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Developmental mouse brain common coordinate framework

Author

Listed:
  • 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)

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.

Suggested Citation

  • 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 Heo, 2024. "Developmental mouse brain common coordinate framework," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-53254-w
    DOI: 10.1038/s41467-024-53254-w
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