A high-resolution CT image of both hindlimbs is acquired. At Biospective, we have developed a fully-automated "pipeline" for quantitative image analysis. The CT images are first preprocessed to remove the acquisition bed from the scans. Each preprocessed image is then registered to a population average mouse template using a combination of linear and non-linear transformations. These transformations are inverted and are used to map an atlas defining the various leg muscles on the mouse template back onto the individual CT images to obtain native muscle volumes.