Elsevier

Neuroscience

Volume 135, Issue 4, 2005, Pages 1203-1215
Neuroscience

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

https://doi.org/10.1016/j.neuroscience.2005.07.014Get rights and content

Abstract

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.

Section snippets

Specimen preparation

Formalin perfusion-fixed mouse brains were selected to build our first atlas database owing to the advantages of ex vivo samples on MRM signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) compared with in vivo imaging (Benveniste and Blackband, 2002). Mice of the inbred strain C57BL/6J were used (12–14-week old males, weight range of 25–30g obtained from The Jackson Laboratory, Bar Harbor, ME, USA). All animal protocols for live animal experiments were approved by the Institutional

Anatomical segmentation of the reference brain

A typical anatomical segmentation performed on the T2⁎-weighted MRM images is shown in Fig. 1 with different renderings. Note that although the MRM images have good spatial resolution (47×47×47μm) and high CNRs, certain parts of the selected ROI were difficult to define visually even with expert anatomical knowledge. This challenge was particularly true for the boundaries of the posterior hypothalamic area, the boundary of the thalamus and pretectum and the fine extensions of fiber tracts like

Discussion

The major goal of this work was the construction of a fundamental C57BL6/J brain atlas database that can serve as a new computational framework for future quantitative atlas-based studies. The database contains three different atlas formats for the C57BL6/J high priority mouse strain: 10 individualized brain atlases, a minimal deformation atlas and a probabilistic atlases as well as derived quantitative structural and group variability data.

As expected, among the 10 genetically identical

Conclusion

The database presented comprises MRM-based brain atlases for the important inbred mouse strain C57BL/J. The database is completely digital and encompasses 10 individualized atlases, a minimal deformation atlas and a probabilistic atlas through a combination of nonlinear registration and interactively corrected semi-automated segmentation. Our database can be browsed and visualized online on the database browser. The in vitro based atlases augment ongoing efforts to construct an in vivo C57BL/J

Acknowledgments

The authors would like to acknowledge the financial support of the NIH through grants R01 EB 00233–04 and P41 RR16105 and the National High Magnetic Field Laboratory. MRI data were obtained at the Advanced Magnetic Resonance Imaging and Spectroscopy (AMRIS) facility in the McKnight Brain Institute of the University of Florida. The authors would like than Karen Law, Mei Yu and Hai-dee Lee for their assistance in manual anatomical tracing, William Janssen for histological processing,

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