Whole-body muscle segmentation in the browser
MuscleMap is a browser-based tool for automatic muscle segmentation from MRI or CT using an official MONAI 2D UNet model.
All computation runs locally in your browser using ONNX Runtime Web. Patient data is not uploaded to any server.
Download the Neurodesk container while online, then run segmentation locally without an internet connection. The container includes the whole-body v1.4 model and its runtime dependencies.
Use an x86_64 Linux computer or cluster with Apptainer installed. Follow the Neurodesk container setup instructions before going offline. Singularity users can replace apptainer with singularity in the command below.
Download musclemap_1.4.0_20260827.simg (6.54 GB). Keep the file on your computer or transfer it to your offline machine.
The Zenodo release record lists the MD5 checksum. Verify the download before use:
Put the container and your NIfTI scan in the same writable folder. Open a terminal in that folder and replace image.nii.gz with your scan's filename. This command uses the CPU and writes results to that folder.
For an NVIDIA GPU with working host drivers, add --nv after exec and change -g N to -g Y.