Waxholm Space atlas of the Sprague Dawley rat brain

Neuroimage. 2014 Aug 15:97:374-86. doi: 10.1016/j.neuroimage.2014.04.001. Epub 2014 Apr 12.


Three-dimensional digital brain atlases represent an important new generation of neuroinformatics tools for understanding complex brain anatomy, assigning location to experimental data, and planning of experiments. We have acquired a microscopic resolution isotropic MRI and DTI atlasing template for the Sprague Dawley rat brain with 39 μm isotropic voxels for the MRI volume and 78 μm isotropic voxels for the DTI. Building on this template, we have delineated 76 major anatomical structures in the brain. Delineation criteria are provided for each structure. We have applied a spatial reference system based on internal brain landmarks according to the Waxholm Space standard, previously developed for the mouse brain, and furthermore connected this spatial reference system to the widely used stereotaxic coordinate system by identifying cranial sutures and related stereotaxic landmarks in the template using contrast given by the active staining technique applied to the tissue. With the release of the present atlasing template and anatomical delineations, we provide a new tool for spatial orientation analysis of neuroanatomical location, and planning and guidance of experimental procedures in the rat brain. The use of Waxholm Space and related infrastructures will connect the atlas to interoperable resources and services for multi-level data integration and analysis across reference spaces.

Keywords: Diffusion tensor imaging; Digital brain atlas; Magnetic resonance imaging; Neuroinformatics; Rat brain template; Segmentation; Sprague Dawley; Waxholm Space.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Atlases as Topic*
  • Brain / anatomy & histology*
  • Diffusion Magnetic Resonance Imaging
  • Gray Matter / anatomy & histology
  • Image Processing, Computer-Assisted
  • Information Dissemination
  • Internet
  • Male
  • Rats
  • Rats, Sprague-Dawley / anatomy & histology*
  • Spinal Cord / anatomy & histology
  • White Matter / anatomy & histology