ImageJ

One of the main missions of the Fiji project is to bring advanced computer vision algorithms into the hands of biologists. For that to happen it is necessary that computer vision researchers contribute their algorithms and plugins to the platform.

This process has started and one example is the MosaicSuite of image processing algorithms developed by the MOSAIC group headed by Ivo Sbalzarini at MPI-CBG in Dresden. The suite includes tools for segmentation, particle tracking and more. Some of the algorithms are described in these papers:

Shivanandan, A., Radenovic A., Sbalzarini I. F. MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis BMC Bioinformatics, 14, pp. 1-10, (2013)

A. Rizk, G. Paul, P. Incardona, M. Bugarski, M. Mansouri, A. Niemann, U. Ziegler, P. Berger, and I. F. Sbalzarini. Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh. Nature Protocols, 9(3):586–596, 2014.

G. Paul, J. Cardinale, and I. F. Sbalzarini. Coupling image restoration and segmentation: A generalized linear model/Bregman perspective. Int. J. Comput. Vis., 104(1):69–93, 2013.

J. Cardinale, G. Paul, and I. F. Sbalzarini. Discrete region competition for unknown numbers of connected regions. IEEE Trans. Image Process., 21(8):3531–3545, 2012.

J. A. Helmuth, G. Paul, and I. F. Sbalzarini. Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. BMC Bioinformatics, 11:372, 2010.

I. F. Sbalzarini and P. Koumoutsakos. Feature Point Tracking and Trajectory Analysis for Video Imaging in Cell Biology, Journal of Structural Biology 151(2):182-195, 2005.

All information on how to install the tools, documentation and developer information is available on the MOSAIC group website.

The plugins are available in Fiji through a dedicated update site.

We are looking forward to more contributions from the MOSAIC group in the future.