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Related Experiment Video

Updated: Jul 15, 2025

Whole-Brain Single-Cell Imaging and Analysis of Intact Neonatal Mouse Brains Using MRI, Tissue Clearing, and Light-Sheet Microscopy

Whole-Brain Single-Cell Imaging and Analysis of Intact Neonatal Mouse Brains Using MRI, Tissue Clearing, and Light-Sheet Microscopy

Published on: August 1, 2022

Developmental Mouse Brain Common Coordinate Framework.

Fae A Kronman¹, Josephine K Liwang¹, Rebecca Betty¹

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

Biorxiv : the Preprint Server for Biology

|September 25, 2023

Summary

This summary is machine-generated.

A new 3D developmental common coordinate framework (DevCCF) provides standard reference brains for mouse development. This resource enables large-scale data integration for a comprehensive understanding of brain development.

Keywords:

GABA neurons anatomical segmentation brain development common coordinate framework (CCF)multimodal registration reference atlas

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Microdissection of Mouse Brain into Functionally and Anatomically Different Regions

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Published on: February 15, 2021

Area of Science:

Neuroscience
Developmental Biology
Bioinformatics

Background:

Standard 3D reference brains are crucial for brain research and data interoperability.
A lack of standardized 3D atlases for developing mouse brains has limited progress in understanding brain development.

Approach:

Developed a multimodal 3D developmental common coordinate framework (DevCCF) covering key embryonic and postnatal stages (E11.5-P56).
Created undistorted, morphologically averaged atlas templates using MRI and light sheet fluorescence microscopy.
Incorporated expert-curated 3D anatomical segmentations based on an updated prosomeric model and a developmental ontology.

Key Points:

The DevCCF includes co-registered high-resolution templates and an interactive 3D web-visualizer.
Used DevCCF to study the emergence of GABAergic neurons in embryonic brains.
Integrated Allen CCFv3 and mapped spatial transcriptome data to the P56 template.

Conclusions:

The DevCCF is an openly accessible resource for integrating diverse developmental neuroscience datasets.
Facilitates a comprehensive understanding of mouse brain development through standardized spatial referencing.
Enables advanced research in developmental neurobiology and comparative studies.