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Updated: Jun 11, 2026
A Polished and Reinforced Thinned-skull Window for Long-term Imaging of the Mouse Brain
Published on: March 7, 2012
Waxholm space: an image-based reference for coordinating mouse brain research
G Allan Johnson1, Alexandra Badea, Jeffrey Brandenburg
1Duke Center for In Vivo Microscopy, Radiology, Duke University Medical Center, Durham, NC 27710, USA. gjohnson@duke.edu
Abstract:
We describe an atlas of the C57BL/6 mouse brain based on MRI and conventional Nissl histology. Magnetic resonance microscopy was performed on a total of 14 specimens that were actively stained to enhance tissue contrast. Images were acquired with three different MR protocols yielding contrast dependent on spin lattice relaxation (T1), spin spin relaxation (T2), and magnetic susceptibility (T2*). Spatial resolution was 21.5 mum (isotropic). Conventional histology (Nissl) was performed on a limited set of these same specimens and the Nissl images were registered (3D-to-3D) to the MR data. Probabilistic atlases for 37 structures are provided, along with average atlases. The availability of three different MR protocols, the Nissl data, and the labels provides a rich set of options for registration of other atlases to the same coordinate system, thus facilitating data-sharing. All the data is available for download via the web.
Insights
This study presents a C57BL/6 mouse brain atlas using MRI and Nissl histology. The atlas offers detailed anatomical data for enhanced neuroscience research and data sharing.
Area of Science:
- Neuroscience
- Medical Imaging
- Comparative Anatomy
Background:
- Accurate anatomical atlases are crucial for interpreting neuroimaging data.
- Previous mouse brain atlases may lack sufficient resolution or multimodal data integration.
Purpose of the Study:
- To create a high-resolution, multimodal atlas of the C57BL/6 mouse brain.
- To facilitate data sharing and registration of other atlases within a standardized coordinate system.
Main Methods:
- Magnetic resonance microscopy (MRM) was performed on 14 C57BL/6 mouse brains.
- MRM utilized T1, T2, and T2* contrast protocols at 21.5 µm isotropic resolution.
- Conventional Nissl histology was performed and registered to the MR data.
Main Results:
- A probabilistic atlas of 37 brain structures was generated.
- Average atlases were created from the registered MR and Nissl data.
- All data, including MR images and Nissl histology, is available for download.
Conclusions:
- The developed atlas provides a valuable resource for mouse brain research.
- The multimodal approach enhances anatomical detail and registration capabilities.
- Open data access promotes collaborative research and data integration in neuroscience.
