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

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Harry Carey, Sébastien Piluso, Ingvild Bjerke, Xiaoyun Gui, Sharon Yates, Sophia Pieschnik, Signý Benediktsdóttir, Archana Golla, Maja Puchades, Timo Dickscheid, Trygve Leergaard, Simon McMullan, Henry Markram, Daniel Keller, Jan G. Bjaalie

Published: 21 Jan 2026, Last Modified: 27 Feb 2026CrossrefEveryoneRevisionsCC BY-SA 4.0
Abstract: h3>Abstract</h3> <p>The Allen Mouse Brain Atlas provides gene expression data for over 20,000 genes and has been extensively used in neuroscience. However, it’s constrained by a resolution of 200 µm<sup>3</sup>. We improved this to 25 µm<sup>3</sup> 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.</p>