Multiscale spatial atlas of human basal ganglia cell types and communities.

A multi-region spatial transcriptomic atlas of the human basal ganglia resolves 60 transcriptionally distinct cell types from ~7.9 million cells across four neurotypical donors.

• Why it matters: The basal ganglia’s nuclei differ functionally, yet their cell-type composition and spatial organization have lacked a comprehensive, subcellular-resolution map.
• What they did: The study integrated MERFISH+ with Stereo-seq across caudate, putamen, nucleus accumbens, and globus pallidus, then used subcellular RNA localization and community analyses to link cell types to spatial architecture.
• The result: It shows region-selective diversification of spiny projection neurons and non-neuronal populations, with astrocyte and oligodendrocyte subclusters enriched at striosome–matrix borders and primate-expanded interneurons confined to matrix; cross-species comparisons reveal conserved striosome–matrix organization and dorsolateral-to-ventromedial transcriptional gradients.

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