Segmentation, Registration, and Deformation Analysis of 3D MR Images of Mice

We demonstrate our mouse MR image and shape analysis pipeline. The long term goal of our work is the description of structural shape variations in normal, genetically identical mice and the subsequent detection of pathological phenotypes in genetically modified mice. The pipeline begins with the acquisition and reconstruction of high resolution MR images of mice. Regions of the images containing organs under study are enhanced via edge-preserving smoothing and mouse organs are segmented using a deformable mesh model. Images are registered using a multi-resolution approach and displacement fields are used to calculate local volume changes. Detailed descriptions and results for each step of the pipeline are presented.