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

BMC Bioinformatics

Software

Benjamin Schmid¹  Martin Heisenberg¹  Albert Cardona²  Johannes Schindelin³  Mark Longair⁴ 

[1]Department of Neurobiology and Genetics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany

[2]Institute of Neuroinformatics, Uni/ETH Zürich, Winterthurerstrasse 190, Zürich, Switzerland

[3]Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden, Germany

[4]School of Informatics, University of Edinburgh, 10 Crichton Street, Edinburgh, UK

关键词: Image Volume;    Application Programming Interface;    Volume Rendering;    Scene Graph;    Volume Editing;   

DOI  :  10.1186/1471-2105-11-274

 received in 2010-01-13, accepted in 2010-05-21,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundCurrent 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.ResultsHere 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.ConclusionsOur 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.

【 授权许可】

CC BY   
© Schmid et al; licensee BioMed Central Ltd. 2010