The Human and Mammalian Brain Atlas (HMBA) is a major atlas of the BRAIN Initiative Cell Atlas Network (BICAN) that proposes to establish a comprehensive, highly granular cell atlas in complete adult human, macaque, and marmoset brains that links brain structure, function and cellular architecture. We are pleased to share a new cross-species atlas release now available to the community.
Atlas Release: Basal Ganglia
The first atlas release from the HMBA consortium delivers a cross-species cell type taxonomy, a massive annotated single-cell dataset, and tools for accessing, exploring, and utilizing the taxonomy and data. Read more about the release here: HMBA Release: Basal Ganglia .
The consensus basal ganglia cell type taxonomy is the result of iterative clustering and cross-species integration of transcriptomic data from single-nucleus 10x Genomics multiomic profiling. The taxonomy encompasses neurons from key structures within the basal ganglia, including the caudate (Ca), putamen (Pu), nucleus accumbens (NAc), the external and internal segments of the globus pallidus (GPe, GPi), ventral pallidus (VeP), subthalamic nucleus (STN), and substantia nigra (SN). By combining data from multiple primate and rodent species, this consensus taxonomy highlights both conserved and species-specific cell types. The taxonomy was validated through marker gene expression analysis, comparison with previously published taxonomies, and self-projection, ensuring the accuracy and robustness of each level in the taxonomic hierarchy.
HMBA Basal Ganglia Data, Tools and Resources on the Allen Institute’s Brain Knowledge Platform
Explore the data now in the ABC Atlas:
Map your own data to the new consensus taxonomy using MapMyCells
Programmatic access including downloads and tutorial notebooks are at abc_atlas_access on GitHub
As always, thank you for being part of the AIBS community. Please let us know how we can improve the ABC Atlas to better serve your needs.