Torchio
Medical imaging processing for AI applications.
Install / Use
/learn @TorchIO-project/TorchioREADME
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<p align="center">
<a href="https://docs.torchio.org/">
<img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/source/favicon_io/for_readme_2000x462.png" alt="TorchIO logo">
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<!-- markdownlint-disable --> <table align="center"> <tr> <td align="left"> <b>Package</b> </td> <td align="center"> <a href="https://pypi.org/project/torchio/"> <img src="https://img.shields.io/pypi/dm/torchio.svg?label=PyPI%20downloads&logo=python&logoColor=white" alt="PyPI downloads"> </a> <a href="https://pypi.org/project/torchio/"> <img src="https://img.shields.io/pypi/v/torchio?label=PyPI%20version&logo=python&logoColor=white" alt="PyPI version"> </a> <a href="https://anaconda.org/conda-forge/torchio"> <img src="https://img.shields.io/conda/v/conda-forge/torchio.svg?label=conda-forge&logo=conda-forge" alt="Conda version"> </a> </td> </tr> <tr> <td align="left"> <b>CI</b> </td> <td align="center"> <a href="https://github.com/TorchIO-project/torchio/actions/workflows/tests.yml"> <img src="https://github.com/TorchIO-project/torchio/actions/workflows/tests.yml/badge.svg" alt="Tests status"> </a> <a href="https://github.com/TorchIO-project/torchio/actions/workflows/docs.yml"> <img src="https://github.com/TorchIO-project/torchio/actions/workflows/docs.yml/badge.svg" alt="Documentation status"> </a> <a href="https://app.codecov.io/github/TorchIO-project/torchio"> <img src="https://codecov.io/gh/TorchIO-project/torchio/branch/main/graphs/badge.svg" alt="Coverage status"> </a> </td> </tr> <tr> <td align="left"> <b>Code</b> </td> <td align="center"> <a href="https://docs.astral.sh/ruff/"> <img src="https://camo.githubusercontent.com/bb88127790fb054cba2caf3f3be2569c1b97bb45a44b47b52d738f8781a8ede4/68747470733a2f2f696d672e736869656c64732e696f2f656e64706f696e743f75726c3d68747470733a2f2f7261772e67697468756275736572636f6e74656e742e636f6d2f636861726c6965726d617273682f727566662f6d61696e2f6173736574732f62616467652f76312e6a736f6e" alt="Code style"> </a> <a href="https://scrutinizer-ci.com/g/TorchIO-project/torchio/?branch=main"> <img src="https://img.shields.io/scrutinizer/g/TorchIO-project/torchio.svg?label=Code%20quality&logo=scrutinizer" alt="Code quality"> </a> </td> </tr> <tr> <td align="left"> <b>Tutorials</b> </td> <td align="center"> <a href="https://github.com/TorchIO-project/torchio/blob/main/tutorials/README.md"> <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Google Colab"> </a> </td> </tr> <tr> <td align="left"> <b>Community</b> </td> <td align="center"> <a href="https://www.youtube.com/watch?v=UEUVSw5-M9M"> <img src="https://img.shields.io/youtube/views/UEUVSw5-M9M?label=watch&style=social" alt="YouTube"> </a> <a href="https://github.com/TorchIO-project/torchio#contributors"> <img src="https://img.shields.io/github/all-contributors/TorchIO-project/torchio?color=ee8449&style=flat-square" alt="All Contributors"> </a> </td> </tr> </table>
<p align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html"> <img style="width: 600px; overflow: hidden;" src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/fpg_progressive.gif" alt="Progressive artifacts"> </a> </p> <p align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html"> <img style="width: 360px; height: 360px; overflow: hidden;" src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/augmentation.gif" alt="Augmentation"> </a> </p>
<table align="center"> <tr> <td align="center">Original</td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomblur">Random blur</a> </td> </tr> <tr> <td align="center"><img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/1_Lambda_mri.png" alt="Original"></td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomblur"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/2_RandomBlur_mri.gif" alt="Random blur"> </a> </td> </tr> <tr> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomflip">Random flip</a> </td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomnoise">Random noise</a> </td> </tr> <tr> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomflip"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/3_RandomFlip_mri.gif" alt="Random flip"> </a> </td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomnoise"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/4_Compose_mri.gif" alt="Random noise"> </a> </td> </tr> <tr> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomaffine">Random affine transformation</a> </td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomelasticdeformation">Random elastic transformation</a> </td> </tr> <tr> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomaffine"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/5_RandomAffine_mri.gif" alt="Random affine transformation"> </a> </td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomelasticdeformation"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/6_RandomElasticDeformation_mri.gif" alt="Random elastic transformation"> </a> </td> </tr> <tr> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randombiasfield">Random bias field artifact</a> </td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randommotion">Random motion artifact</a> </td> </tr> <tr> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randombiasfield"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/7_RandomBiasField_mri.gif" alt="Random bias field artifact"> </a> </td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randommotion"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/8_RandomMotion_mri.gif" alt="Random motion artifact"> </a> </td> </tr> <tr> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomspike">Random spike artifact</a> </td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomghosting">Random ghosting artifact</a> </td> </tr> <tr> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomspike"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/9_RandomSpike_mri.gif" alt="Random spike artifact"> </a> </td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomghosting"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/10_RandomGhosting_mri.gif" alt="Random ghosting artifact"> </a> </td> </tr> </table>
<p align="center"> <a href="https://docs.torchio.org/patches/patch_training.html#queue"> <img style="width: 640px; height: 360px; overflow: hidden;" src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/queue.gif" alt="Queue"> </a> </p>
Tools like TorchIO are a symptom of the maturation of medical AI research using deep learning techniques.
