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Segmentation models for cancer metastasis in brain MR.

Project description

AURORA

Python Versions Stable Version Documentation Status tests License

Deep learning models for brain cancer metastasis segmentation based on the manuscripts:

Installation

With a Python 3.8+ environment, you can install brainles_aurora directly from pypi.org:

pip install brainles-aurora

Recommended Environment

Usage

BrainLes features Jupyter Notebook tutorials with usage instructions.

A minimal example could look like this:

    from brainles_aurora.inferer import AuroraInferer, AuroraInfererConfig

    config = AuroraInfererConfig(
        tta=False, cuda_devices="4"
    )  # disable tta for faster inference in this showcase
    inferer = AuroraInferer(config=config)

    inferer.infer(
        t1="t1.nii.gz",
        t1c="t1c.nii.gz",
        t2="t2.nii.gz",
        fla="fla.nii.gz",
        segmentation_file="segmentation.nii.gz",
        whole_tumor_unbinarized_floats_file="whole_network.nii.gz",
        metastasis_unbinarized_floats_file="metastasis_network.nii.gz",
        log_file="aurora.log",
    )

Citation

Please support our development by citing the following manuscripts:

Identifying core MRI sequences for reliable automatic brain metastasis segmentation

@article{buchner2023identifying,
  title={Identifying core MRI sequences for reliable automatic brain metastasis segmentation},
  author={Buchner, Josef A and Peeken, Jan C and Etzel, Lucas and Ezhov, Ivan and Mayinger, Michael and Christ, Sebastian M and Brunner, Thomas B and Wittig, Andrea and Menze, Bjoern H and Zimmer, Claus and others},
  journal={Radiotherapy and Oncology},
  volume={188},
  pages={109901},
  year={2023},
  publisher={Elsevier}
}

also consider citing the original AURORA manuscript, especially when using the vanilla model (all 4 modalities as input):

Development and external validation of an MRI-based neural network for brain metastasis segmentation in the AURORA multicenter study

@article{buchner2022development,
  title={Development and external validation of an MRI-based neural network for brain metastasis segmentation in the AURORA multicenter study},
  author={Buchner, Josef A and Kofler, Florian and Etzel, Lucas and Mayinger, Michael and Christ, Sebastian M and Brunner, Thomas B and Wittig, Andrea and Menze, Bj{\"o}rn and Zimmer, Claus and Meyer, Bernhard and others},
  journal={Radiotherapy and Oncology},
  year={2022},
  publisher={Elsevier}
}

Contact / Feedback / Questions

If possible please open a GitHub issue here.

For inquiries not suitable for GitHub issues:

Florian Kofler florian.kofler [at] tum.de

Josef Buchner j.buchner [at] tum.de

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