Iterative co-creation of harmonized human and non-human primate cellular and structural ontologies and 3D common coordinate frameworks for the basal ganglia

Ding, S.-L.; Bhandiwad, A.; Rosen, B.; Seeman, S. C.; Long, B.; Johansen, N. J.; Bayindir, U.; Facer, B.; Fu, Y.; Halimi, Y.; Hou, Y.; Hu, D.; Huang, M.; Ikeda, T.; Kalmbach, B.; Kruse, L.; Lesnar, P.; Liu, X.-P.; Luo, Z.; Ray, P.; Royall, J. J.; Schmitz, M. T.; Uematsu, A.; Vezoli, J.; Yazdani, F.; Bakken, T. E.; Freiwald, W.; Hayashi, T.; Hodge, R. D.; Kennedy, H.; Mollenkopf, T.; Ng, L.; Osumi-Sutherland, D.; Thompson, C. L.; Hawrylycz, M.; Glasser, M. F.; Van Essen, D. C.; Zeng, H.; Lein, E. S.

doi:10.64898/2026.07.30.741796

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bioRxiv · 10.64898/2026.07.30.741796

Iterative co-creation of harmonized human and non-human primate cellular and structural ontologies and 3D common coordinate frameworks for the basal ganglia

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Abstract

A major goal of the BRAIN Initiative Cell Atlas Network (BICAN) is to create a suite of foundational reference cell atlases and associated standards for human and non-human primate brains. Central to this goal is the creation of cross-species harmonized cellular taxonomies and structural parcellations with formal ontologies that can be mapped into 3D reference frameworks bridging neuroimaging and cellular and histological resolutions. We describe here an iterative approach, focused initially on the basal ganglia, to co-create structural and cellular ontologies in human, macaque and marmoset brains, including a Harmonized Ontology of Mammalian Brain Anatomy (HOMBA), and to map and refine structural parcellations into neuroimaging-based common coordinate frameworks. These references provide the framework for documenting and mapping all experimental sampling in BICAN, allowing analyses of cellular and molecular variation as a function of topographic position, and enabling comparisons of cellular, molecular and neuroimaging-based functional variation within and between primate species. HighlightsO_LIA hierarchical Harmonized Ontology of Mammalian Brain Anatomy (HOMBA) covering 2348 structures C_LIO_LIHOMBA-annotated 3D common coordinate frameworks (CCFs) of the basal ganglia across species C_LIO_LIHistologically informed 3D parcellation/atlas of 280 human subcortical structures indexed by HOMBA C_LIO_LIMapping and integration of structural, cellular and functional data with HOMBA and CCFs C_LI

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Ding, S.-L., Bhandiwad, A., Rosen, B., Seeman, S. C., Long, B., Johansen, N. J., Bayindir, U., Facer, B., Fu, Y., Halimi, Y., Hou, Y., Hu, D., Huang, M., Ikeda, T., Kalmbach, B., Kruse, L., Lesnar, P., Liu, X.-P., Luo, Z., Ray, P., Royall, J. J., Schmitz, M. T., Uematsu, A., Vezoli, J., Yazdani, F., Bakken, T. E., Freiwald, W., Hayashi, T., Hodge, R. D., Kennedy, H., Mollenkopf, T., Ng, L., Osumi-Sutherland, D., Thompson, C. L., Hawrylycz, M., Glasser, M. F., Van Essen, D. C., Zeng, H., Lein, E. S.. 2026-08-04. Iterative co-creation of harmonized human and non-human primate cellular and structural ontologies and 3D common coordinate frameworks for the basal ganglia. https://doi.org/10.64898/2026.07.30.741796

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