Developmental mouse brain common coordinate framework

Fae N. Kronman, Josephine K. Liwang, Rebecca Betty, Daniel J. Vanselow, Yuan-Ting Wu, Nicholas J. Tustison, Ashwin Bhandiwad, Steffy B. Manjila, Jennifer A. Minteer, Donghui Shin, Choong Heon Lee, Rohan Patil, Jeffrey T. Duda, Jian Xue, Yingxi Lin, Keith C. Cheng, Luis Puelles, James C. Gee, Jiangyang Zhang, Lydia Ng and Yongsoo Kim ()
Additional contact information
Fae N. Kronman: The Pennsylvania State University
Josephine K. Liwang: The Pennsylvania State University
Rebecca Betty: The Pennsylvania State University
Daniel J. Vanselow: The Pennsylvania State University
Yuan-Ting Wu: The Pennsylvania State University
Nicholas J. Tustison: University of Virginia
Ashwin Bhandiwad: Allen Institute for Brain Science
Steffy B. Manjila: The Pennsylvania State University
Jennifer A. Minteer: The Pennsylvania State University
Donghui Shin: The Pennsylvania State University
Choong Heon Lee: New York University School of Medicine
Rohan Patil: The Pennsylvania State University
Jeffrey T. Duda: University of Pennsylvania
Jian Xue: University of Texas Southwestern Medical Center
Yingxi Lin: University of Texas Southwestern Medical Center
Keith C. Cheng: The Pennsylvania State University
Luis Puelles: and Murcia Arrixaca Institute for Biomedical Research (IMIB)
James C. Gee: University of Pennsylvania
Jiangyang Zhang: New York University School of Medicine
Lydia Ng: Allen Institute for Brain Science
Yongsoo Kim: The Pennsylvania State University

Nature Communications, 2024, vol. 15, issue 1, 1-17

Abstract: Abstract 3D brain atlases are key resources to understand the brain’s spatial organization and promote interoperability across different studies. However, unlike the adult mouse brain, the lack of developing mouse brain 3D reference atlases hinders advancements in understanding brain development. Here, we present a 3D developmental common coordinate framework (DevCCF) spanning embryonic day (E)11.5, E13.5, E15.5, E18.5, and postnatal day (P)4, P14, and P56, featuring undistorted morphologically averaged atlas templates created from magnetic resonance imaging and co-registered high-resolution light sheet fluorescence microscopy templates. The DevCCF with 3D anatomical segmentations can be downloaded or explored via an interactive 3D web-visualizer. As a use case, we utilize the DevCCF to unveil GABAergic neuron emergence in embryonic brains. Moreover, we map the Allen CCFv3 and spatial transcriptome cell-type data to our stereotaxic P56 atlas. In summary, the DevCCF is an openly accessible resource for multi-study data integration to advance our understanding of brain development.

Date: 2024
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DOI: 10.1038/s41467-024-53254-w

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