RodCellJ

A 2D/3D ImageJ plugin to segment and track fluorescently labeled structures in rod-shaped cells

Daniel Schmitter and Daniel Sage at the Biomedical Image Group (BIG), EPFL, Switzerland
Paulina Wachowicz at the Cell Cycle Control Laboratory, EPFL, Switzerland

Outline

RodCellJ is freely available to the community as a package of several ImageJ plugins to simultaneously analyze the behavior of a large number of rod-shaped cells in an extensive manner. The integration of different image-processing techniques in a single package, as well as the development of novel algorithms does not only allow to speed up the analysis with respect to the usage of existing tools, but also accounts for higher accuracy. Its utility was demonstrated on both 2D and 3D static and dynamic images to study the septation initiation network of the yeast Schizosaccharomyces pombe. More generally, it can be used in any kind of biological context where fluorescent-protein labeled structures need to be analyzed in rod-shaped cells.

Reference

Daniel Schmitter, Paulina Wachowicz, Daniel Sage, Anastasia Chasapi, Ioannis Xenarios, Viesturs Simanis and Michael Unser " A 2D/3D image analysis system to track fluorescently labeled structures in rod-shaped cells: application to measure spindle pole asymmetry during mitosis" Cell Division 2013, 8:6 doi:10.1186/1747-1028-8-6.

Available Software

Video Tutorial

ImageJ prerequirement

The software provided here is a plugin for ImageJ, a general purpose image-processing and image-analysis package. ImageJ has a public domain licence; it runs on several plateforms: Unix, Linux, Windows, Mac OS 9 and Mac OS X. It doesn't take more than a couple of minutes to install.

Download and install

Download RodCellJ.zip, unzip it into the ImageJ plugins folder. The plugin consists to 4 jar files:

RodCellJ.jar: the main application
big.jar: internal Java library
Jama-1.0.2.jar: Java Matrix Package
colt.jar: Open Source Libraries for High Performance Scientific and Technical Computing in Java

Conditions of use

You are free to use this software for research purposes, but you should not redistribute it without our consent.
In addition, we expect you to include adequate citations and acknowledgments whenever you present or publish results that are based on it.

Acknowledgment

This research was supported by the Swiss national foundation (NSF) through a SYNERGIA grant No 132392.