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This is a collaborative effort of six laboratories. See other information section below for detail.


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. 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.


DATA Queries
One of the main goals of the Mouse BIRN collaboration is to make querying and accessing multiple data types and sources within the context of a digital atlas easy and intuitive. To achieve these goals, there are two new query options available.
Concept-based Queries
The query interface allows the use to search data by date type, subject, and experiment related terms. A query may return multiple types of data most of which can be viewed within MBAT. For those that cannot, a link to an external website may be provided.
Spatial-based Queries
Spatial-based queries allow the user to search data based on a region of interest in the atlas. This query system has been built suing functionality developed for UCSD's SmartAtlas. The system access 2D images that have been registered using tools developed by the UCSD group
Expression Queries
Expression queries allow the user to search for microarray gene expression data from different databases. This includes the GeneNetwork database and the BIRN Microarray database The return of the query is shown as color values corresponding to gene expression levels for some areas of the brain.
MBAT is distributed in two different versions, a standalone version and a full atlas version.The atlas version is packaged with an MR data file, a delineation (MDA2006), 3D surfaces that can be viewed with MBAT 3D Viewer and Surface Manager, and a structural hierarchy that can be viewed and navigated through using the BrainGraph tool. Several additional atlas delinations are available for download at
MBAT provides the user with the option of downloading several different data volumes for visualization purposes. These data volumes were created by the Mouse BIRN group and are available in the Analyze image 7.5 format. It also is possible to load other types of image volumes/datasets into the main MBAT viewer. These datasets can be found on the BIRN download site BIRN site.
BrainGraph is a flexible, extensible, graph-based data model that integrates, organizes and directly accesses numerous types of data. It allows simultaneous storage of multiple labeling schemes and study-specific graph traversal schemes. The BrainGraph editor has been integrated into the MBAT application. BrainGraph adds colored label nodes that correspond to the label volume and label index. This makes it easier for the user to identify and navigate the brain structures. Also, the new tree view option provides clearer and organized hierarchical information of structures to view the brain.
MBAT offers different Workspaces that optimize the configuration of the interface for specific tasks. The MBAT Startup Page points the user to the various Workspaces. The quicklinks offered from the Startup Page include Search by Region of Interest, Query Data, Open Data, View Atlas and Create Atlas.
NIfTI-1 support
Mouse BIRN
Jyl Boline
How to get
You can download these datasets and get more information at the BIRN website, or LONI website
Current version
v2.0.13 Beta
Current version release date
Open source
BIRN License
Available free of charge
JRE 1.5+, Java3D 1.3+
Technical publications
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

Applications publications
Other information

Partner Institutions in Mouse BIRN

Mouse BIRN integrates activities of six laboratories:

This project is supported by Grant U24 RR021760 to the Mouse Biomedical Informatics Research Network (BIRN,, that is funded by the National Center for Research Resources (NCRR) at the National Institutes of Health (NIH).

atlas, BIRN, visualization, volume
Java, Linux, MacOS, UNIX, Windows
IATR listing last updated
22 Feb 2008