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift Sergey Ioffe Christian Szegedy OOD 432 43,234 0 11 Feb 2015