Current Protocols in Molecular Biology For Chapter 29 Ms#CP-16-0221 Automated computational processing of 3D MR images of mouse brain for phenotyping of living animals

摘要

Magnetic resonance (MR) imaging provides a method to obtain anatomical information from the brain in vivo not amenable to optical imaging because of its opacity. MR is non-destructive and obtains deep tissue contrast with 100 µm³ voxel resolution or better. Manganese-enhanced MRI (MEMRI) may be used to observe axonal transport and localized neural activity in the living rodent and avian brain. Such enhancement enables researchers to investigate differences in functional circuitry or neuronal activity in images of brains of different animals. Moreover, once MR images of a number of animals are aligned into a single matrix, statistical analysis can be done comparing MR intensities between different multi-animal cohorts, comprised of individuals from different mouse strains, different transgenic animals, or between different time points after an experimental manipulation. Although preprocessing steps for such comparisons (including skull-stripping and alignment) are automated for human imaging, no such automated processing has previously been readily available for mouse or other widely used experimental animals and most investigators use in-house custom processing. This protocol describes a step-wise method to perform such preprocessing for mouse.