Original Research Article
Three-dimensional atlas system for mouse and rat brain imaging data
Trine Hjornevik 1, Trygve B. Leergaard 1, Dmitri Darine 1, Olve Moldestad 1, Anders M. Dale 2, 3, Frode Willoch 1, 4 and Jan G. Bjaalie 1*
1 Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, University of Oslo, Norway
2 Departments of Neurosciences and Radiology, University of California, USA
3 Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, USA
4 Department of Radiology, Aker University Hospital, Norway
2 Departments of Neurosciences and Radiology, University of California, USA
3 Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, USA
4 Department of Radiology, Aker University Hospital, Norway
Tomographic neuroimaging techniques allow visualization of functionally and structurally specific signals in the mouse and rat brain. The interpretation of the image data relies on accurate determination of anatomical location, which is frequently obstructed by the lack of structural information in the data sets. Positron emission tomography (PET) generally yields images with low spatial resolution and little structural contrast, and many experimental magnetic resonance imaging (MRI) paradigms give specific signal enhancements but often limited anatomical information. Side-by-side comparison of image data with conventional atlas diagram is hampered by the 2-D format of the atlases, and by the lack of an analytical environment for accumulation of data and integrative analyses. We here present a method for reconstructing 3-D atlases from digital 2-D atlas diagrams, and exemplify 3-D atlas-based analysis of PET and MRI data. The reconstruction procedure is based on two seminal mouse and brain atlases, but is applicable to any stereotaxic atlas. Currently, 30 mouse brain structures and 60 rat brain structures have been reconstructed. To exploit the 3-D atlas models, we have developed a multi-platform atlas tool (available via The Rodent Workbench, http://rbwb.org) which allows combined visualization of experimental image data within the 3-D atlas space together with 3-D viewing and user-defined slicing of selected atlas structures. The tool presented facilitates assignment of location and comparative analysis of signal location in tomographic images with low structural contrast.
Keywords: 3-D reconstruction, atlas, brain, imaging, magnetic resonance imaging, positron emission tomography, stereotaxic, visualization
Copyright: © 2007 Hjornevik, Leergaard, Darine, Moldestad, Dale, Willoch and Bjaalie. This is an open-access article subject to an exclusive license agreement between the authors and the Frontiers Research Foundation, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are credited.
*Correspondence: Jan G. Bjaalie, Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, University of Oslo, Norway. e-mail:j.g.bjaalie@medisin.uio.no
Citation: Hjornevik T, Leergaard TB, Darine D, Moldestad O, Dale AM, Willoch F and Bjaalie JG (2007) Three-dimensional atlas system for mouse and rat brain imaging data. Front. Neuroinform. (2007) 1:4. doi:10.3389/neuro.11.004.2007
Received: 05 September 2007; paper pending published: 24 September 2007; accepted: 09 October 2007; published online: 02 November 2007.
Edited by:
Maryann E. Martone, University of California San Diego, USA
Reviewed by:
Richard A. Baldock, Medical Ressearch Council Human Genetics Unit, UK
James F. Brinkley, University of Washington, USA
James F. Brinkley, University of Washington, USA
*Correspondence: Jan G. Bjaalie, Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, University of Oslo, Norway. e-mail:j.g.bjaalie@medisin.uio.no
