Molecularly defined cellular atlas of the entire mouse brain with isotropic single-cell resolution.

The mammalian brain comprises a vast number of neurons, exhibiting remarkable diversity in both molecular composition and spatial distribution. However, a comprehensive understanding of how these neurons are organized within the brain remains elusive, largely due to the lack of systematic studies providing three-dimensional coverage of molecularly defined neurons across the entire brain. In this study, we utilized transgenic mice and fMOST imaging to map the spatial distribution of glutamatergic, GABAergic, and modulatory neurons at the single-cell level throughout the whole brain. Our approach enabled precise registration of individual cells to the standardized brain coordinate framework, facilitating the construction of whole-brain cell atlases for commonly used Cre recombinase driver lines. Analysis revealed diverse cellular composition patterns across the brain, aligning with the boundaries of known brain regions in some areas while uncovering previously uncharacterized subdivisions in others. Notably, cortical and subcortical nuclei as small as approximately one millimeter in size exhibited intricate three-dimensional organization, suggesting the presence of finer functional zones.