A three-dimensional digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy

A comprehensive three-dimensional digital atlas database of the C57BL/6J mouse brain was developed based on magnetic resonance microscopy images acquired on a 17.6-T superconducting magnet. By using both manual tracing and an atlas-based semi-automatic segmentation approach, T2⁎-weighted magnetic re...

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Bibliographic Details
Published in:	Neuroscience Vol. 135; no. 4; pp. 1203 - 1215
Main Authors:	Ma, Y., Hof, P.R., Grant, S.C., Blackband, S.J., Bennett, R., Slatest, L., McGuigan, M.D., Benveniste, H.
Format:	Journal Article
Language:	English
Published:	Oxford Elsevier Ltd 2005 Elsevier
Subjects:	Anatomy, Artistic - methods Animals Biological and medical sciences brain Brain - anatomy & histology computational biology Databases, Factual Fundamental and applied biological sciences. Psychology Imaging, Three-Dimensional Magnetic Resonance Imaging magnetic resonance microscopy Medical Illustration Mice Mice, Inbred C57BL - anatomy & histology phenotype Vertebrates: nervous system and sense organs phenotype computational biology MPD magnetic resonance microscopy MR atlas CNR MRM AIR brain mice ROI 3D 2D RF SI SNR Rodentia Central nervous system Encephalon Vertebrata Phenotype Mammalia Microscopy Mouse Animal
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Summary:	A comprehensive three-dimensional digital atlas database of the C57BL/6J mouse brain was developed based on magnetic resonance microscopy images acquired on a 17.6-T superconducting magnet. By using both manual tracing and an atlas-based semi-automatic segmentation approach, T2⁎-weighted magnetic resonance microscopy images of 10 adult male formalin-fixed, excised C57BL/6J mouse brains were segmented into 20 anatomical structures. These structures included the neocortex, hippocampus, amygdala, olfactory bulbs, basal forebrain and septum, caudate-putamen, globus pallidus, thalamus, hypothalamus, central gray, superior colliculi, inferior colliculi, the rest of midbrain, cerebellum, brainstem, corpus callosum/external capsule, internal capsule, anterior commissure, fimbria, and ventricles. The segmentation data were formatted and stored into a database containing three different atlas types: 10 single-specimen brain atlases, an average brain atlas and a probabilistic atlas. Additionally, quantitative group information, such as variations in structural volume, surface area, magnetic resonance microscopy image intensity and local geometry, were computed and stored as an integral part of the database. The database augments ongoing efforts with other high priority strains as defined by the Mouse Phenome Database focused on providing a quantitative framework for accurate mapping of functional, genetic and protein expression patterns acquired by a myriad of technologies and imaging modalities.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0306-4522 1873-7544
DOI:	10.1016/j.neuroscience.2005.07.014