title: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: MRC Human Genetics Unit, Western General Hospital, Crewe Road, EH4 2XU, Edinburgh, UK. Guangjie.Feng@hgu.mrc.ac.uk <Guangjie.Feng@hgu.mrc.ac.uk>
authors.forename: Guangjie
authors.initials: G
authors.lastname: Feng
authors.forename: Nick
authors.initials: N
authors.lastname: Burton
authors.forename: Bill
authors.initials: B
authors.lastname: Hill
authors.forename: Duncan
authors.initials: D
authors.lastname: Davidson
authors.forename: Janet
authors.initials: J
authors.lastname: Kerwin
authors.forename: Mark
authors.initials: M
authors.lastname: Scott
authors.forename: Susan
authors.initials: S
authors.lastname: Lindsay
authors.forename: Richard
authors.initials: R
authors.lastname: Baldock
mesh_terms: D000715:Anatomy; D019412:Anatomy, Cross-Sectional; D000818:Animals; D001921:Brain / Q000033:anatomy & histology; D001270:Cervical Atlas; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003198:Computer Simulation; D003194:Computer-Assisted Instruction; D003201:Computers; D003626:Data Display; D030562:Databases, Protein; D006801:Humans; D007090:Image Interpretation, Computer-Assisted; D007091:Image Processing, Computer-Assisted; D021621:Imaging, Three-Dimensional; D016247:Information Storage and Retrieval; D051379:Mice; D008953:Models, Anatomic; D011381:Programming Languages; D012984:Software; D014584:User-Computer Interface