High resolution volumetric atlas of the rat hippocampal region and its subdivisions
Lisa J Kjonigsen (Centre for Molecular Biology and Neuroscience, Institute of Basic Medical Sciences, UIO, Oslo), Trygve B Leergaard (Centre for Molecular Biology and Neuroscience, Institute of Basic Medical Sciences, UIO, Oslo), G Allan Johnson (Center for In Vivo Microscopy, Duke University Medical Center, Durham, NC), Menno P Witter (The Kavli Institute for Systems Neuroscience & Centre for the Biology of Memory, NTNU, Trondheim), Jan G Bjaalie (Centre for Molecular Biology and Neuroscience, Institute of Basic Medical Sciences, UIO, Oslo)
We here present a 3D atlas of the rat hippocampus based on high-resolution ex vivo MRI anatomical (T2*) images with 39 μm isotropic voxels and diffusion tensor imaging (DTI) volumes with 78 μm isotropic voxels from an 80 day old male Sprague-Dawley rat. The boundaries of 18 hippocampal structures were identified and delineated based on image contrast in the volume data, and comparison with cyto- and chemoarchitectonic features in histological images present in an earlier 2D histological atlas of the rat hippocampus. We provide a comprehensive 3D atlas of the rat hippocampal region and describe several boundaries that can be identified on basis of T2* or DTI contrast.
Spatial reference is provided by the application of Waxholm Space, a standard atlas space recently defined by the International Neuroinformatics Coordinating Facility (INCF). The use of Waxholm Space connects the atlas to an infrastructure of interoperable resources and services for multi-level data integration and analysis across reference spaces.