Mouse BIRN Atlasing Toolkit Information

Description
Reference biological/biomedical imagery has always been critically important for providing context for observations and experimentation. 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 it?s plugin architecture.
Features
  • 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.
Usage
System Requirements
OS: any except Mac OS X 10.5 (Leopard), Memory: 512 Mb, Processor: N/a, Other: MBAT requires installation of JRE 1.4+. One may also install Java3D 1.3+ (to visualize 3D surfaces)
Installation

To replace the existing version of MBAT, uninstall the old version prior starting the installation.

To run the different versions of MBAT simultaneously, you have to install MBAT under a separate directory.

-- Windows
1. Unzip the installation program in your local hard drive.
2. Click the MBAT_windows_.exe to start the installation.

-- Mac
1. Click the MBAT_macos_.dmg to start the installation.

-- UNIX/Linux
1. Un-tar or gunzip the installation program in your local hard drive.
2. Run the MBAT_unix_.sh to start the installation.

Atlas and Volume subfolders will be created under the MBAT program folder after the installation.

Purpose

MBAT allows a user to view their data and offers the ability to interface with data offered by Mouse BIRN. 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 http://www.nbirn.net/bdr/bdr_current_data.shtm. Additional data volumes may also be downloaded in Analyze image 7.5 format.

The Concept Query accesses multiple databases and downloads data based on user input. This data can then be incorporated with the user's own data, juxtaposed and analyzed. The databases provide a variety of different data types and are available regardless of the user's location or affiliation with the Mouse BIRN.

Online Support
Forum
Please submit your questions about Mouse BIRN Atlasing Toolkit to the forum.

Documentation
Consult the software documentation for more detailed information not covered on this page.
 
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