epDevAtlas: mapping GABAergic cells and microglia in the early postnatal mouse brain

Josephine K. Liwang, Fae N. Kronman, Hyun-Jae Pi, Yuan-Ting Wu, Daniel J. Vanselow, Steffy B. Manjila, Deniz Parmaksiz, Donghui Shin, Yoav Ben-Simon, Michael Taormina, Sharon W. Way, Hongkui Zeng, Bosiljka Tasic, Lydia Ng and Yongsoo Kim ()
Additional contact information
Josephine K. Liwang: The Pennsylvania State University
Fae N. Kronman: The Pennsylvania State University
Hyun-Jae Pi: The Pennsylvania State University
Yuan-Ting Wu: The Pennsylvania State University
Daniel J. Vanselow: The Pennsylvania State University
Steffy B. Manjila: The Pennsylvania State University
Deniz Parmaksiz: The Pennsylvania State University
Donghui Shin: The Pennsylvania State University
Yoav Ben-Simon: Allen Institute for Brain Science
Michael Taormina: Allen Institute for Brain Science
Sharon W. Way: Allen Institute for Brain Science
Hongkui Zeng: Allen Institute for Brain Science
Bosiljka Tasic: Allen Institute for Brain Science
Lydia Ng: Allen Institute for Brain Science
Yongsoo Kim: The Pennsylvania State University

Nature Communications, 2025, vol. 16, issue 1, 1-18

Abstract: Abstract During development, brain regions follow encoded growth trajectories. Compared to classical brain growth charts, high-definition growth charts could quantify regional volumetric growth and constituent cell types, improving our understanding of typical and pathological brain development. Here, we create high-resolution 3D atlases of the early postnatal mouse brain, using Allen CCFv3 anatomical labels, at postnatal days (P) 4, 6, 8, 10, 12, and 14, and determine the volumetric growth of different brain regions. We utilize 11 different cell type-specific transgenic animals to validate and refine anatomical labels. Moreover, we reveal region-specific density changes in γ-aminobutyric acid-producing (GABAergic) neurons, cortical layer-specific cell types, and microglia as key players in shaping early postnatal brain development. We find contrasting changes in GABAergic neuronal densities between cortical and striatal areas, stabilizing at P12. Moreover, somatostatin-expressing and vasoactive intestinal peptide-expressing cortical interneurons undergo regionally distinct density changes. Remarkably, microglia transition from high density in white matter tracks to gray matter at P10, and show selective density increases in sensory processing areas that correlate with the emergence of individual sensory modalities. Lastly, we create an open-access web-visualization ( https://kimlab.io/brain-map/epDevAtlas ) for cell-type growth charts and developmental atlases for all postnatal time points.

Date: 2025
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DOI: 10.1038/s41467-025-64549-x

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