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Hardware-accelerated 3D visualization for ImageJ.

In the fields of biology and medicine, ImageJ has become a popular image processing tool, particularly for data acquired by microscopy. In both
fields, such data is not restricted to two dimensions. On the contrary,
many imaging techniques (for example Computed Tomography, MRI, confocal
microscopy, etc.) produce 3D data sets. While ImageJ can handle these data by treating them as stacks of 2D slices, it lacks capabilities to visualize and process them as real 3D data.
To fill this gap, we developed an ImageJ plugin for 3D visualization, which
allows the user to display stacks as surfaces, volume renderings or orthoslices. It supports both perspective as well as orthogonal projection.
The application focuses on interactive, hardware-accelerated display of 3D data. Additionally, it offers functionality for animation and movie recording as well as a flexible interface for handling transformations of displayed 3D objects. Displayed volumes can be edited directly in the viewport by projective filling of freely defined Regions of Interest. The user can select landmark points, which may be used for alignment of 3D objects.
Existing 3D visualization solutions for ImageJ are either not hardware-accelerated (like VolumeJ), or are dependent on third party libraries (like ij-wtk). In contrast to these, our tool is purely based on Java and Java3D. This facilitates installation and the performance necessary for interactive usage. Other plugins can easily use the viewer as a library and in this way benefit from 3D visualization.

ImageJ, Java3D, 3D, visualization

Benjamin Schmid

University of Wuerzburg


Short Biography
Focus of research:
* 3D visualization
* 3D image processing in general
* 3D image registration of Drosophila fly brains obtained
by Confocal microscopy.
* PhD student at the University of Wuerzburg
* 2005: Final year project at the University of Cambridge:
Analyzing gene expression data in Arabidopsis Thaliana.
* 2001 - 2005: Study of bioinformatics at the University of Applied
Sciences Weihenstephan.

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