ABOUT THE MOUSE BIRN ATLASING TOOLKIT (MBAT)

General Description

The Mouse BIRN Atlasing Toolkit is designed to view multiple types of multiscale data, access and query databases associated with the Mouse BIRN, and process some of these data types.

This is a collaborative effort by the groups of 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 user location or affiliation with the Mouse BIRN.

Report Bugs at http://bugzilla.nbirn.net/bugzilla/enter_bug.cgi. You must have an account on this site

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Features

DATA VOLUMES

Packaged with a 3D mouse MRI volume reference data set and the ability to load other brain volumes into the main viewer.

Atlases

Packaged with 2 different atlas delineations, one based on Swanson 1998, and the other on Paxinos 2001. The Swanson-based atlas also includes 3D surfaces that can be viewed with the 3D viewer and surface manager, and a structural hierarchy that can be viewed and navigated using BrainGraph. Roughly registered contours are overlaid on the other images. These contours can be located locally or accessed over the web.

QUERY DATA

A major goal of this tool is to provide access to remote databases for querying and viewing multiscale data.

CCDB query tool

High resolution cell fills and brain maps spatially linked to the MBAT atlases can be located, viewed, and downloaded through this tool. This tool accesses the database at http://ccdb.ucsd.edu/CCDBWebSite/index.html. Movie demonstrating CCDB query tool

GeneNetwork query tool

This tool queries microarray gene expression data from the GeneNetwork database (http://www.genenetwork.org). The return of the query is shown as color values corresponding to gene expression levels for some areas of the brain. Movie demonstrating GeneNetwork query tool

BAMS connection Tool

This tool connects to the Brain Architecture Management System (BAMS) at http://brancusi.usc.edu/bkms/ and allows you to search their information about structures.

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DOWNLOAD MBAT

RELEASE DATE 11/23/05: The Mouse BIRN is pleased to announce a beta version release of the Mouse BIRN Atlasing Toolkit (MBAT). It was officially released at the 2005 Society for Neuroscience Meeting and is available to everyone. This version may be downloaded from the BIRN site, or on the LONI site. Contact Jyl Boline.

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