Objective: To integrate the NeuroCommons Google Map API ABA demo into MBAT and if successful, use this same method for other types of data CONCEPT Query Initiation ...

Table of Contents TOC MBAT 3.0 Build Instructions If you are using Eclipse then all the configuration and build scripts should automatically compile, archive the plugins ...

Table of Contents TOC Cart Manager Cart Manager is the mechanism using which objects are passed in different workspaces in !MBAT. !MBAT !API users can add new plugins ...

Coding Policies To maintain good team development and coding standards, all developers must adhere to the following policies: 1. Comment all commits 1. Comment code ...

Creating mbat.jar This section gives instructions on how to create the mbat.jar application file using Eclipse. The Ant build file used in these instructions is located ...

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TOC{title "Table of Content"} Required Software 1 Java SDK 1.6: http://java.sun.com/javase/downloads/index.jsp 2 JOGL JSR231-1.1.1: 3 Eclipse: http://www.eclipse ...

File Formats The following file formats are currently supported by MBAT. Image volume files Analyze(tm) ( .img, .hdr): http://www.mayo.edu/bir/PDF/ANALYZE75.pdf Nifti ...

Table of Contents TOC MBAT 3.0 File Formats Atlas File Format The .atlas file format is an XML based file format to specify a labelled atlas object which consists ...

Functional Specifications: Graph manager

Table of Contents TOC Graph Manager The Graph Manager presents hierarchical anatomical structure information using a radial tree display that is synchronized with ...

Table of Contents TOC Registration workspace Using registration workspace, users can align a source image with respect to a template image. Following diagram shows ...

TOC File menu options Introduction This page describes the functional specifications for "File" menu items. The File menu contains following menu options: File Open ...

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In-Person Programmer Meeting General Information Dates: June 25-26, 2007 Location: UCSD — BIRN-CC 9500 Gilman Drive Mailcode 0715 Holly Building La Jolla, CA 92093 ...

Table of Contents TOC JxBrowser Eclipse Setup 1. Set the native library locations for jniwrap. 1. Run Configurations Environment tab . Set the appropriate environmental ...

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Requirements AHM Plan (Oct. 20) Mockups 1 Workflows 1 Workspace 1 Workspace 1 Terms Feature Requests Data Sources Registration View BrainGraph Viewer Search Plugin ...

Supporting Large 3D Datasets in MBAT We need to pick at least one data format for large (larger than available RAM, larger than a 32-bit address space) 3D image volumes ...

ABOUT THE MOUSE BIRN ATLASING TOOLKIT (MBAT) GENERAL DESCRIPTION: Reference biological/biomedical imagery has always been critically important for providing context ...

MBAT 3.0 Architecture The !MBAT 3.0 Architecture is an extensible design built on a scalable plugin architecture. It consists of a core framework (utlity libraries ...

MBAT Client Documentation Modules Supported Formats Volumes Viewing Gene Expression Brain Graph Surface Rendering CCDB Search Development Environment Requirement ...

TOC Introduction This page describes the functionality provided by the !MouseBIRN Atlasing Toolkit (MBAT) application. It is developed as a bioinformatics framework ...

Minutes from All MBAT Programmer Meetings Link to Mouse BIRN Programmers Working Page General decisions: 03/09/06: Decided that in general, people will work on modules ...

SteveAnderson^? 07 Feb 2008 Creating an MBAT Build from the Subversion Repository A full MBAT build currently consists of several separate modules that are included ...

Created on 26 Jun 2007 MBAT Upcoming Features Data Collaboration Conceptual Query Dynamically access data from multiple modalities. Access data from one central location ...

ABOUT THE MOUSE BIRN ATLASING TOOLKIT (MBAT) Version 1.1.0 Release Date November 2007 GENERAL DESCRIPTION: The Mouse BIRN Atlasing Toolkit is designed to view multiple ...

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 ...

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 ...

Table of Contents TOC mbManagerCart Design This section describes how to access and retrive data from the !MBAT cart, the mechanism that allows the sharing of objects ...

