brats 0.0.6

BraTS algorithms

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.