Automated segmentation of the actively stained mouse brain using multi-spectral MR microscopy.

Magnetic resonance microscopy (MRM) has created new approaches for high-throughput morphological phenotyping of mouse models of diseases. Transgenic and knockout mice serve as a test bed for validating hypotheses that link genotype to the phenotype of diseases, as well as developing and tracking treatments. We describe here a Markov random fields based segmentation of the actively stained mouse brain, as a prerequisite for morphological phenotyping.

Enhanced T2 contrast for MR histology of the mouse brain.

A 3D Carr-Purcell-Meiboom-Gill (CPMG) sequence was implemented to obtain enhanced T(2) contrast in actively stained (perfusion with fixative and contrast agent) mouse brains at 9.4 T. Short interecho spacing was used to minimize diffusion and susceptibility losses.