BraTS Orchestrator
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Providing the top-performing algorithms from the Brain Tumor Segmentation (BraTS) challenges, through an easy-to-use Python API.
Documentation
|
Quickstart Get up and running in minutes. Go to Quickstart |
Segmentation Adult glioma, meningioma, metastases, and more. Go to Segmentation |
|
Inpainting Synthesize healthy tissue in tumor regions. Go to Inpainting |
Missing MRI Generate missing MRI sequences. Go to Missing MRI |
Installation
pip install brats
# Python >= 3.10 required for preprocessing:
pip install brats[preprocessing]
[!IMPORTANT] BraTS Orchestrator requires Docker or Singularity to run algorithm containers. Most algorithms also need GPU support (NVIDIA Container Toolkit). See the installation docs for full setup instructions.
Quick Example
from brats import AdultGliomaPreAndPostTreatmentSegmenter
segmenter = AdultGliomaPreAndPostTreatmentSegmenter(cuda_devices="0")
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",
)
Citation
If you use BraTS Orchestrator in your research, please cite:
Kofler, F., et al. (2025). BraTS orchestrator: Democratizing and Disseminating state-of-the-art brain tumor image analysis. arXiv:2506.13807
@misc{kofler2025bratsorchestratordemocratizing,
title={BraTS orchestrator: Democratizing and Disseminating state-of-the-art brain tumor image analysis},
author={Florian Kofler and others},
year={2025},
eprint={2506.13807},
archivePrefix={arXiv},
primaryClass={eess.IV},
url={https://arxiv.org/abs/2506.13807},
}
Contributing
We welcome contributions! Please open a new issue here or have a look at our CONTRIBUTING.md.
License
2 maintainers
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