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Unformatted text preview: A histology-based atlas of the C57BL/6J mouse brain deformably registered to in vivo MRI for localized radiation and surgical targeting This article has been downloaded from IOPscience. Please scroll down to see the full text article. 2009 Phys. Med. Biol. 54 7315 (http://iopscience.iop.org/0031-9155/54/24/005) Download details: IP Address: 184.108.40.206 The article was downloaded on 16/03/2010 at 10:40 Please note that terms and conditions apply. The Table of Contents and more related content is available Home Search Collections Journals About Contact us My IOPscience IOP PUBLISHING PHYSICS IN MEDICINE AND BIOLOGY Phys. Med. Biol. 54 (2009) 7315–7327 doi:10.1088/0031-9155/54/24/005 A histology-based atlas of the C57BL / 6J mouse brain deformably registered to in vivo MRI for localized radiation and surgical targeting David Purger 1 , Todd McNutt 1 , Pragathi Achanta 2 , Alfredo Qui˜nones-Hinojosa 2 , John Wong 1 and Eric Ford 1 , 3 1 Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, 401 North Broadway, Suite 1440, Baltimore, MD 21231, USA 2 Department of Neurosurgery, Johns Hopkins University, Cancer Research Building II, 1550 Orleans Street, Room 247, Baltimore, MD 21231, USA E-mail: [email protected] Received 3 April 2009, in final form 27 September 2009 Published 20 November 2009 Online at stacks.iop.org/PMB/54/7315 Abstract The C57BL / 6J laboratory mouse is commonly used in neurobiological research. Digital atlases of the C57BL / 6J brain have been used for visualization, genetic phenotyping and morphometry, but currently lack the ability to accurately calculate deviations between individual mice. We developed a fully three-dimensional digital atlas of the C57BL / 6J brain based on the histology atlas of Paxinos and Franklin ( 2001 The Mouse Brain in Stereotaxic Coordinates 2nd edn (San Diego, CA: Academic)). The atlas uses triangular meshes to represent the various structures. The atlas structures can be overlaid and deformed to individual mouse MR images. For this study, we selected 18 structures from the histological atlas. Average atlases can be created for any group of mice of interest by calculating the mean three-dimensional positions of corresponding individual mesh vertices. As a validation of the atlas’ accuracy, we performed deformable registration of the lateral ventricles to 13 MR brain scans of mice in three age groups: 5, 8 and 9 weeks old. Lateral ventricle structures from individual mice were compared to the corresponding average structures and the original histology structures. We found that the average structures created using our method more accurately represent individual anatomy than histology-based atlases alone, with mean vertex deviations of 0.044 mm versus 0.082 mm for the left lateral ventricle and 0.045 mm versus 0.068 mm for the right lateral ventricle. Our atlas representation gives direct spatial deviations for structures of interest. Our results indicate that MR-deformable histology-based atlasesof interest....
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- Spring '10
- RNA, Magnetic resonance imaging, Ventricular system, Lateral ventricles, mouse brain