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

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

3. 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.

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

5. MBAT-Download Download MBAT at http://nbirn.net/tools/mbat/index.shtm http://nbirn.net/tools/mbat/index.shtm Several datasets and atlases are packaged with MBAT Additional data at http://nbirn.net/bdr/bdr_current_data.shtm http://nbirn.net/bdr/bdr_current_data.shtm Users may also view their own datasets and create their own atlases

6. Compatibility and Requirements Requires installation of JRE 1.5 –Download and install the appropriate version at http://java.com/en/download/index.jsphttp://java.com/en/download/index.jsp Optional: Java3D 1.3+ (3D surfaces) –Download and install Java 3D at https://java3d.dev.java.net/binary- builds.html https://java3d.dev.java.net/binary- builds.html

7. 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

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

9. 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

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

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

12. View an Atlas Open atlas and navigate in windows or BrainGraph

13. Open Data Open image volume data and navigate in windows

14. 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

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

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

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

18. 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

19. Compare Results to Atlas Register data to Atlas

20. Compare Results to Atlas Apply atlas labels to image

21. Compare Results to Atlas Apply gene expression analysis

22. 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

23. 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

24. 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)

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

26. 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

27. Mouse BIRN Information Additional Information: BIRN: –http://www.nbirn.net/research/mousehttp://www.nbirn.net/research/mouse –http://www.loni.ucla.edu/BIRN/Projects/Mousehttp://www.loni.ucla.edu/BIRN/Projects/Mouse MBAT: –http://www.nbirn.net/tools/mbathttp://www.nbirn.net/tools/mbat –http://www.loni.ucla.edu/MBAThttp://www.loni.ucla.edu/MBAT Contact Information: PI: Arthur Toga, toga@loni.ucla.edutoga@loni.ucla.edu Project Manager: Jyl Boline, jboline@loni.ucla.edujboline@loni.ucla.edu