title: A high-level 3D visualization API for Java and ImageJ.
abstract: BACKGROUND
  Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set.
  
  
  RESULTS
  Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts.
  
  
  CONCLUSIONS
  Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de.
authors.affiliation: Department of Neurobiology and Genetics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany. b.schmid@biozentrum.uni-wuerzburg.de
authors.forename: Benjamin
authors.initials: B
authors.lastname: Schmid
authors.forename: Johannes
authors.initials: J
authors.lastname: Schindelin
authors.forename: Albert
authors.initials: A
authors.lastname: Cardona
authors.forename: Mark
authors.initials: M
authors.lastname: Longair
authors.forename: Martin
authors.initials: M
authors.lastname: Heisenberg
mesh_terms: D003196:Computer Graphics; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D018613:Microscopy, Confocal / Q000379:methods; D010363:Pattern Recognition, Automated / Q000379:methods; D011381:Programming Languages; D012984:Software