Nature Methods: EBRAINS hosts the world's most complete open-access atlas of the rat brain

This open-access 3D multimodal rat brain atlas, offered through different viewers available via the EBRAINS research infrastructure, has now expanded to include annotations of 222 structures, including 112 new annotations and 57 revised ones. The work, supported by the Human Brain Project and conducted by researchers from the University of Oslo, Autónoma de Madrid University, and Amsterdam University Medical Center, was published in Nature Methods.

Until recently, a publicly available digital atlas with complete coverage of the rat brain had been missing. The WHS rat brain atlas fills this gap, providing neuroscientists with a detailed volumetric open-source reference atlas, covering all major systems of the brain.

“The Nature Methods publication marks a significant milestone, making this highly advanced brain atlas available to the scientific community in its most refined form,” says Jan Bjaalie, one of the authors of the study and EBRAINS Data Services leader.

Digital 3D brain atlases are used to plan and perform neuroscientific experiments and analyses, visualise and disseminate data, and integrate new with already available data. The WHS rat brain atlas supports these functionalities through its compatibility with analytical workflows. Incorporated in tools and workflows offered by EBRAINS, it allows researchers to accurately visualise and navigate brain structures, and enables the comparison of datasets in the same model species.

This open-access approach facilitates the integration of data into the atlas, benefiting both individual researchers and the broader scientific community.

Previous versions of the WHS rat brain atlas had high-level annotations focused on major brain regions. Now, its version 4 includes a more complete segmentation, offering full-brain coverage, with 222 detailed and functionally relevant annotations. The authors have focused on expanding annotations in cortical, thalamic, striatopallidal, and midbrain regions, which play important roles in sensorimotor processing, information flow, habit formation, motor behaviour, and reward processing. These regions are also linked to various neurological and neuropsychiatric diseases.

To delineate these annotations, the authors combined interpretation of the structural magnetic resonance imaging (sMRI) and diffusion tensor imaging (DTI) datasets of the atlas template with multimodal cyto-, chemo- and myeloarchitecture, other reference atlases, and literature. The study also presents explicit criteria for structure identification and provides a consistent organisation hierarchical scheme.

Previous versions of the WHS rat brain atlas have already supported a wide range of studies and analysis of structural and functional data at multiple scales. Motivated by the success stories of the users of this tool, the team of researchers remains committed to the further development of the atlas, not least to solve problems related to uncharted regions and alternative interpretations.

This study used no new animal data, but reused data from previous studies, all generated in compliance with ethical regulations for animal research.

Read the paper:
Waxholm Space atlas of the rat brain: a 3D atlas supporting data analysis and integration
Kleven, H., Bjerke, I.E., Clascá, F. et al. Waxholm Space atlas of the rat brain: a 3D atlas supporting data analysis and integration. Nat Methods (2023). https://doi.org/10.1038/s41592-023-02034-3