SpotTacker

An ImageJ plugin for tracking single particle over noisy images sequence

Written by Daniel Sage at the Biomedical Image Group (BIG), Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland

A moving particle in a cell nucleus

Path in red over one specific XY image

Path in red over X(t) maximum intensity projection

Description

SpotTracker is a robust and fast computational procedure for tracking fluorescent markers in time-lapse microscopy. The algorithm is optimized for finding the time-trajectory of single particles in very noisy image sequences. The optimal trajectory of the particle is extracted by applying a dynamic programming optimization procedure. In addition, SpotTracker includes a optimal filter to enhance a Gaussian-like spot while attenuating the background noise.

Reference

D. Sage, F.R. