torchio

Tools for medical image processing with PyTorch

291 个版本 Python >=3.10

TorchIO contributors

安装

pip install torchio

poetry add torchio

pipenv install torchio

conda install torchio

描述

Tools like TorchIO are a symptom of the maturation of medical AI research using deep learning techniques.

Jack Clark, Policy Director at OpenAI (link).

Package
CI
Code
Tutorials
Community

Original	Random blur

Random flip	Random noise

Random affine transformation	Random elastic transformation

Random bias field artifact	Random motion artifact

Random spike artifact	Random ghosting artifact

(Queue for patch-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 in PyTorch, 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 to MRI magnetic field inhomogeneity or k-space motion artifacts.

This package has been greatly inspired by NiftyNet, which is not actively maintained anymore.

Credits

If 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 was originally 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 started

See Getting started for installation instructions and a Hello, World! example.

Longer usage examples can be found in the tutorials.

Read the documentation for more information.

Please create an issue if you think something is missing.

Contributors

Thanks 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 🐛	_{Amin Alam} 📖
_marius-sm 🤔	_haarisr 💻	_{Chris Winder} 🐛	_{Ricky Walsh} 💻	_{Keerthi Sravan Ravi} 🐛	_{Rahul Kurian Jacob} 📖	_{Ethan Rooke} 📖
_{David Kucher} 💻	_StijnvWijn 💻 🐛	_Toufiq 💻	_bcrobo 🐛	_{Emmanuel Ferdman} 🐛	_{Anders Dahl Henriksen} 🚧	_{Eike Petersen} 🐛
_{AlexanderHBerger} 🐛	_{Rhys \| Senior DevOps Engineer \| 3x AWS Certified \| CKA \| Terraform Certified} 🐛	_{Vicent Caselles-Ballester} 📖	_{Arsalaan Ahmad} 📖