A mouse brain atlas based on dendritic microenvironments

Abstract Brain atlases map the spatial organization of neural tissue and serve as anatomical references. Current mouse brain atlases define regions based primarily on cell density patterns but overlook how neurons extend their branches (dendrites) to form local networks. Here we show that mapping dendrites enhanced by their local neighborhoods—which we call microenvironments—reveals a finer-grained brain organization. We analyzed dendrite patterns from more than 100,000 neurons across 111 mouse brains and discovered that neurons group into distinct microenvironments that subdivide known brain regions, nearly doubling the number of identifiable areas compared with the standard Allen Common Coordinate Framework. Remarkably, hippocampal neurons with similar local dendrite arrangements tend to form long-range connections to similar distant targets, suggesting that local structure predicts global connectivity. This microenvironment atlas complements existing resources by revealing previously hidden subdivisions and correlations that align with functional differences, offering new insights into how brain structure relates to function.