BrainJ3DBrainJ3D

What is it?What is it?

• A tool to visualize the brain. Including A tool to visualize the brain. Including structural volumes, functional volumes, structural volumes, functional volumes, surfaces, veins/arteries and photos.surfaces, veins/arteries and photos.

• Allows mapping of points.Allows mapping of points.

• It is written in Java/Java3D so it is cross It is written in Java/Java3D so it is cross platform.platform.

• Utilizes Java RMI to provide client/server Utilizes Java RMI to provide client/server and standalone modes with one code and standalone modes with one code base.base.

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• It will replace:It will replace:– Brain MapperBrain Mapper– Visualization AppletVisualization Applet

• It will be more maintainable.It will be more maintainable.• It will reduce dependence on It will reduce dependence on

Skandha4.Skandha4.• It support SPM file types It support SPM file types

– We can leverage functionality We can leverage functionality – It increases user base.It increases user base.

Where is it?Where is it?

• It has most of the functionality of the It has most of the functionality of the Brain Mapper and the Applet that we Brain Mapper and the Applet that we want to implement.want to implement.

• It is not ready to replace them yet.It is not ready to replace them yet.– It doesn’t support saving of data.It doesn’t support saving of data.– It doesn’t generate veins or arteries.It doesn’t generate veins or arteries.

ArchitectureArchitecture

Client/ServerClient/Server

• Uses Java RMI.Uses Java RMI.

• One server can serve multiple One server can serve multiple clients.clients.

• Uses the Java3D offscreen option for Uses the Java3D offscreen option for rendering.rendering.

• Uses same code base, so it often Uses same code base, so it often works without much additional work.works without much additional work.

MilestonesMilestones

• M1:M1:– Create a workspace that organizes data. Create a workspace that organizes data. – Show functional activation.Show functional activation.– Fully implements mapping (display, Fully implements mapping (display,

interface, loading and saving (not done)). interface, loading and saving (not done)). – Support more file types – Matlab 5 (not Support more file types – Matlab 5 (not

done), 3D formats done.done), 3D formats done.– Implement a cutaway view.Implement a cutaway view.

WorkspaceWorkspace

• Organizes and Organizes and manages patient’s manages patient’s datadata

• XML format, so it is XML format, so it is easy to read and easy to read and edit.edit.

• Categories can be Categories can be added and removed.added and removed.

• Names can be Names can be changed.changed.

WorkspaceWorkspace

• Future versions will use the Future versions will use the workspace to manage coordinate workspace to manage coordinate systems (space)systems (space)– Data should be displayed in a consistent Data should be displayed in a consistent

space, but it is often imported in space, but it is often imported in different spaces.different spaces.

– So we can have the workspace So we can have the workspace transform the data as needed.transform the data as needed.

Functional ActivationFunctional Activation

• Functional data can now be overlayed Functional data can now be overlayed on structural data.on structural data.

• An arbitrary number can be An arbitrary number can be overlayed.overlayed.

• Transparency is supported.Transparency is supported.

• Different color schemes can be Different color schemes can be chosen for each functional volume, chosen for each functional volume, i.e.. Warm or green or cold.i.e.. Warm or green or cold.

MappingMapping

• You can map points You can map points and label the brainand label the brain

• You can display text You can display text and/or a choice of and/or a choice of shapes.shapes.

• It supports marked It supports marked nodes.nodes.

• You can pick up and You can pick up and move points.move points.

• It supports multiple It supports multiple maps.maps.

MappingMapping

• Saving is not yet implemented.Saving is not yet implemented.

• It only loads the skanda4 file format.It only loads the skanda4 file format.– This doesn’t support all the functionality This doesn’t support all the functionality

that BrainJ3D has.that BrainJ3D has.– So it isn’t an ideal format for saving.So it isn’t an ideal format for saving.

File FormatsFile Formats

• It interfaces to Java3D file loaders, so it It interfaces to Java3D file loaders, so it supports almost all 3D formats to some supports almost all 3D formats to some extent.extent.

• But SPM produces files in Matlab 5 But SPM produces files in Matlab 5 format.format.– The specifications for this is huge.The specifications for this is huge.– No file loaders in Java are readily available.No file loaders in Java are readily available.– They are available in C.They are available in C.

• Minc is not supported.Minc is not supported.

CutawayCutaway

• You can cutaway the You can cutaway the brain and “look brain and “look inside”inside”

• It uses the structural It uses the structural volume and a brain volume and a brain mask to achieve this.mask to achieve this.

• You can overlay fMRI You can overlay fMRI onto these structures onto these structures in the same way as in the same way as the volume viewer.the volume viewer.

Remote modeRemote mode

• Almost everything works perfectly in Almost everything works perfectly in client/server modeclient/server mode– the cutaway does not work. A bug in the cutaway does not work. A bug in

how I’m using Java3D in offscreen mode.how I’m using Java3D in offscreen mode.– Everything else works fine with some Everything else works fine with some

expected performance loss.expected performance loss.– Security issues – need to implement a Security issues – need to implement a

security manager for user level security.security manager for user level security.

NextNext

• Generate surface models of both Generate surface models of both cortex and arteries/veins.cortex and arteries/veins.– Probably require dilating the brain mask.Probably require dilating the brain mask.

• Fix the user interface.Fix the user interface.– Including a help system and meaningful Including a help system and meaningful

exception handling.exception handling.

• Document code.Document code.• Saving files.Saving files.

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• Level of Detail nodes. We can have Level of Detail nodes. We can have two different models and then switch two different models and then switch them when we need faster rendering.them when we need faster rendering.

• Have underlying fMRI be visible on Have underlying fMRI be visible on the surface model by changing the the surface model by changing the surface color in some areas.surface color in some areas.

• Creating crude brain masks.Creating crude brain masks.• Synchronize interfaces.Synchronize interfaces.

Future StuffFuture Stuff

• Try and utilize the FMTry and utilize the FM– I’m not really sure how, but it could be a I’m not really sure how, but it could be a

good resource.good resource.

• Connect to the brain map database.Connect to the brain map database.

• Interface to the Talarach daemon.Interface to the Talarach daemon.

Where to now?Where to now?

• Tonga, The Friendly Tonga, The Friendly IslandsIslands– 15-23 S & 173-177 W15-23 S & 173-177 W– Only Polynesian Only Polynesian

Monarchy.Monarchy.– Never a colonial Never a colonial

presensepresense– Consists of 171 Consists of 171

islands 45 are islands 45 are inhabited.inhabited.

IslandsIslands

• 4 Island groups:4 Island groups:– Tongatapu is the Tongatapu is the

business centerbusiness center– Vava’u in the north Vava’u in the north

is a tropical is a tropical paradiseparadise

– Ha’apai is in the Ha’apai is in the middle.middle.

– Niuas are good for Niuas are good for culture.culture.

– New Island 6/1995New Island 6/1995

The Friendly IslandsThe Friendly Islands

• Dubbed that by Dubbed that by Captain Cook.Captain Cook.

• The Friendliness The Friendliness was a failed plot to was a failed plot to kill him and take all kill him and take all his stuff.his stuff.

• They were the They were the Vikings of the Vikings of the Pacific.Pacific.