MIC-MAC: High-throughput analysis of three-dimensional microglia morphology in mammalian brains

ABSTRACT Microglia, the resident immune cells of the brain, exhibit complex and diverse phenotypes depending on their physiological context including brain regions and disease states. While single-cell RNA-sequencing has recently resolved this heterogeneity, it does not capture tissue and intercellular mechanisms. Our complementary imaging-based approach enables automatic 3D-morphology characterization and classification of thousands of individual microglia in situ and revealed species- and disease-specific morphological phenotypes in mouse and human brain samples.