A high-level 3D visualization API for Java and ImageJ

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 a...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Benjamin Schmid, Johannes E. Schindelin, Albert Cardona, Mark Longair, Martin Heisenberg
• Keywords: Biological Image, BMCBI 2010, Image, Image Analysis Tools