BraTS algorithms
Project description
BraTS
Providing the top performing algorithms from the Brain Tumor Segmentation (BraTS) challenges, through an easy to use Python API powered by docker.
Features
- Access to top-performing algorithms from recent BraTS challenges
- Easy-to-use minimal API
- Extensive documentation and examples
Installation
With a Python 3.8+ environment, you can install brats
directly from PyPI:
pip install brats
Docker and NVIDIA Container Toolkit Setup
To run brats
you need a working Docker installation.
Most algorithms also require GPU support (NVIDIA Docker).
Installation instructions:
- Docker: Installation instructions on the official website
- NVIDIA Container Toolkit: Refer to the NVIDIA install guide and the official GitHub page
Use Cases and Tutorials
A minimal example to create a segmentation could look like this:
from brats import AdultGliomaSegmenter
segmenter = AdultGliomaSegmenter()
segmenter.infer_single(
t1c="path/to/t1c.nii.gz",
t1n="path/to/t1n.nii.gz",
t2f="path/to/t2f.nii.gz",
t2w="path/to/t2w.nii.gz",
output_file="segmentation.nii.gz",
)
For more examples and details please refer to our extensive Notebook tutorials [TODO]
Algorithms
Challenge | Year | Position | Authors | Paper | CPU support |
---|---|---|---|---|---|
Meningioma Segmentation | 2023 | 1st | Andriy Myronenko, et al. | N/A | :heavy_multiplication_x: |
2023 | 2nd | Ziyan Huang | N/A | :white_check_mark: | |
2023 | 3rd | Zhifan Jiang et al. | N/A | :heavy_multiplication_x: | |
Pediatric Segmentation | 2023 | 1st | Zhifan Jiang et al. | N/A | :heavy_multiplication_x: |
2023 | 2nd | Andriy Myronenko, et al. | N/A | :heavy_multiplication_x: | |
2023 | 3rd | Yubo Zhou | N/A | :heavy_multiplication_x: | |
Adult Glioma Segmentation | 2023 | 1st | André Ferreira, et al. | Link | :heavy_multiplication_x: |
2023 | 2nd | Andriy Myronenko, et al. | N/A | :heavy_multiplication_x: | |
2023 | 3rd | Fadillah Adamsyah Maani, et al. | N/A | :heavy_multiplication_x: |
Citation
If you use BraTS in your research, please cite it to support the development!
TODO: citation will be added asap
Contributing
We welcome all kinds if contributions from the community!
Reporting Bugs, Feature Requests and Questions
Please open a new issue here.
Code contributions
Nice to have you on board! Please have a look at our CONTRIBUTING.md file.
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.