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High resolution volumetric atlas of the rat hippocampal region and its subdivisions

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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)

Considering the complexity of the rat parahippocampal- and hippocampal region, precise neuroanatomical knowledge and access to high quality reference material are required for experimental planning as well as for data analysis. Several two-dimensional (2D) atlas resources exist (including The Rat Hippocampal Atlas,, but these are typically insufficient for three-dimensional (3D) analysis of the region needed to fully comprehend spatial organization. Moreover, with increasing access to small animal magnetic resonance imaging (MRI) instruments, it is necessary to determine to which extent different hippocampal subregions can be defined from MRI data.
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.
Preferred presentation format: Demo
Why demo: We would like a live demo in order to fully demonstrate the three-dimensional representation online, to go through the volume data & histological section images that we have used to segment the hippocampal region, and examples of use.
Topic: Digital atlasing

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