INCF at SfN 2013: Jan Bjaalie presents the Waxholm Space atlas of the Sprague Dawley rat brain
Channel: INCF
Date: 2013-11-26

Computer demo at SfN 2013, San Diego.
Presenter: Jan Bjaalie, University of Oslo, Norway.
Title: Waxholm Space atlas of the Sprague Dawley rat brain

Abstract:
Three-dimensional digital brain atlases are important neuroinformatics tools for understanding complex brain anatomy, assigning location to experimental data, and planning of experiments. The most recent generation of atlases typically use volumetric images of the brain, acquired using magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI), as templates. 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 (main areas, nuclei, regions, and fiber tracts) throughout the brain. More detailed parcellations are currently ongoing for the hippocampus. Structures were delineated using ITK-SNAP software based on multiple types of image contrasts and anatomical reference information. White matter structures were readily distinguished from grey matter, and several structural differences could also be observed within gray matter. Delineations were aided by information from classical 2D atlases and collections of histological images from brains of comparable animals, and delineation criteria were defined for all structures.

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.