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JAtlas View: A Java atlas-viewer for browsing biomedical 3D images and atlases

Lookup NU author(s): Dr Janet Kerwin, Mark Scott, Emerita Professor Susan Lindsay



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. © 2005 Feng et al; licensee BioMed Central Ltd.

Publication metadata

Author(s): Feng G, Burton N, Hill B, Davidson D, Kerwin JM, Scott M, Lindsay S, Baldock R

Publication type: Article

Publication status: Published

Journal: BMC Bioinformatics

Year: 2005

Volume: 6

Issue: 47

Pages: 7

Print publication date: 09/03/2005

ISSN (electronic): 1471-2105

Publisher: BioMed Central


DOI: 10.1186/1471-2105-6-47


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Funder referenceFunder name
G9826762Medical Research Council
MC_U127527203Medical Research Council