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.

Our offer

  • 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 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. 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 shared 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 118 brain regions, accompanied by a label file with the name and ID of each region.


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.

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