Brain Imaging Techniques in Rodent Models

Preclinical brain imaging in rodents employs a spectrum of modalities to interrogate structure, function and connectivity at high resolution. Structural approaches such as magnetic resonance imaging (MRI) and X-ray microtomography yield detailed three-dimensional maps of grey and white matter, ventricles and fibre tracts. Functional techniques, including manganese-enhanced MRI and functional MRI, provide insight into activity patterns and neurophysiological changes over time. Optical methods, such as two-photon microscopy and light-sheet fluorescence imaging, enable cellular-level visualisation of neural circuits in cleared tissue. Central to these efforts are digital brain atlases and common coordinate frameworks that standardise spatial reference spaces, permitting integration of multimodal datasets. Advances in automated image registration, machine-learning-driven segmentation and probabilistic mapping have accelerated data processing and reproducibility. Together, these tools support longitudinal studies of development, disease models and therapeutic interventions, fostering translational insights from rodent systems to human neuroscience.

Research from Nature Portfolio

Recent studies have expanded and refined digital atlases and registration workflows to streamline rodent neuroimaging. A comprehensive update of a rat brain volumetric atlas now covers over 200 anatomical structures with revised annotations, accompanied by open-access tools for integration and analysis of diverse experimental datasets. A deep-learning–based framework has been developed to register histological sections from mouse brains to a standard coordinate space with accuracy comparable to expert manual alignment but at over a thousand-fold increase in speed. In addition, high-resolution MRI templates and probabilistic tissue maps for the rat brain have been introduced, providing sub-150-micrometre isotropic images for structural segmentation and voxel-based morphometry applications. These resources enhance consistency across laboratories and enable more precise localisation of anatomical and functional changes in rodent models.

Brain Imaging Techniques in Rodent Models publication trend

The graph below shows the total number of articles in brain imaging techniques in rodent models across all publications each year (not limited to Nature Index journals).

Technical terms

Volumetric atlas: A three-dimensional reference map of brain structures segmented and annotated for spatial analysis.

Image registration: The process of aligning different images or modalities into a common coordinate system.

Common Coordinate Framework: A standardized three-dimensional reference space enabling integration of diverse neuroimaging data.

Isotropic resolution: Imaging resolution where voxel dimensions are equal in all three spatial axes, ensuring uniform detail.

Microtomography: High-resolution X-ray imaging technique producing detailed three-dimensional reconstructions at micrometre scale.

Parcellation: Division of the brain into distinct regions or parcels based on anatomical or functional criteria.

References

1. Waxholm Space atlas of the rat brain: a 3D atlas supporting data analysis and integration. Nature Methods (2023).
2. DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas. Nature Communications (2023).
3. The SIGMA rat brain templates and atlases for multimodal MRI data analysis and visualization. Nature Communications (2019).
4. Synchrotron Radiation‐Based Tomography of an Entire Mouse Brain with Sub‐Micron Voxels: Augmenting Interactive Brain Atlases with Terabyte Data. Advanced Science (2025).
5. An in vivo MRI Template Set for Morphometry, Tissue Segmentation, and fMRI Localization in Rats. Frontiers in Neuroinformatics (2011).