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.

Version: MBAT 1.1.5 beta, release May 2007

Report Bugs at The BIRN help page, or at the MBAT forum

• MBAT.jpg:
  

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FEATURES:

DATA VOLUMES

This version includes the option to download several different data volumes created by the Mouse BIRN group for visualization. Most of the data volumes are Analyze image 7.5 format. However, it is possible to load several other types of images into the main viewer. These datasets can be downloaded from the BIRN site or here.

ATLASES

It is packaged with 3 different atlas delineations: one based on Swanson 1998, another one on Paxinos 2001, and one on Swanson 2004 and Paxinos and Franklin 2001. Some of these atlases also include 3D surfaces that can be viewed with the 3D viewer and Surface Manager, and the structural hierarchies can be viewed and navigated using BrainGraph tool.

QUERY DATA

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

Expression query tool

This tool queries 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. Movie demonstrating GeneNetwork query tool Microarray data upload tutorial document or See the flash tutorial here. From this interface it is also possible to query and view the high resolution cell fills and brain maps from the CCDB. Right click on the anatomical structure in the query return to launch this.

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HIGHLIGHTS:

BrainGraph

This version of BrainGraph tool adds colored label nodes which correspond to the label volume and label index to make it more visually enriched and easily identify and navigate the brain structures. Also, the new tree view option provides clearer and organized hierarchical information of structures to view the brain.

FlexDock

FlexDock gives users the flexibility to dock multiple windows dynamically. Users can now view the data all at once without switching back and forth different windows.

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REFERENCES FOR MBAT:

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

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DOWNLOAD MBAT:

RELEASE DATE: 05/07. The Mouse BIRN is pleased to announce a beta version 1.1.5 release of the Mouse BIRN Atlasing Toolkit(MBAT). This version may be downloaded from the BIRN site, or on the LONI site. Contact Jyl Boline.

To download the full MBAT package, visit the BIRN downloads page

• MBATreadme.txt: MBAT v1.1 Beta Readme File
• MBAT_v1.1_beta_tutorial.pdf: Users documentation
• MBAT_release.zip: MBAT program zipped

Download the Atlases and Data zip files and place the Atlases and Volume folders in your MBAT folder for additional atlases and data.

• MBAT_Atlases.zip: Additional atlases for visualization in MBAT
• MBATdata.zip: Additional data for display in MBAT

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VISIT the MBAT Forum:

A forum space for users to ask questions, report bugs, and make comments and suggestions.

VISIT the MBAT Programmers Page:

A space for additional technical information about MBAT

MBAT Design Page

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Link to the Older version of MBAT: MBAT 1.1.0 beta, released November 2007 and MBAT 1.0.0 beta, released October 2006