Volumetric Waxholm Space atlas of the rat brain for spatial integration of experimental image data
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1
University of Oslo, Department of Anatomy, Institute of Basic Medical Sciences, Norway
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2
Duke University Medical Center, Center for In Vivo Microscopy, United States
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3
NTNU, Center for the Biology of Memory, Norway
Brain atlases are important tools for understanding complex brain anatomy and widely used for planning of experiments and interpretation of experimental data. Several volumetric atlas templates based on magnetic resonance imaging (MRI) data have been developed for the rat brain to facilitate assignment of anatomical location to data and comparison across experiments. Important limitations of these atlases have been the lack of a standardized spatial reference given by internal landmarks and a lack of anatomic delineations directly corresponding to underlying image features. Recently, a standard reference space (Waxholm Space) was defined for the mouse brain by the International Neuroinformatics Coordinating Facility (INCF), connecting several mouse brain atlases for spatial integration of experimental data. As a contribution to a novel atlasing resource for the rat brain, we have implemented Waxholm Space in the rat, and created a volumetric atlas of the SpragueDawley brain based on ex vivo MRI anatomical (T2*) images with 39 μm isotropic voxels and diffusion tensor imaging (DTI) volumes with 78 μm isotropic voxels acquired from an 80 day old male SpragueDawley rat. The atlas covers 83 anatomical structures, including 16 substructures of the hippocampus, distinguished on the basis of image contrast observed in MRI and DTI, aided by information from traditional brain atlases and cyto and chemoarchitectonic data from other animals. The atlas and the underlying MRI and DTI image volumes are shared via the INCF Software Center. Waxholm Space connects the atlas to a growing infrastructure of interoperable resources and services for multilevel data integration and analysis across reference spaces.
Keywords:
Waxholm Space,
digital brain atlas,
MRI,
DTI,
Sprague Dawley rat
Conference:
Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.
Presentation Type:
Poster
Topic:
Digital atlasing
Citation:
Papp
EA,
Kjonigsen
LJ,
Lillehaug
S,
Johnson
GA,
Witter
MP,
Leergaard
TB and
Bjaalie
JG
(2013). Volumetric Waxholm Space atlas of the rat brain for spatial integration of experimental image data.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2013.
doi: 10.3389/conf.fninf.2013.09.00003
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Received:
05 Jun 2013;
Published Online:
11 Jul 2013.
*
Correspondence:
Ms. Eszter A Papp, University of Oslo, Department of Anatomy, Institute of Basic Medical Sciences, Oslo, Norway, e.a.papp@medisin.uio.no