A common cross-species atlas of cortical gray matter

Venkadesh, S.; Tian, Y.; Linn, W.-J.; Martinez, J. B.; Mansour, H.; Cook, J.; Schaeffer, D. J.; Szczupak, D.; Silva, A. C.; Johnson, G. A.; Yeh, F.-c.

doi:10.1101/2025.09.08.675002

bioRxiv · 10.1101/2025.09.08.675002

A common cross-species atlas of cortical gray matter

Venkadesh, S.·Tian, Y.·Linn, W.-J.·Martinez, J. B.·Mansour, H.·Cook, J.·Schaeffer, D. J.·Szczupak, D.·Silva, A. C.·Johnson, G. A.·Yeh, F.-c.

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Abstract

Translational neuroscience requires consistent anatomical frameworks to compare brain organization across species despite differences in size and specialization. Existing atlases are species-specific, limiting cross-species analyses. Here we developed a hierarchical common atlas delineating homologous cortical and subcortical gray matter regions across mouse, rat, marmoset, rhesus macaque, and human, built upon population-averaged minimal deformation templates and uniform tissue segmentation. The atlas was validated through cross-atlas Dice similarity against established human parcellations, cross-scale containment against species-specific atlases, cross-species geometric consistency of regional positioning, and comparison of independent mouse and marmoset invasive tracer connectivity, with a per-region homology confidence index quantifying the strength of each regional assignment. Cross-species tracer comparison revealed a structured gradient of correspondence, with sensorimotor connections showing strong conservation and association connections showing progressive divergence. This freely available atlas provides a unified coordinate system for comparative neuroscience, enabling quantitative evaluation of where cross-species correspondence holds and where species-specific divergence emerges.

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Venkadesh, S., Tian, Y., Linn, W.-J., Martinez, J. B., Mansour, H., Cook, J., Schaeffer, D. J., Szczupak, D., Silva, A. C., Johnson, G. A., Yeh, F.-c.. 2025-09-09. A common cross-species atlas of cortical gray matter. https://doi.org/10.1101/2025.09.08.675002

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