Collaborative Mouse BIRN tools for sharing and visualizing multimodal, multi-scale data

Informatics Center for Mouse Neurogenetics UCSD (NCMIR) Duke (CIVM) Caltech (Beckman) UCLA LONI Participants (UTHSC) (Drexel)

Mouse BIRN Atlasing Toolkit (MBAT) One of the main goals of the Mouse BIRN collaboration is to make query, access, and visualization of multiple data types and sources easy and intuitive within the context of a digital atlas.

SRB Local Databases Visualize DescribeOrganize Remote Databases Data Acquisition Database Management Data Upload IntegrateShare Discover Analyze Data Integration Framework Processing

MBAT-Download Download MBAT at Several datasets and atlases are packaged with MBAT Additional data at Users may also view their own datasets and create their own atlases

Compatibility and Requirements Requires installation of JRE 1.5 –Download and install the appropriate version at Optional: Java3D 1.3+ (3D surfaces) –Download and install Java 3D at builds.html builds.html

Installation To run MBAT with full functionality, un-tar or unzip the full MBAT folder to the user’s hard drive Other atlases and data may be read from anywhere, but it is easier to place it in the MBAT folder

Launching MBAT Double-click.jar file Command line: from MBAT directory “java –jar MBAT.jar”

File Formats: Volume Image Volumes (Data Layer) File that contains image data Analyze Image 7.5 (.img,.hdr) Nifti (.niiI) Medical Imaging NetCDF (.mnc) Bruker format (reco, 2Dseq) CIVM format (.headfile) (large volumes) Biorad (PIC) Tagged Image File Format (TIFF) –regular single layer –ImageJ image stack Label Volumes (Paint Layer) These special volumes contain the delineations that are the foundation of atlases Overlay of Image and Label Volumes

File Formats: Integrated Label Format.ilf Create.ilf files using BrainGraph Editor (to be released Nov 1)

Getting Started-the Launch page Options offered on Launch page to aid tasks

View an Atlas Open atlas and navigate in windows or BrainGraph

Open Data Open image volume data and navigate in windows

Docking Resize panels by dragging panel boundaries drag a panel, drag the title bar at top or the tool tab at the bottom to start the drag-n-drop operation to move the panel to another desired location Hide tools using Pin icon

Query data Open Query data Workspace Set search criteria by selecting search groups

Review Results Choose data for examination by adding it to the Comparison Cart

Examine Selected Results Examine selected results in comparison window in relation to the MBAT atlas

Examine Selected Results You may navigate Volumes using the toolbar at the top Page Up/Dn will move through a volume quickly Open a Larger View by clicking the Window icon in the upper right

Compare Results to Atlas Register data to Atlas

Compare Results to Atlas Apply atlas labels to image

Compare Results to Atlas Apply gene expression analysis

Query: by Region Open Query by Region Workspace Navigate to brain area or interest Change to Draw Mode. Select New to create a new Region. Use ctrl + left button drag to delineate a Region

Create Atlas Create a new Label Volume Create a new Label Index and select the Label color Select paint brush and brush size in the Drawing Tool Drag left mouse button to paint the area

Query: Bonfire/BAMs Connections to Information Sources The BONFIRE browser allows a user to search the ontologies available on the BIRN CC ontology system The BAMS connection allows a user to search the structure hierarchies onstructed by the Brain Architecture Center (BAC)

Atlas: View 3D surfaces Some MBAT atlases come with associated 3D surfaces Open Surface View, Surface manager, and.atlas3D file

Mouse BIRN Data Freely available, powerful extensible Tools –MBAT and integration tools Multiplatform Java 372 downloads as of September 2007 –Facilitate sharing other types of data Mouse BIRN Resources

Mouse BIRN Information Additional Information: BIRN: – – MBAT: – – Contact Information: PI: Arthur Toga, Project Manager: Jyl Boline,