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Mouse Brain Atlas Database

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Authors and Collaborators

MR microscopy @ AMRIS/NHMFL, University of Florida

To take advantage of the information emerging from the mouse genome sequencing efforts, it has become necessary to systematically collect normative phenotypic information at all biological levels. Accordingly, an international collaboration, the Mouse Phenome Database (MPD) project, was created to establish a collection of baseline phenotypic data from commonly used inbred mice, such as the C57BL/6J, 129S1/SvlmJ, DBA/2J and BALB/cByJ strains.

The National Institutes of Health (NIH) neuroimaging phenotyping informatics emphasis has similarly been directed toward designing comprehensive three dimensional (3D) digital brain atlases of commonly used mice strains including variability of brain structures across a given strain.

As part of this world-wide effort, we have constructed an adult male C57BL/6J mouse brain atlas database derived directly from T2*-weighted 3D magnetic resonance microscopy images acquired on a 17.6-T magnet @ University of Florida. The 3D neuroanatomical information of twenty segmented structures including structure variability data, are integrated into a comprehensive database with the following framework:

• Multiple brain samples with T2*-weighted 3D magnetic resonance microscopy images.
• Individual 3D digital anatomical atlases and associated quantitative structural information.
• Probabilistic atlases.
• Minimal Deformation (Average Shape) Atlas.
• Downloadable visualization tool.

This development, although lacking the histological resolution of traditional mouse brain atlases, is intended to circumvent the shortcomings of currently available 2D and 3D atlases and to provide new quantitative anatomical information as well as additional computational templates for integrating other related information such as function and gene expression patterns.

In addition, to overcome the possible sample distortion caused by in vitro approaches, we newly constructed an in vivo MRI based C57BL/6J mouse atlas database. The in vivo atlases not only provide the users with a comprehensive platform for analyzing in vivo neurological data, they also provide the necessary framework to compare in vitro and in vivo studies. The in vivo mouse brain MRI template is inherently the natural template for longitudinal MRM studies, which are usually carried out at a similar or a lower spatial resolution level. Therefore the in vivo atlases will have wide usage in computational morphometry and quantitative phenotyping of mice. Using our templates for pilot segmentation, users can also easily modify and create their own mouse brain atlases to meet their own special needs.

For more details about this database, please see:

[1] Ma Y, Hof PR, Grant SC, Blackband SJ, Bennett R, Slatest L, McGuigan MD, Benveniste H. A three-dimensional digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy. Neuroscience. 2005;135(4):1203-15

[2] Ma Y, Smith D, Hof PR, Foerster B, Hamilton S, Blackband SJ, Yu M and Benveniste H. In vivo 3D digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy. Front. Neuroanat. 2008; 2:1. doi:10.3389/neuro.05.001.2008
 

Last Modified: Aug. 2008