Rat Brain Atlas

3D anatomical atlas that provides detailed information about brain regions, connectivity, and function, to support neuroanatomy research.

  • Explore detailed 3D delineations of brain regions in an intuitive web-based atlas viewer.
  • Find your brain region of interest easily with the linked brain region hierarchy.
  • Find and access data shared through EBRAINS and registered to the Waxholm Space Rat Brain Atlas.
  • Use the atlas embedded in other EBRAINS tools, allowing data integration and automated spatially linked image analysis.

The Waxholm Space rat brain atlas is a detailed volumetric atlas of the rat brain, to which a wide range of anatomical and functional data have been registered, including detailed data showing cellular distributions, axonal pathways, and gene expression patterns. EBRAINS provides a visualization interface, enabling researchers to explore and compare different aspects of the rat brain in 3D space.

Explore or download the Waxholm Space Atlas of the Sprague Dawley Rat Brain

The Waxholm Space (WHS) Rat Brain Atlas contains comprehensive anatomical delineations of the adult rat brain's brain regions and fibre tracts. The atlas was acquired from an 80-day-old male Sprague Dawley rat using high-resolution ex vivo magnetic resonance and diffusion tensor imaging (MRI/DTI) at the Duke Center for In Vivo Microscopy (Durham, NC, USA). It includes spatial coordinates and the position of bregma and lambda, facilitating conversion to stereotaxic coordinates.

Screenshot of the Rat Brain Atlas

The atlas, the MRI/DTI volumes, and the diffusion tensor data are available, along with labels and configuration files for ITK-SNAP, the Mouse BIRN Atlasing Toolkit, and PMOD. The atlas is shared in a standard volumetric format (NIfTI) containing delineations of 222 brain regions, accompanied by a label file with the name and ID of each region.

Waxholm Space Rat Brain Atlas from NITRC
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Atlas dataset and publications
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Related tools

The Waxholm Space Rat Brain Atlas is the backbone of spatially-focused workflows and tools that support spatial registration of new data to the atlas template, semi-automatic analyses using the brain region hierarchy and delineations, and visualisation of extracted data in 3D.

The atlas is incorporated in the QuickNII tool for spatial registration of serial 2D images, and employed in the QUINT workflow for extracting and quantifying labelled objects from images registered to the atlases.

Learn more about the QuickNII tool

Learn more about the QUINT workflow

Connect to atlas developers and the user community

The Waxholm Space rat brain atlas is in active development by the atlasing team at the Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, with contributions from experts on the anatomy of individual brain regions. The level of detail in the atlas is evolving, with each subsequent version offering new and refined anatomical delineations.

Downloads

As of October 2023, the WHS rat brain atlas has been downloaded 33000 times.

Contributors

Over 20 anatomists, experimental neuroscientists, students of medicine and neuroscience, software developers.

Work around the rat brain atlas

The atlas repository at the NeuroImaging Tools & Resources Collaboratory (NITRC) is accompanied by a public forum that gives you the opportunity to ask questions, suggest improvements, and contribute to the discussion around the use and development of the atlas. A brief introduction to the latest developments is given in the atlas wiki.

The anatomical delineations, the MRI template, as well as surface representations of each anatomical structure have also been incorporated into the Analysis of Functional NeuroImages (AFNI) toolbox. For AFNI-specific issues, please refer to the AFNI message board.

Join the discussion on NITRC

User forum

See the latest developments

Wiki

Learn more about using the atlas in AFNI

Message board
 

Related Publications

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Research article

Waxholm Space atlas of the rat brain: a 3D atlas supporting data analysis and integration

Kleven, H., Bjerke I.E., Clascá, F., Groenewegen, H.J., Bjaalie, J.G., Leergaard, T.B. (2023). Nature Methods 20: 1822–1829
Research article

Waxholm Space atlas of the rat brain auditory system: Three-dimensional delineations based on structural and diffusion tensor magnetic resonance imaging

Osen, K.K., Imad J., Wennberg, A.E., Papp, E.A., Leergaard, T.B. (2019). NeuroImage: 199, 38-56.
Research article

Waxholm Space atlas of the rat brain hippocampal region: Three-dimensional delineations based on magnetic resonance and diffusion tensor imaging

Kjonigsen, L.J., Lillehaug, S., Bjaalie, J.G., Witter, M.P., Leergaard, T.B. (2015). NeuroImage 108: 441-449.
Research article

Addendum to "Waxholm Space atlas of the Sprague Dawley rat brain" [NeuroImage 97 (2014) 374-386]

Papp, E.A., Leergaard, T.B., Calabrese, E., Johnson, G.A., Bjaalie, J.G. (2015). NeuroImage 105, 561–562.
Research article

Waxholm Space atlas of the Sprague Dawley rat brain

Papp, E.A., Leergaard, T.B., Calabrese, E., Johnson, G.A., Bjaalie, J.G. (2014). NeuroImage 97, 374-386.
Launch online

Related Resources

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WHS rat brain atlas v1.01 (Papp et al., 2015)

The main focus of our original article was to describe the anatomical delineations constituting the first version of the WHS Sprague Dawley atlas, apply the Waxholm Space coordinate system, and publish the associated MRI/DTI template and segmentation volume in their original format. To increase usability of the dataset, we have recently shared an updated version of the volumetric image material (v1.01). The aims of this addendum are to inform about the improvements in the updated dataset, in particular related to navigation in the WHS coordinate system, and provide guidance for transforming coordinates acquired in the first version of the atlas.

Other Tools

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siibra-explorer

siibra-explorer is built around an interactive 3D view of the brain displaying a unique selection of detailed templates and parcellation maps for the human, macaque, rat or mouse brain, including BigBrain as a microscopic resolution human brain model at its full resolution of 20 micrometres.

QuickNII

QuickNII is a stand-alone tool for user guided affine spatial registration (anchoring) of sectional image data, typically high resolution microscopic images, to a 3D reference atlas space. QuickNII is one of several tools developed by the Human Brain Project (HBP) with the aim of facilitating brain atlas based analysis and integration of experimental data and knowledge about the human and rodent brain. A key feature in the tool is the capability to generate user defined cut planes through the atlas templates, matching the orientation of the cut plane of the 2D experimental image data. The reference atlas is transformed to match anatomical landmarks in the corresponding experimental images. In this way, the spatial relationship between experimental image and atlas is defined, without introducing transformations in the original experimental images. Following anchoring of a limited number of sections containing key landmarks, transformations are propagated across the entire series of images to reduce the amount of manual steps required.

siibra-explorer

siibra-explorer is built around an interactive 3D view of the brain displaying a unique selection of detailed templates and parcellation maps for the human, macaque, rat or mouse brain, including BigBrain as a microscopic resolution human brain model at its full resolution of 20 micrometres.

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