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

Harry Carey, Heidi Kleven, Martin Øvsthus, Sharon C. Yates, Gergely Csucs, Maja A. Puchades, Simon McMullan, Jan G. Bjaalie, Trygve B. Leergaard and Ingvild E. Bjerke ()
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Harry Carey: University of Oslo
Heidi Kleven: University of Oslo
Martin Øvsthus: University of Oslo
Sharon C. Yates: University of Oslo
Gergely Csucs: University of Oslo
Maja A. Puchades: University of Oslo
Simon McMullan: Macquarie University
Jan G. Bjaalie: University of Oslo
Trygve B. Leergaard: University of Oslo
Ingvild E. Bjerke: University of Oslo

Nature Communications, 2025, vol. 16, issue 1, 1-13

Abstract: Abstract 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 was created by using existing brain templates for six developmental time points and interpolating intermediate ages. DeMBA is incorporated in software for spatial registration and analysis, enabling brain-wide quantification of features of interest. Furthermore, we provide the software package 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.

Date: 2025
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DOI: 10.1038/s41467-025-63177-9

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