An interactive 3D atlas of gene expression in the mouse brain

Carey, H.; Piluso, S.; Bjerke, I.; Gui, X.; Yates, S.; Pieschnik, S.; Benediktsdottir, S.; Golla, A.; Puchades, M.; Dickscheid, T.; Leergaard, T.; McMullan, S.; Markram, H.; Keller, D.; Bjaalie, J. G.

doi:10.64898/2026.01.20.700446

bioRxiv · 10.64898/2026.01.20.700446

An interactive 3D atlas of gene expression in the mouse brain

Carey, H.·Piluso, S.·Bjerke, I.·Gui, X.·Yates, S.·Pieschnik, S.·Benediktsdottir, S.·Golla, A.·Puchades, M.·Dickscheid, T.·Leergaard, T.·McMullan, S.·Markram, H.·Keller, D.·Bjaalie, J. G.

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Abstract

The Allen Mouse Brain Atlas provides gene expression data for over 20,000 genes and has been extensively used in neuroscience. However, its constrained by a resolution of 200 {micro}m3. We improved this to 25 {micro}m3 for 4,083 genes by re-registering 401,660 sections to atlas space. From this, we produced an atlas with regions defined by shared molecular signatures and built an interactive online platform allowing exploration of gene expression patterns.

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Carey, H., Piluso, S., Bjerke, I., Gui, X., Yates, S., Pieschnik, S., Benediktsdottir, S., Golla, A., Puchades, M., Dickscheid, T., Leergaard, T., McMullan, S., Markram, H., Keller, D., Bjaalie, J. G.. 2026-01-21. An interactive 3D atlas of gene expression in the mouse brain. https://doi.org/10.64898/2026.01.20.700446

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