BrainJ3D is a cross-platform Java/Java3D software toolkit for processing and visualizing brain imaging data, which 1) contains general purpose tools for reconstructing, mapping and visualizing integrated structural and functional images and 2) leverages Java's Remote Method Invocation to provide both a standalone and a client/server mode

Brinkley, James F

Moore, Eider B

Poliakov, Andrew V

English

University of Washington Structural Informatics Group Publications

 
 Brain Visualization in Java3D 
Eider Moore
a, Andrew Poliakov
a, PhD, James F. Brinkley
a,b,c , MD, PhD 
Structural Informatics Group,
 Departments of  
aBiological Structure, 
bMedical Education and Biomedical Informatics, 
 and 
cComputer Science and Engineering,  University of Washington, Seattle, USA 
 
 
BrainJ3D is a cross-platform Java/Java3D software toolkit 
for processing and visualizing brain imaging data, which 1) 
contains general purpose tools for reconstructing, mapping  
and visualizing integrated structural and functional images 
and 2) leverages Java’s Remote Method Invocation to provide 
both a standalone and a client/server mode. 
Keywords: 3D visualization, brain imaging, web-enabled, 
neuroinformatics. 
BrainJ3D is a next-generation 3-D visualization 
package we are developing as a follow-on to the successful 
use of our custom but non-portable software by neuroscience 
researchers
1 (see also the companion poster by Poliakov et al). 
BrainJ3D provides two major pieces of functionality: 1) 3-D 
reconstruction, mapping, and visualization of integrated data, 
and 2) client-server operation.  Given appropriate image vol-
umes as input, BrainJ3D can generate and render in real-time 
(on the local workstation in standalone mode) an anatomically 
correct 3-D model of the brain.  Using this surface model the 
user can map functional data onto the brain – such as cortical 
stimulation mapping (CSM) sites from a surgical photo [Fig 
1] – or fMRI overlays [Fig 2].   
Client-server mode, on the other hand,  is designed to 
make it easier to share and view MRI and fMRI data over the 
Internet, thereby  facilitating collaboration between labs, and 
improving the usefulness of central data repositories. 
 
Figure 1. Mapping CSM sites from a photograph. 
Sharing data is crucial to collaboration, but there are 
several roadblocks for sharing of neuroimaging data, includ-
ing a sense of ownership over the studies, the physical diffi-
culty in sharing and transferring extremely large studies, and a 
desire to maintain control of the data. BrainJ3D addresses 
these roadblocks in several ways. To reduce the need to 
transmit large studies client/server mode is designed using the 
off screen rendering feature of Java3D, so that renderings are 
computed on the server, and only snapshots are exported to 
the client.  Such an approach means the clients do not need 
overly fast network connections, nor expensive hardware or 
complicated software installations. 
   In addition, client-server operation permits fine-tuned 
control over data sharing.  Because BrainJ3D supports various 
levels of security on the user level, the sharing lab can set up 
restrictions on which datasets can be viewed by certain indi-
viduals.  This feature allows labs to share more data with 
trusted collaborators and to add restrictions to the general 
public or less trusted collaborators.  The lab maintains control 
of the data because only snapshots of the models or slices are 
exported to other computers, whereas the data stay local. 
  Although initially designed as a follow-on to existing 
tools within our own group, BrainJ3D was also designed to be 
flexible, expandable and interoperable with popular software 
tools (including SPM).  We believe that current and future 
versions will provide an increasingly valuable visualization 
and data sharing tool for users, fMRI data repositories and 
individual labs. 
 
Figure 2. Cutaway of surface model with fMRI activation. 
Supported by Human Brain Project grant MH/DC02310. 
 
1.  Poliakov, A.V., Albright, E., Corina, D., Ojemann, G., 
Martin, R.F. and Brinkley, J.F. 2001 Server-based 
approach to web visualization of integrated 3-D medical 
image data. Proc AMIA Symposium 2001, pp 533-537. 

Brain Visualization in Java3D

http://sigpubs.biostr.washington.edu/archive/00000151/

Brain Visualization in Java3D

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