swin-unetr-mlx

Segment 13 abdominal organs in CT with MONAI SwinUNETR and native MLX.

Docs · MedMLX

Abdominal CT → multi-organ segmentation.

Apple Silicon · Metal · Python 3.13 / 3.14 · uv

Quick start

uv venv --python 3.13
source .venv/bin/activate
repo="https://github.com/MedMLX/swin-unetr-mlx"
uv pip install \
  "swin-unetr-mlx[conversion] @ git+$repo" \
  huggingface-hub

Download and convert the checkpoint once, then run:

from pathlib import Path

from huggingface_hub import hf_hub_download
from swin_unetr_mlx import convert_checkpoint
from swin_unetr_mlx.medmlx import run

checkpoint = hf_hub_download("MONAI/swin_unetr_btcv_segmentation", "models/model.pt")
convert_checkpoint(Path(checkpoint), Path("model.safetensors"))

result = run(image_path="ct.nii.gz", weights_path="model.safetensors", output_dir="out")
print(result["outputs"]["mask"])

License

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

For research and education. Outputs require human review.