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Updated: Mar 1, 2026
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
An ontologically consistent MRI-based atlas of the mouse diencephalon
Charles Watson1, Andrew L Janke2, Carlo Hamalainen3
1The Australian Mouse Brain Mapping Consortium, The University of Queensland, Brisbane, Australia; Health Sciences, Curtin University, Perth, Western Australia, Australia; Neuroscience Research Australia and The University of New South Wales, Sydney, Australia.
This study introduces a new volumetric mouse brain atlas detailing 89 diencephalon structures. The atlas aids researchers in analyzing the diencephalon (the brain region between the hypothalamus and midbrain) and its nuclei.
Area of Science:
- Neuroscience
- Medical Imaging
- Anatomy
Background:
- The diencephalon, located between the hypothalamus and midbrain, comprises three segments: pretectum, thalamus, and prethalamus.
- Existing MRI-based mouse brain atlases lack detailed segmentation of diencephalon segments and their nuclei.
Purpose of the Study:
- To present a novel volumetric MRI-based atlas of the mouse diencephalon.
- To identify and map 89 distinct structures within the diencephalon of the C57BL/6J mouse model.
Main Methods:
- Acquisition of high-resolution (16.4T) MRI scans from 18 male C57BL/6J mice (12 weeks old).
- Generation of an average volumetric atlas representing the diencephalon's segmented structures.
- Development of an FSL package for nonlinear registration and automated segmentation.
Main Results:
- A comprehensive atlas of the mouse diencephalon, detailing 89 anatomical structures.
- The atlas is based on averaged MR scans, providing a robust representation.
- A downloadable atlas (www.imaging.org.au/AMBMC) and registration tools are provided.
Conclusions:
- This new atlas provides unprecedented detail of the mouse diencephalon's segmented structures.
- The accompanying software facilitates the integration of new data with the atlas.
- This resource will advance research in mouse brain anatomy and function.
