Three-dimensional atlas system for mouse and rat brain data
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1
CMBN & IMB, University of Oslo, Norway
Three-dimensional (3-D) tomographic neuroimaging techniques (e.g. Positron Emission Tomography (PET) and Magnetic Resonance Imaging (MRI)) as well as histological techniques deliver enormous amount of information about the structural and functional organization of the brain. Interpretation of data relies to a large extent on accurate determination of anatomical location. Comparison of experimental data with conventional atlas diagrams is hampered by the two-dimensional (2-D) format of the atlases, and by the lack of an analytical environment for accumulation of data and integrative analyses. Access to seminal high-resolution atlases reconstructed in 3-D, and software tools for comparison of experimental data with atlas frameworks, is thus needed. We have recently published a multi-platform atlas tool (available via The Rodent Workbench, http://rbwb.org) which provides a new dynamic environment for comparing experimental rodent brain data with a 3-D atlas framework. Currently, 30 mouse brain structures and 60 rat brain structures have been reconstructed from "The Mouse Brain in Stereotaxic Coordinates" by Paxinos & Franklin (2001) and "The Rat Brain in Stereotaxic Coordinates" by Paxinos & Watson (2005). The Java3D based atlas tool allows visualization of experimental data within the 3-D atlas space together with 3-D viewing and 2-D user-defined slicing, at any angle and orientation, of both selected atlas structures and 3-D image data. We demonstrate the use of the atlas tool for assigning localization to tomographic and histological data. Examples include comparative analysis of signal location in 3-D tomographic images with low structural contrast as well as user-defined slicing of the atlases to match the orientation of histological sections from a given experimental material. The system presented provides an environment for analyses of 2-D and 3-D rodent brain data in relation to standardized atlas space.
Acknowledgements:
Supported by grants from the Research Council of Norway
Conference:
Neuroinformatics 2008, Stockholm, Sweden, 7 Sep - 9 Sep, 2008.
Presentation Type:
Poster Presentation
Topic:
Digital Atlasing
Citation:
Hjornevik
T,
Darine
D,
Qu
H,
Willoch
F,
Leergaard
TB and
Bjaalie
JG
(2008). Three-dimensional atlas system for mouse and rat brain data.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2008.
doi: 10.3389/conf.neuro.11.2008.01.052
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Received:
25 Jul 2008;
Published Online:
25 Jul 2008.
*
Correspondence:
Trine Hjornevik, CMBN & IMB, University of Oslo, Oslo, Norway, trine.hjornevik@medisin.uio.no