Table of Contents TOC MBAT Common Datatype Class Interface The fundamental datatype that can be exchanged among all the workspaces and all the core libraries is defined ...

Table of Contents TOC mbSecurity Design Overview mbSecurity framework is a singleton class that can be called by all workspace plugins. Its goal is to provide the ...

Table of Contents TOC Comparison Viewer Overview The Comparison Viewer workspace in !MBAT3.0 is built on the concept of layers which can be composited together. Each ...

MBAT Plugins API Specify well-defined Input/Output data model for plugins TOC I. !DocManager Core 1. File reader plugin Input: Classtype: metafile,2D/3D Image, numeric ...

Minutes of !MouseBIRN Programmers Meeting 30 May 2008 TOC Attendees Main., Main., Main., Main. 1. !MBAT cores effected DocManager/Search/Viewer/Analysis 2. Plugin ...

Table of Contents TOC MouseBIRN Partner Plugins This page contains the documentation and functional specifications for the plugins developed by the MouseBIRN partners ...

Go to Mouse BIRN Wiki Table of Contents MouseBIRN Atlasing: Atlasing Working Pages Table of Contents The tool integration and prioritization taskforce has interoperable ...

Table of Contents TOC Spring 2009 AHM Deliverables (May 21, 2009) This document lists the deliverables for each institution to be delivered by the Spring !MouseBIRN ...

Table of Contents TOC Fall 2009 Deliverables (Oct 21, 2009) This document lists the deliverables for each institution to be delivered by Oct 21, 2009. CalTech Goal ...

TOC{title "Table of Contents"} MouseBIRN Schedule This document lists the major tasks, the organizations responsible for leading the efforts, and the timeline for ...

TOC{title "Table of Contents"} GUI Builder Java 1.5 Compatibility 1. Look at form in design view. 1. Go to Inspector panel. Click on Form. Right-click and go to properties ...

Minutes of !MouseBIRN AHM Meetings New topic: (Must be WikiWord: two or more words with initial capitals, run together) SEARCH{"^ MeetingMinutes " scope "topic" type ...

TOC Overview This page describes the design and technical details of "Save/Open workspace" functionality. We have used XStream library for implementing this functionality ...

TOC{title "Table of Contents"} Search Datasource Plugin This document describes the search datasource plugin architecture and how to create and add a datasource plugin ...

Table of Contents TOC Search workspace In the search workspace, users can specify a single query that searches across multiple data sources. Searches can be by keyword ...

Server Protocols ArcIMS ArcXML Programmer's Reference Guide for ArcIMS 9.1 Neuroterrain Atlas Server Network Protocols Web Services Description Language (Axis Client ...

TOC{title "Table of Contents"} Spatial Registration Plugin This document describes the registration plugin architecture and how to create and add a new spatial registration ...

svn+ssh on command line (Windows) Required Software 1. PuTTY, Plink, Pageant: 2. svn.exe: http://subversion.tigris.org Installation 1. Setup ssh (see http://tortoisesvn ...

Table of Contents TOC Trouble Shooting Below are some common problems you may encounter when building and running !MBAT: 1 SVN error: org.tigris.subversion.javahl ...

TOC{title "Table of Contents"} Upload Data Plugin This document describes the upload plugin architecture and how to create and add a new upload plugin to the !MBAT ...

Table of Contents TOC Comparison Viewer Rendering Plugin This document describes the comparison viewer rendering plugin architecture and how to create and add a new ...

Comparison Viewer Workspace In the comparison viewer workspace, users can view one or more images and perform various image manipulation tasks. The viewer workspace ...

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Web Services Providers used by MBAT 1. BIRN Miroarry DB API Methods: URI: http://microarray.nbirn.net/get data.php? Parameters: 1. cmd get probes get my probes 1 ...

Functional Specifications: Welcome workspace On starting the application, the user gets directed to this workspace by default. Following diagram shows the welcome ...

TOC{title "Table of Contents"} Workspace Plugin This document describes the workspace plugin architecture and how to create and add a new workspace plugin to the ...