Developmental mouse brain common coordinate framework

Area of Science:

• Neuroscience
• Developmental Biology
• Bioinformatics

Background:

• 3D brain atlases are crucial for understanding brain organization and data interoperability.
• A lack of 3D reference atlases for the developing mouse brain impedes research into brain development.

Purpose of the Study:

• To present a 3D developmental common coordinate framework (DevCCF) for the mouse brain across multiple developmental stages.
• To provide an accessible resource for integrating diverse neurodevelopmental datasets.

Main Methods:

• Creation of undistorted, morphologically averaged atlas templates using magnetic resonance imaging and light sheet fluorescence microscopy.
• Development of a 3D developmental common coordinate framework (DevCCF) spanning embryonic day (E)11.5 to postnatal day (P)56.
• Co-registration of atlas templates and 3D anatomical segmentations.

Main Results:

• The DevCCF includes atlas templates for E11.5, E13.5, E15.5, E18.5, P4, P14, and P56.
• An interactive 3D web-visualizer and downloadable data are available for the DevCCF.
• The DevCCF was used to study GABAergic neuron emergence and map existing datasets (Allen CCFv3, spatial transcriptome data) to the P56 atlas.

Conclusions:

• The DevCCF is an openly accessible resource that facilitates multi-study data integration.
• This framework advances the understanding of mouse brain development by providing a standardized spatial reference.
• The DevCCF supports research into neurodevelopmental trajectories and cell-type distributions.