News: New 3D in vivo MRM based C57BL/6J atlases available here!


Atlas Relaunch January 2010.

Hello Atlas Users!!

Many apologies on lack of feedback with our atlas the last year or so. As is no doubt true for many of you, the last year or two has been interesting and challenging to say the least! we hope you are faring well and will survive the economic downturn.

Regarding this atlas, due to changes and scientific priorities, it will no longer be based and maintained at Brookhaven National Laboratory (BNL). Instead the atlas database has been moved to the University of Florida (UF) and will be maintained by support from UF and the National High Magnetic Field Laboratory (NHMFL), still in collaboration with Benveniste's team at BNL and Stony Brook University. A new UF staff member is assigned to the atlas starting January 16th and will be available for questions and help.

Over the next year we plan to expand the atlas based on our survey of users and their expressed needs, so keep an eye out. Will be sending update emails too. We will be looking for support for the atlas in terms of grants and funding over the next year and may be requesting your input and help facilitating our new visions and goals for the database.

Please note that the in vivo mouse atlas data is now also available at this site.

Finally, this is MR, so a new launch requires a new acronym! Our site is now named the Magnetic Resonance Microimaging Neurological Atlas, "MRM NeAt"

Good luck to all in this new decade, and we look forward to hearing from you!


Steve Blackband and Helene Benveniste.



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.