Rats are one of the most widely used animal models in neuroscience. Atlases of the rat brain are widely used as reference for orientation, planning of experiments, and as tools for assigning location to experimental data and combining and comparing data across experiments. EBRAINS offers the Waxholm Space (WHS) Rat Brain Atlas. You can explore the atlas from any browser with our interactive atlas viewer and locate regions of interest through text search or via the accompanying brain region hierarchy. The WHS Rat Brain Atlas is the backbone of spatially-focused workflows and several other EBRAINS tools for analysing data from the rat brain.

  • Explore detailed 3D delineations of brain regions in an intuitive web-based atlas viewer
  • The atlas is built on a high-resolution, high-quality, volumetric image template
  • Find easily your brain region of interest 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


Waxholm Space Atlas

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 brain regions and fibre tracts of the adult rat brain. 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.

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.


Connect to atlas developers and the user community



As of June 2021, the WHS rat brain atlas has been downloaded over 15 000 times



Anatomists, experimental neuroscientists, students of medicine and neuroscience, software developers

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.

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.

Related publications

Osen K.K., Imad J., Wennberg A.E., Papp E.A., Leergaard T.B. (2019) Waxholm Space atlas of the rat brain auditory system: Three-dimensional delineations based on structural and diffusion tensor magnetic resonance imaging. NeuroImage 199, 38-56. https://doi.org/10.1016/j.neuroimage.2019.05.016

Papp E.A., Leergaard T.B., Calabrese E., Johnson G.A., Bjaalie J.G. (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97, 374-386.

Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2015) Addendum to "Waxholm Space atlas of the Sprague Dawley rat brain" [NeuroImage 97 (2014) 374-386]. NeuroImage 105, 561–562. DOI: 10.1016/j.neuroimage.2014.10.017

Kjonigsen LJ, Lillehaug S, Bjaalie JG, Witter MP, Leergaard TB (2015) Waxholm Space atlas of the rat brain hippocampal region: Three-dimensional delineations based on magnetic resonance and diffusion tensor imaging. NeuroImage 108, 441-449. DOI: 10.1016/j.neuroimage.2014.12.080

Osen KK, Imad J, Wennberg AE, Papp EA, Leergaard TB (2019) Waxholm Space atlas of the rat brain auditory system: Three-dimensional delineations based on structural and diffusion tensor magnetic resonance imaging. NeuroImage 199, 38-56. DOI: 10.1016/j.neuroimage.2019.05.016

Kleven H, Bjerke IE, Imad J, Clasca F, Groenewegen HJ, Bjaalie JG, Leergaard TB, Manuscript in preparation

Access all EBRAINS services