Human and Mammalian Brain Atlas (HMBA) - Marmoset Subcortex: Taxonomy and Data

Human and Mammalian Brain Atlas (HMBA) - Marmoset Subcortex: Taxonomy and Data#

The Marmoset Subcortical Cell Atlas (MSCA), is a multiomic atlas of the common marmoset (Callithrix jacchus) subcortex that integrates single nucleus transcriptomics, chromatin accessibility, and spatial transcriptomics. Part of the Human and Mammalian Brain Atlas (HMBA) effort within the NIH’s BRAIN Initiative® Cell Atlas Network (BICAN), this dataset comprehensively samples key subcortical structures in the non-human primate, including the hippocampal formation, amygdala, olfactory areas, basal forebrain, thalamus, hypothalamus, midbrain, and major hindbrain structures (excluding cerebellar cortex).

The MSCA reference cell type taxonomy clustered ~680k snRNA-seq cells to resolve 1,737 transcriptomic Clusters, which are hierarchically organized in 212 Groups and 17 Classes. Mapping 5.6 million Xenium spatial transcriptomics cells to these Clusters provided anatomical anchoring and nomenclature to the annotated Group and Class levels. Clusters localized to basal ganglia nuclei inherited their Group labels from the companion HMBA Basal Ganglia Cross-Species Consensus Taxonomy.

For more information on the MSCA cell type taxonomy and the associated 10X Multiome and Xenium spatial transcriptomics datasets, please refer to the publication: Dan, Turner, DeBerardine, et al. (2026). Spatial and regulatory organization of cell identity across the primate subcortex. Cell. https://doi.org/10.1016/j.cell.2026.10.007.

More information about the cell type taxonomy and datasets: