Open Access Highly Accessed Software

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

Benjamin Schmid1*, Johannes Schindelin2, Albert Cardona3, Mark Longair4 and Martin Heisenberg1

Author Affiliations

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

2 Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden, Germany

3 Institute of Neuroinformatics, Uni/ETH Zürich, Winterthurerstrasse 190, Zürich, Switzerland

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

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BMC Bioinformatics 2010, 11:274  doi:10.1186/1471-2105-11-274

Published: 21 May 2010



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.


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.


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 webcite.