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Updated: Jul 1, 2026
Preparation of Mouse Brain Tissue for Immunoelectron Microscopy
Published on: July 21, 2010
Protocol for tissue processing and paraffin embedding of mouse brains following ex vivo MRI
Adele Smart1, Cristiana Tisca2, Istvan N Huszar2
1Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, OX3 9DU Oxford, UK; Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, OX3 9DU Oxford, UK.
Abstract:
Combining histology and ex vivo MRI from the same mouse brain is a powerful way to study brain microstructure. Mouse brains prepared for ex vivo MRI are often kept in storage solution for months, potentially becoming brittle and showing reduced antigenicity. Here, we describe a protocol for mouse brain dissection, tissue processing, paraffin embedding, sectioning, and staining. We then detail registration of histology to ex vivo MRI data from the same sample and extraction of quantitative histological measurements.
Insights
This study presents a protocol for preparing mouse brains for both histology and ex vivo MRI, enabling detailed brain microstructure analysis. The method ensures tissue integrity and antigenicity for accurate quantitative histological measurements.
Area of Science:
- Neuroscience
- Biomedical Imaging
- Histology
Background:
- Combining ex vivo MRI and histology offers powerful insights into brain microstructure.
- Long-term storage of mouse brains for MRI can compromise tissue integrity and antigenicity.
- A standardized protocol is needed to preserve tissue quality for multimodal analysis.
Purpose of the Study:
- To develop and describe a comprehensive protocol for processing mouse brains for both ex vivo MRI and histology.
- To ensure tissue quality, including integrity and antigenicity, after storage.
- To enable accurate registration and quantitative histological measurements from the same sample.
Main Methods:
- Detailed protocol for mouse brain dissection, tissue processing, and paraffin embedding.
- Sectioning and staining techniques for histological analysis.
- Registration of histological data to ex vivo MRI from the identical sample.
Main Results:
- Successful implementation of a protocol preserving mouse brain tissue for multimodal analysis.
- Demonstration of accurate registration between ex vivo MRI and histology.
- Extraction of quantitative histological measurements from processed samples.
Conclusions:
- The described protocol facilitates the combined analysis of ex vivo MRI and histology from the same mouse brain.
- This method supports robust studies of brain microstructure by maintaining tissue quality.
- The protocol enables precise quantitative histological measurements correlated with MRI data.
