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Open Access Software

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

Guangjie Feng1, Nick Burton1, Bill Hill1, Duncan Davidson1, Janet Kerwin2, Mark Scott2, Susan Lindsay2 and Richard Baldock1*

Author Affiliations

1 MRC Human Genetics Unit, Western General Hospital, Crewe Road, EH4 2XU, Edinburgh, UK

2 The Institute of Human Genetics, University of Newcastle, International Centre for Life, Central Parkway, Newcastle-upon-Tyne, NE1 3BZ, UK

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BMC Bioinformatics 2005, 6:47  doi:10.1186/1471-2105-6-47

Published: 9 March 2005

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.