Mouse BIRN Atlasing Toolkit


MBAT provides a workflow environment bringing together online resources, a user's image data and biological atlases in a concise, unified and intuitive workspace. MBAT is written in java so it is platform independent and is extensible through its plugin architecture.


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Atlas Viewer Screenshot


  • MBAT is designed with a Search Workspace to enable users to submit a query to multiple databases simultaneously.
  • The Registration Workspace performs 2D and 3D image alignment (spatial registration).
  • The Viewer Workspace displays and composites images and image volumes using high performance graphics hardware.
  • A major feature of the Viewer Workspace is the Atlas Viewer module; a generic volumetric atlas viewer. This module allows navigation and interrogation of volumetric atlases.


Mouse BIRN Atlasing Toolkit Support


Download Details

Version: 3.1.4
Release Date:  2011-03-11
Developer(s): CIT- BIC, UCLA - LONI, Duke - CIVM, UCSD - NCMIR, Informatics Center for Mouse Neurogenetics at UTHSC, Drexel, and BIDMC
License: LONI Software License
File Size: 43 MB
SYSTEM REQUIREMENTS Memory: 2 GB, Processor: Any
Lee, D, Ruffins, S, Ng, Q, Sane, N, Anderson, S, Toga (2010) MBAT: A scalable informatics system for unifying digital atlasing workflows, BMC Bioinformatics, 11:608, doi: 10.1186/1471-2105-11-608, PMCID: PMC3023809
Ruffins SW, Lee D, Larson SD; Zaslavsky I, Ng L, and Toga AW (2010). MBAT at the Confluence of Waxholm Space. Frontiers in Neuroscience, Vol. 4, p.5., doi:10.3389/conf.fnins.2010.13.00132
Swanson L.W (1998) Brain Maps: Structure of the Rat Brain: A Laboratory Guide with Printed and Electronic Templates for Data, Models, and Schematics, 2nd Revised Edition, pp vii, 267. Elsevier, Amsterdam; New York
Paxinos G and Franklin K BJ (2001) The Mouse Brain in Stereotaxic Coordinates, 2nd Edition, pp xxi, 264. Academic Press, San Diego.
Bug WJ, Wong W, Badea A, Brandenburg J, Gustafson C, MacKenzie-Graham A, Memon A, Price D, Rosen G, Yuan H, Zaslavsky I, Boline J, Johnson GA, Martone ME, Nissanov J, Toga AW, Williams RW (2007). The BIRN Atlasing System Interoperability Service: an inte
Boline JK, Zaslavsky I, Bug WJ, Williams RW, Martone ME, Anderson S, Wong W, Yuan H, Memon A, Ng Q, Grethe JS, Sforza DM, MacKenzie-Graham A, Nissanov J, Gustafson C, Toga AW (2007). Accessing a sharing infrastructure with the Mouse BIRN atlasing toolki
Boline JK, MacKenzie-Graham A, Shattuck D, Yuan H, Anderson S, Sforza DM, Wang J, Williams RW, Wong W, Martone ME, Zaslavsky I, Toga AW (2006). A Digital Atlas and Neuroinformatics Framework for Query and Display of Disparate Data. Society for Neuroscie
This work was supported by:
NIH/USC U24 RR025736
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