Elsevier

NeuroImage

Volume 97, 15 August 2014, Pages 374-386
NeuroImage

Waxholm Space atlas of the Sprague Dawley rat brain

https://doi.org/10.1016/j.neuroimage.2014.04.001Get rights and content
Under a Creative Commons license
open access

Highlights

  • High-resolution MRI and DTI template for the Sprague Dawley rat brain

  • Atlas of major anatomical structures with detailed delineation criteria

  • Internal landmarks for implementing ‘Waxholm Space’ spatial reference system

  • Cranial landmarks for translation to stereotaxic coordinate system

  • The template and atlas form a new tool for spatial orientation in the rat brain.

Abstract

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 orientationanalysis 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

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

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