segresnet-mlx

Segment brain tumors, renal structures and whole-body CT anatomy with MONAI SegResNet models in native MLX.

Docs · BraTS weights · Renal weights · MedMLX

Apple Silicon · Metal · Python 3.13 / 3.14 · uv

Install

uv venv --python 3.13
source .venv/bin/activate
uv pip install "segresnet-mlx @ git+https://github.com/MedMLX/segresnet-mlx.git@f60afe77518f5e617145cc4ccfa8eaa59e9eeb3e"

This source revision validates NIfTI units, voxel values and geometry before inference; PyPI 0.3.0 predates those checks.

Run

from segresnet_mlx.medmlx import brats

result = brats(
    t1c_path="t1c.nii.gz", t1_path="t1.nii.gz", t2_path="t2.nii.gz",
    flair_path="flair.nii.gz", output_dir="out",
)
print(result["outputs"]["mask"])

The registered models are segresnet-brats and segresnet-renal-cect. Their brats and renal_cect runners select the matching bundle internally and download MedMLX/segresnet-brats-mlx or MedMLX/segresnet-renal-cect-mlx when weights_path is omitted. An explicit folder contains segresnet-brats.safetensors for BraTS or segresnet-renal-cect.safetensors for renal CECT. The renal runner takes arterial_path, venous_path and excretory_path. Keep each model's input volumes on one voxel grid.

The standalone run(bundle=..., weights_path=...) interface remains available for explicit local checkpoints, including the whole-body CT variants. Published native weights are also available for renal CECT and whole-body CT.

Downloaded commits are returned in details.weights_revision; explicit local weights report null unless the folder carries a MedMLX download revision.

License

Apache-2.0. See third-party notices. Model weights retain their publisher terms.

For research and education. Outputs require human review.