a

Mouse BIRN Atlasing Toolkit (MBAT) 2.0 BETA



Overview

This document describes the Mouse BIRN Atlasing Toolkit (MBAT) 2.0 BETA, which was built from the combined efforts of groups within the Mouse BIRN. For more information, visit the MBAT home page at http://cms.loni.ucla.edu/MBAT/

 

Short Description

The Mouse BIRN Atlasing Toolkit (MBAT) 2.0 BETA is a JAVA application designed to view multiple types of multiscale data, access and query databases associated with the Mouse BIRN, and process some of these data types.

 

Logo

birn logo

mousebirn logo

 

 

Figure

figure

 

Categories and Keywords

Application, tool, atlasing, viewer

 

Longer Overview

This is a collaborative effort by groups within the Mouse BIRN to create an interoperable tool that offers an intuitive way to access the functionality offered by the individual efforts.  The goal of the MBAT is to act as an intuitive, interoperable interface for viewing, accessing, processing, and analyzing multimodal data with emphasis on functionality across distributed locations and diverse databases.   

This tool allows a user to view their data and offers the ability to interface with data offered by Mouse BIRN.  Future plans include the option to incorporate and compare a variety of different data types, regardless of the user’s location or affiliation with the mouse BIRN.

This new release (2.0 BETA) includes several improvements and updates. Of particular note are the powerful query tools which access several data and information sources.  This version of MBAT improves and expands the previous query capability of MBAT.  The query interface can be used for multiple data types and expands the primarily microarray data sources accessed in the previous version of MBAT to include image data from multiple sources.  In addition, MBAT can also be used to access information from web-resources including the BIRN Ontology Tool (Bonfire) and the Brain Architecture Management System (BAMS) at USC.

This release also includes many interface improvements such as a Launch Page, Workspaces that are configured for specific tasks, a new docking framework, and easy access to Mouse BIRN resources for data upload.

To access or download this tool, visit the BIRN Portal, www.nbirn.net.  For additional information about the MBAT project, visit the MBAT wiki page, http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/MBAT or the new MBAT home page at http://cms.loni.ucla.edu/MBAT/.

 

User Manual

To access the user manual for this tool see the BIRN website www.nbirn.net, or the MBAT wiki page, http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/MBAT or visit the new MBAT home page at http://cms.loni.ucla.edu/MBAT/.

 

Register for Download

Much of the data offered by the BIRN group can be visualized using this tool.  You can download these datasets and get more information at the BIRN website www.nbirn.net.

 

Installation Information

  1. Make sure Java 1.5 or higher is installed on your computer, if you need to install it, download it from http://java.com/en/
  2. To run MBAT with full functionality, un-tar or unzip the full MBAT folder to the user’s hard drive.
  3. If you wish to include the extra data files, download and unzip the files into the MBAT directory. Other atlases and data may be read from anywhere, but it may be easier to place it in the MBAT folder.
  4. To run the program, double click the MBAT.2.0.jar file.
  5. If you wish to have the program on your desktop, create a shortcut that points to the MBAT.2.0.jar file.

 

References for the Software

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 toolkit (MBAT).”  Society for Neuroscience, Abstract #100.12.

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 interface for exchange of registration coordinates, segmentation geometries, and registered images amongst neuroanatomical atlasing systems.”  Society for Neuroscience, Abstract #100.13.

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 Neuroscience, Abstract #100.12

Contributors/Authors

The Mouse BIRN Atlasing Tool was created from the activities of six laboratories:

  • The MRI Center in the Biological Imaging Center (BIC) at the California Institute of Technology (CIT)
  • The Center for In Vivo Microscopy (CIVM) at Duke University
  • The Laboratory of Neuro Imaging (LONI) at the University of California at Los Angeles (UCLA)
  • The National Center for Microscopy and Imaging Research (NCMIR) at the University of California at San Diego (UCSD)
  • The Informatics Center for Mouse Neurogenetics:
  • GeneNetwork (UTHSC) at University of Tennessee Health Sciences Center
  • Laboratory for Bioimaging and Anatomical Informatics (Drexel) at Drexel College of Medicine, Philadelphia, PA

Technical Contacts

Jyl Boline jyl.boline@loni.ucla.edu

 

Acknowledgements and Fundings Sciences

This project is supported by U24 RR021760 funded by the National Center for Research Resources (NCRR) at the National Institutes of Health (NIH).

 

To download the CHANGE, please go to the download form.