Bjerke, I. | bioRxiv Science

bioRxiv2026

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

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.

neuroscience↗

bioRxiv2024

DeMBA: a developmental atlas for navigating the mouse brain in space and time

Studies of the adult mouse brain have benefited from three-dimensional (3D) atlases providing standardised frameworks for data analysis and integration. However, few 3D atlases exist for the developing mouse brain, and none cover more than a few ages. This fails to represent the dynamic nature of development and is insufficient for researchers whose data fall between the ages of existent atlases. Existing atlases also neglect the spatial correspondence between ages, making comparison across ages difficult. We present the Developmental Mouse Brain Atlas (DeMBA), a 4D atlas encompassing every postnatal day from 4 to 56. DeMBA is incorporated in software for spatial registration and analysis, enabling brain-wide quantification of features of interest. Furthermore, we provide a software package, the CCF translator, allowing coordinates or image volumes to be transformed between ages for comparison. These resources provide age-specific spatial frameworks incorporated in accessible analytic pipelines for developmental mouse brain data.

neuroscience↗