Jack Clark, Policy Director at OpenAI (link).
<!-- markdownlint-disable --> <table align="center"> <tr> <td align="left"> <b>Package</b> </td> <td align="center"> <a href="https://pypi.org/project/torchio/"> <img src="https://img.shields.io/pypi/dm/torchio.svg?label=PyPI%20downloads&logo=python&logoColor=white" alt="PyPI downloads"> </a> <a href="https://pypi.org/project/torchio/"> <img src="https://img.shields.io/pypi/v/torchio?label=PyPI%20version&logo=python&logoColor=white" alt="PyPI version"> </a> <a href="https://anaconda.org/conda-forge/torchio"> <img src="https://img.shields.io/conda/v/conda-forge/torchio.svg?label=conda-forge&logo=conda-forge" alt="Conda version"> </a> </td> </tr> <tr> <td align="left"> <b>CI</b> </td> <td align="center"> <a href="https://github.com/TorchIO-project/torchio/actions/workflows/tests.yml"> <img src="https://github.com/TorchIO-project/torchio/actions/workflows/tests.yml/badge.svg" alt="Tests status"> </a> <a href="https://github.com/TorchIO-project/torchio/actions/workflows/docs.yml"> <img src="https://github.com/TorchIO-project/torchio/actions/workflows/docs.yml/badge.svg" alt="Documentation status"> </a> <a href="https://app.codecov.io/github/TorchIO-project/torchio"> <img src="https://codecov.io/gh/TorchIO-project/torchio/branch/main/graphs/badge.svg" alt="Coverage status"> </a> </td> </tr> <tr> <td align="left"> <b>Code</b> </td> <td align="center"> <a href="https://docs.astral.sh/ruff/"> <img src="https://camo.githubusercontent.com/bb88127790fb054cba2caf3f3be2569c1b97bb45a44b47b52d738f8781a8ede4/68747470733a2f2f696d672e736869656c64732e696f2f656e64706f696e743f75726c3d68747470733a2f2f7261772e67697468756275736572636f6e74656e742e636f6d2f636861726c6965726d617273682f727566662f6d61696e2f6173736574732f62616467652f76312e6a736f6e" alt="Code style"> </a> <a href="https://scrutinizer-ci.com/g/TorchIO-project/torchio/?branch=main"> <img src="https://img.shields.io/scrutinizer/g/TorchIO-project/torchio.svg?label=Code%20quality&logo=scrutinizer" alt="Code quality"> </a> </td> </tr> <tr> <td align="left"> <b>Tutorials</b> </td> <td align="center"> <a href="https://github.com/TorchIO-project/torchio/blob/main/tutorials/README.md"> <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Google Colab"> </a> </td> </tr> <tr> <td align="left"> <b>Community</b> </td> <td align="center"> <a href="https://www.youtube.com/watch?v=UEUVSw5-M9M"> <img src="https://img.shields.io/youtube/views/UEUVSw5-M9M?label=watch&style=social" alt="YouTube"> </a> <a href="https://github.com/TorchIO-project/torchio#contributors"> <img src="https://img.shields.io/github/all-contributors/TorchIO-project/torchio?color=ee8449&style=flat-square" alt="All Contributors"> </a> </td> </tr> </table>
<p align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html"> <img style="width: 600px; overflow: hidden;" src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/fpg_progressive.gif" alt="Progressive artifacts"> </a> </p> <p align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html"> <img style="width: 360px; height: 360px; overflow: hidden;" src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/augmentation.gif" alt="Augmentation"> </a> </p>
<table align="center"> <tr> <td align="center">Original</td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomblur">Random blur</a> </td> </tr> <tr> <td align="center"><img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/1_Lambda_mri.png" alt="Original"></td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomblur"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/2_RandomBlur_mri.gif" alt="Random blur"> </a> </td> </tr> <tr> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomflip">Random flip</a> </td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomnoise">Random noise</a> </td> </tr> <tr> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomflip"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/3_RandomFlip_mri.gif" alt="Random flip"> </a> </td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomnoise"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/4_Compose_mri.gif" alt="Random noise"> </a> </td> </tr> <tr> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomaffine">Random affine transformation</a> </td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomelasticdeformation">Random elastic transformation</a> </td> </tr> <tr> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomaffine"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/5_RandomAffine_mri.gif" alt="Random affine transformation"> </a> </td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomelasticdeformation"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/6_RandomElasticDeformation_mri.gif" alt="Random elastic transformation"> </a> </td> </tr> <tr> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randombiasfield">Random bias field artifact</a> </td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randommotion">Random motion artifact</a> </td> </tr> <tr> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randombiasfield"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/7_RandomBiasField_mri.gif" alt="Random bias field artifact"> </a> </td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randommotion"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/8_RandomMotion_mri.gif" alt="Random motion artifact"> </a> </td> </tr> <tr> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomspike">Random spike artifact</a> </td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomghosting">Random ghosting artifact</a> </td> </tr> <tr> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomspike"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/9_RandomSpike_mri.gif" alt="Random spike artifact"> </a> </td> <td align="center"> <a href="https://docs.torchio.org/transforms/augmentation.html#randomghosting"> <img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/10_RandomGhosting_mri.gif" alt="Random ghosting artifact"> </a> </td> </tr> </table>
<p align="center"> <a href="https://docs.torchio.org/patches/patch_training.html#queue"> <img style="width: 640px; height: 360px; overflow: hidden;" src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/queue.gif" alt="Queue"> </a> </p>
(Queue for patch-based training)
<!-- markdownlint-restore -->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 tra
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