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Developmental mouse brain common coordinate framework

Affiliations
  • 1Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA, USA.
  • 2Department of Pathology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA.
  • 3Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA.
  • 4Allen Institute for Brain Science, Seattle, WA, USA.
  • 5Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA.
  • 6Department of Radiology, Penn Image Computing and Science Lab, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
  • 7Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
  • 8Department of Human Anatomy and Psychobiology, Faculty of Medicine, Universidad de Murcia, and Murcia Arrixaca Institute for Biomedical Research (IMIB), Murcia, Spain.
  • 9Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA, USA. yuk17@psu.edu.

Published on:

October 21, 2024

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.