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BrainJ3D: Advanced Brain Visualization Tool for Structural and Functional Mapping

BrainJ3D is a cutting-edge visualization tool designed to enhance the study of the brain by providing structural volumes, functional overlays, surfaces, and vascular mapping. Developed in Java and Java3D, it supports multiple operating systems and facilitates client/server and standalone modes. While still in development, it aims to replace existing tools like Brain Mapper with improved maintainability and enhanced functionality. Key features include mapping capabilities, workspace data organization, support for various file types, and the ability to visualize functional data in conjunction with structural images.

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BrainJ3D: Advanced Brain Visualization Tool for Structural and Functional Mapping

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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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