Package: torchio
Tools like TorchIO are a symptom of the maturation of medical AI research using deep learning techniques.Jack Clark, Policy Director
atOpenAI(link).PackageCICodeTutorialsCommunityOriginalRandom blurRandom flipRandom noiseRandom affine transformationRandom elastic transformationRandom bias field artifactRandom motion artifactRandom spike artifactRandom ghosting artifact(Queueforpatch-based training)TorchIO is a Python package containing a set of tools to efficiently
read, preprocess, sample, augment, and write 3D medical images in deep learning applications
written inPyTorch,
including intensity and spatial transforms
for data augmentation and preprocessing.
Transforms include typical computer vision operations
such as random affine transformations and also domain-specific ones such as
simulation of intensity artifacts due toMRI magnetic field inhomogeneityork-space motion artifacts.This package has been greatly inspired by NiftyNet,which is not actively maintained anymore.CreditsIf you like this repository, please click on Star!If you use this package for your research, please cite our paper:F. Pérez-García, R. Sparks, and S. Ourselin.TorchIO: a Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning. Computer Methods and Programs in Biomedicine (June 2021), p. 106236. ISSN: 0169-2607.doi:10.1016/j.cmpb.2021.106236.BibTeX entry:@article{perez-garcia_torchio_2021,title={TorchIO: a Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning},journal={Computer Methods and Programs in Biomedicine},pages={106236},year={2021},issn={0169-2607},doi={https://doi.org/10.1016/j.cmpb.2021.106236},url={https://www.sciencedirect.com/science/article/pii/S0169260721003102},author={P{\'e}rez-Garc{\'i}a, Fernando and Sparks, Rachel and Ourselin, S{\'e}bastien},}This project is supported by the following institutions:Engineering and Physical Sciences Research Council (EPSRC) & UK Research and Innovation (UKRI)EPSRC Centre for Doctoral Training in Intelligent, Integrated Imaging In Healthcare (i4health)(University College London)Wellcome / EPSRC Centre for Interventional and Surgical Sciences (WEISS)(University College London)School of Biomedical Engineering & Imaging Sciences (BMEIS)(King's College London)Getting startedSeeGetting startedforinstallationinstructions
and aHello, World!example.Longer usage examples can be found in thetutorials.All the documentation is hosted onRead the Docs.Pleaseopen a new issueif you think something is missing.ContributorsThanks goes to all these people (emoji key):Fernando Pérez-García💻📖valabregue🤔👀💻💬🐛GFabien💻👀🤔G.Reguig💻Niels Schurink💻Ibrahim Hadzic🐛ReubenDo🤔Julian Klug🤔David Völgyes🤔💻Jean-Christophe Fillion-Robin📖Suraj Pai🤔Ben Darwin🤔Oeslle Lucena🐛Soumick Chatterjee💻neuronflow📖Jan Witowski📖Derk Mus📖💻🐛Christian Herz🐛Cory Efird💻🐛Esteban Vaca C.🐛Ray Phan🐛Akis Linardos🐛💻Nina Montana-Brown📖🚇fabien-brulport🐛malteekj🐛Andres Diaz-Pinto🐛Sarthak Pati📦📖GabriellaKamlish🐛Tyler Spears🐛DaGuT📖Xiangyu Zhao🐛siahuat0727📖🐛Svdvoort💻Albans98💻Matthew T. Warkentin💻glupol🐛ramonemiliani93📖🐛💻Justus Schock💻🐛🤔👀Stefan Milorad Radonjić🐛Sajan Gohil🐛Ikko Ashimine📖laynr📖Omar U. Espejel🔊James Butler🐛res191🔍nengwp🐛📖susanveraclarke🎨nepersica🐛Sebastian Penhouet🤔Bigsealion🐛Dženan Zukić👀vasl12✅🐛François Rousseau🐛snavalm💻Jacob Reinhold💻Hsu🐛snipdome🐛SmallY🐛guigautier🤔AyedSamy🐛J. Miguel Valverde🤔💻🐛José Guilherme Almeida🤔Asim Usman🐛cbri92🐛Markus J. Ankenbrand🐛Ziv Yaniv📖Luca Lumetti💻📖chagelo🐛mueller-franzes💻🐛Abdelwahab Kawafi🐛Arthur Masson🐛📖양현식💻nicoloesch💻🐛Amund Vedal📖Alabamagan🐛sbdoherty📖Zhack47🐛Blake Dewey📖Doyeon Kim🐛KonoMaxi🐛Laurent Chauvin🐛Christian Hinge🐛zzz123xyz🐛This project follows theall-contributorsspecification. Contributions of any kind welcome!