3.5
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Original Research ARTICLE

Front. Neuroanat., 17 April 2008 | http://dx.doi.org/10.3389/neuro.05.001.2008

In vivo 3D digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy

1
Department of Anesthesiology, Stony Brook University, Stony Brook, NY, USA
2
Medical Department, Brookhaven National Laboratory, Upton, NY, USA
3
Department of Neuroscience and Advanced Imaging Program, Mount Sinai School of Medicine, New York, NY, USA
4
Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
5
The National High Magnetic Field Laboratory, Tallahassee, FL, USA
In this study, a 3D digital atlas of the live mouse brain based on magnetic resonance microscopy (MRM) is presented. C57BL/6J adult mouse brains were imaged in vivo on a 9.4 Tesla MR instrument at an isotropic spatial resolution of 100 μm. With sufficient signal-to noise (SNR) and contrast-to-noise ratio (CNR), 20 brain regions were identified. Several atlases were constructed including 12 individual brain atlases, an average atlas, a probabilistic atlas and average geometrical deformation maps. We also investigated the feasibility of using lower spatial resolution images to improve time efficiency for future morphological phenotyping. All of the new in vivo data were compared to previous published in vitro C57BL/6J mouse brain atlases and the morphological differences were characterized. Our analyses revealed significant volumetric as well as unexpected geometrical differences between the in vivo and in vitro brain groups which in some instances were predictable (e.g. collapsed and smaller ventricles in vitro) but not in other instances. Based on these findings we conclude that although in vitro datasets, compared to in vivo images, offer higher spatial resolutions, superior SNR and CNR, leading to improved image segmentation, in vivo atlases are likely to be an overall better geometric match for in vivo studies, which are necessary for longitudinal examinations of the same animals and for functional brain activation studies. Thus the new in vivo mouse brain atlas dataset presented here is a valuable complement to the current mouse brain atlas collection and will be accessible to the neuroscience community on our public domain mouse brain atlas website.
Keywords:
in vivo mouse brain atlas, magnetic resonance microscopy, mouse brain morphometry, image registration
Citation:
Ma Y, Smith D, Hof PR, Foerster B, Hamilton S, Blackband SJ, Yu M and Benveniste H (2008). In vivo 3D digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy. Front. Neuroanat. 2:1. doi: 10.3389/neuro.05.001.2008
Received:
09 January 2008;
 Paper pending published:
10 March 2008;
Accepted:
08 April 2008;
 Published online:
17 April 2008.

Edited by:

andreas H. Burkhalter, Washington University School of Medicine, USA

Reviewed by:

Kadharbatcha S. Saleem, Washington University School of Medicine, USA
Andreas H. Burkhalter, Washington University School of Medicine, USA
Copyright:
© 2008 Ma, Smith, Hof, Foerster, Hamilton, Blackband, Yu and Benveniste. 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:
Yu Ma, Department of Anesthesiology, Stony Brook University, Stony Brook, NY, USA. e-mail: mayu@bnl.gov