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BrainJ3D

BrainJ3D. What is it?. A tool to visualize the brain. Including structural volumes, functional volumes, surfaces, veins/arteries and photos. Allows mapping of points. It is written in Java/Java3D so it is cross platform.

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BrainJ3D

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  1. BrainJ3D

  2. What is it? • A tool to visualize the brain. Including structural volumes, functional volumes, surfaces, veins/arteries and photos. • Allows mapping of points. • It is written in Java/Java3D so it is cross platform. • Utilizes Java RMI to provide client/server and standalone modes with one code base.

  3. More • It will replace: • Brain Mapper • Visualization Applet • It will be more maintainable. • It will reduce dependence on Skandha4. • It support SPM file types • We can leverage functionality • It increases user base.

  4. Where is it? • It has most of the functionality of the Brain Mapper and the Applet that we want to implement. • It is not ready to replace them yet. • It doesn’t support saving of data. • It doesn’t generate veins or arteries.

  5. Architecture

  6. Client/Server • Uses Java RMI. • One server can serve multiple clients. • Uses the Java3D offscreen option for rendering. • Uses same code base, so it often works without much additional work.

  7. Milestones • M1: • Create a workspace that organizes data. • Show functional activation. • Fully implements mapping (display, interface, loading and saving (not done)). • Support more file types – Matlab 5 (not done), 3D formats done. • Implement a cutaway view.

  8. Workspace • Organizes and manages patient’s data • XML format, so it is easy to read and edit. • Categories can be added and removed. • Names can be changed.

  9. Workspace • Future versions will use the workspace to manage coordinate systems (space) • Data should be displayed in a consistent space, but it is often imported in different spaces. • So we can have the workspace transform the data as needed.

  10. Functional Activation • Functional data can now be overlayed on structural data. • An arbitrary number can be overlayed. • Transparency is supported. • Different color schemes can be chosen for each functional volume, i.e.. Warm or green or cold.

  11. Mapping • You can map points and label the brain • You can display text and/or a choice of shapes. • It supports marked nodes. • You can pick up and move points. • It supports multiple maps.

  12. Mapping • Saving is not yet implemented. • It only loads the skanda4 file format. • This doesn’t support all the functionality that BrainJ3D has. • So it isn’t an ideal format for saving.

  13. File Formats • It interfaces to Java3D file loaders, so it supports almost all 3D formats to some extent. • But SPM produces files in Matlab 5 format. • The specifications for this is huge. • No file loaders in Java are readily available. • They are available in C. • Minc is not supported.

  14. Cutaway • You can cutaway the brain and “look inside” • It uses the structural volume and a brain mask to achieve this. • You can overlay fMRI onto these structures in the same way as the volume viewer.

  15. Remote mode • Almost everything works perfectly in client/server mode • the cutaway does not work. A bug in how I’m using Java3D in offscreen mode. • Everything else works fine with some expected performance loss. • Security issues – need to implement a security manager for user level security.

  16. Next • Generate surface models of both cortex and arteries/veins. • Probably require dilating the brain mask. • Fix the user interface. • Including a help system and meaningful exception handling. • Document code. • Saving files.

  17. More • Level of Detail nodes. We can have two different models and then switch them when we need faster rendering. • Have underlying fMRI be visible on the surface model by changing the surface color in some areas. • Creating crude brain masks. • Synchronize interfaces.

  18. Future Stuff • Try and utilize the FM • I’m not really sure how, but it could be a good resource. • Connect to the brain map database. • Interface to the Talarach daemon.

  19. Where to now? • Tonga, The Friendly Islands • 15-23 S & 173-177 W • Only Polynesian Monarchy. • Never a colonial presense • Consists of 171 islands 45 are inhabited.

  20. Islands • 4 Island groups: • Tongatapu is the business center • Vava’u in the north is a tropical paradise • Ha’apai is in the middle. • Niuas are good for culture. • New Island 6/1995

  21. The Friendly Islands • Dubbed that by Captain Cook. • The Friendliness was a failed plot to kill him and take all his stuff. • They were the Vikings of the Pacific.

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