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Related Experiment Video

Updated: May 10, 2026

Microdissection of Mouse Brain into Functionally and Anatomically Different Regions

Microdissection of Mouse Brain into Functionally and Anatomically Different Regions

Published on: February 15, 2021

Developmental mouse brain common coordinate framework.

Fae N Kronman¹, Josephine K Liwang¹, Rebecca Betty¹

¹Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA, USA.

Nature Communications

|October 21, 2024

Summary

This summary is machine-generated.

A new 3D developmental common coordinate framework (DevCCF) provides a vital resource for studying mouse brain development. This framework enables multi-study data integration to advance our understanding of neurodevelopmental processes.

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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.