Waxholm Space atlas of the Sprague Dawley rat brain.

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Papp, EA; Leergaard, TB; Calabrese, E; Johnson, GA; Bjaalie, JG

Published Date

  • August 15, 2014

Published In

Volume / Issue

  • 97 /

Start / End Page

  • 374 - 386

PubMed ID

  • 24726336

Pubmed Central ID

  • PMC4160085

Electronic International Standard Serial Number (EISSN)

  • 1095-9572

Digital Object Identifier (DOI)

  • 10.1016/j.neuroimage.2014.04.001


  • eng

Conference Location

  • United States