A high-level 3D visualization API for Java and ImageJ
Schmid B, Schindelin J, Cardona A, Longair M, Heisenberg M (2010)
Publication Type: Journal article
Publication year: 2010
Journal
Book Volume: 11
Article Number: 274
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. © 2010 Schmid et al; licensee BioMed Central Ltd.
Authors with CRIS profile
Involved external institutions
Eidgenössische Technische Hochschule Zürich (ETHZ) / Swiss Federal Institute of Technology in Zurich
Switzerland (CH)
Julius-Maximilians-Universität Würzburg
Germany (DE)
University of Edinburgh
United Kingdom (GB)
Max-Planck-Institut für molekulare Zellbiologie und Genetik / Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
Germany (DE)
Switzerland (CH)
Julius-Maximilians-Universität Würzburg
Germany (DE)
University of Edinburgh
United Kingdom (GB)
Max-Planck-Institut für molekulare Zellbiologie und Genetik / Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
Germany (DE)
How to cite
APA:
Schmid, B., Schindelin, J., Cardona, A., Longair, M., & Heisenberg, M. (2010). A high-level 3D visualization API for Java and ImageJ. BMC Bioinformatics, 11. https://doi.org/10.1186/1471-2105-11-274
MLA:
Schmid, Benjamin, et al. "A high-level 3D visualization API for Java and ImageJ." BMC Bioinformatics 11 (2010).
BibTeX: Download