JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases

Abstract

Background: Many three-dimensional (3D) images are routinely collected in biomedical research and a number of digital atlases with associated anatomical and other information have been published. A number of tools are available for viewing this data ranging from commercial visualization packages to freely available, typically system architecture dependent, solutions. Here we discuss an atlas viewer implemented to run on any workstation using the architecture neutral Java programming language.

Results: We report the development of a freely available Java based viewer for 3D image data, descibe the structure and functionality of the viewer and how automated tools can be developed to manage the Java Native Interface code. The viewer allows arbitrary re-sectioning of the data and interactive browsing through the volume. With appropriately formatted data, for example as provided for the Electronic Atlas of the Developing Human Brain, a 3D surface view and anatomical browsing is available. The interface is developed in Java with Java3D providing the 3D rendering. For efficiency the image data is manipulated using the Woolz image-processing library provided as a dynamically linked module for each machine architecture.

Conclusion: We conclude that Java provides an appropriate environment for efficient development of these tools and techniques exist to allow computationally efficient image-processing libraries to be integrated relatively easily.

Figure 1

JAtlasViewer interface. Screen capture of the JAtlasViewer interface. Top-left: main window with 3D visualisation and anatomy tree; RHS: three section views through the data with some high-lighted anatomy; Bottom-left: current list of imported anatomy.

Figure 2

Anatomy manager interface. Anatomy key interface to control displayed colour, anatomy component name and visibilility in the 2D and 3D views.