scBrainScope: cross-species multidimensional brain atlas.

As one of the most evolutionarily complex and functionally diverse organs, the brain is characterized by its intricate structure, developmental alterations, and cellular heterogeneity. Although extensive brain atlases exist, there remains an urgent need for an integration platform that brings together gene expression profiles and analysis tools to explore features across species, brain regions, developmental stages, and pathological conditions. Thus, we developed scBrainScope, a detailed and interactive transcriptomic atlas of the brain. Our platform brings together single cell sequencing data from 135 species, covering 433 brain regions, 198 developmental stages, and 100 neurological diseases. In addition, we compiled 737 bulk RNA sequencing datasets from 275 species, along with 1154 spatial datasets of brain, spinal cord, and embryonic tissues. scBrainScope comprises six atlas modules (AtlasScope, RegionScope, TissueScope, SpaceScope, PathoScope, and AgeScope) and three analytical modules (sPandora, ePandora, and cPandora). Together, these tools enable researchers to investigate cell identity, gene programs, and spatial organization at multiple scales and dimensions. scBrainScope is freely available at http://8.142.154.29/scBrainScope or http://www.brainscopes.org, offering an interactive, data-rich resource for neuroscience, evolutionary biology, and translational medicine.