Open-source toolbox

MuscleMap

Whole-body muscle segmentation and quantitative analysis for large-scale imaging studies.

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Built for researchers, clinicians, and data scientists working with MRI and CT.

Features

Whole-body muscle segmentation

Designed for whole-body and clinical imaging with consistent labelling across muscles and bones, enabling large-scale, multi-region analyses.

Automated muscle quantification

Extract muscle-specific metrics such as volumes or intramuscular fat percentage across multiple MRI contrasts and CT.

Three-dimensional spatial parametric mapping

Visualize and calculate the 3D spatial distribution of intramuscular fat in a standardized muscle template.

3D Slicer extension

Includes a 3D Slicer extension to make MuscleMap easy to run and inspect individual cases for quality control.

Neurodesk web application

Run MuscleMap directly in your browser through Neurodesk. Simply drag and drop NIfTI or DICOM images and click run segmentation. No installation required and all data remains on your local workstation.