Tools for loading, augmenting and writing 3D medical images on PyTorch.
Project description
TorchIO
Tools like TorchIO are a symptom of the maturation of medical AI research using deep learning techniques.
Jack Clark, Policy Director at OpenAI (link).
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(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 the paper:
BibTeX entry:
@misc{fern2020torchio,
title={TorchIO: a Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning},
author={Fernando Pérez-García and Rachel Sparks and Sebastien Ourselin},
year={2020},
eprint={2003.04696},
archivePrefix={arXiv},
primaryClass={eess.IV}
}
Getting started
See Getting started for installation instructions, a Hello, World! example and a comprehensive Jupyter notebook tutorial on Google Colab.
All the documentation is hosted on Read the Docs.
Please open a new 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 🤔 |
This project follows the all-contributors specification. Contributions of any kind welcome!
History
0.17.0 (23-06-2020)
- Add transforms history to
Subjectattributes to improve traceability - Add support to use an initial transformation in
Resample - Add support to use an image file as target in
Resample - Add
meanargument toRandomNoise - Add tensor support for transforms
- Add support to use strings as interpolation argument
- Add support for 2D images
- Add attribute access to
SubjectandImage - Add MNI and 3D Slicer datasets
- Add
intensityargument toRandomGhosting - Add
translationargument toRandomAffine - Add shape, spacing and orientation attributes to
ImageandSubject - Refactor samplers
- Refactor inference classes
- Add 3D Slicer extension
- Add ITK-SNAP datasets
- Add support to take NumPy arrays as transforms input
- Optimize cropping using PyTorch
- Optimizing transforms by reducing number of tensor copying
- Improve representation (
repr()) ofImage - Use lazy loading in
Image
0.16.0 (21-04-2020)
- Add advanced padding options for
RandomAffine - Add reference space options in
Resample - Add probability argument to all transforms
- Add
OneOfandComposetransforms to improve composability
0.15.0 (07-04-2020)
- Refactor
RandomElasticDeformationtransform - Make
Subjectinherit fromdict
0.14.0 (31-03-2020)
- Add
datasetsmodule - Add support for DICOM files
- Add documentation
- Add
CropOrPadtransform
0.13.0 (24-02-2020)
- Add
Subjectclass - Add random blur transform
- Add lambda transform
- Add random patches swapping transform
- Add MRI k-space ghosting artefact augmentation
0.12.0 (21-01-2020)
- Add ToCanonical transform
- Add CenterCropOrPad transform
0.11.0 (15-01-2020)
- Add Resample transform
0.10.0 (15-01-2020)
- Add Pad transform
- Add Crop transform
0.9.0 (14-01-2020)
- Add CLI tool to transform an image from file
0.8.0 (11-01-2020)
- Add Image class
0.7.0 (02-01-2020)
- Make transforms use PyTorch tensors consistently
0.6.0 (02-01-2020)
- Add support for NRRD
0.5.0 (01-01-2020)
- Add bias field transform
0.4.0 (29-12-2019)
- Add MRI k-space motion artefact augmentation
0.3.0 (21-12-2019)
- Add Rescale transform
- Add support for multimodal data and missing modalities
0.2.0 (2019-12-06)
- First release on PyPI.
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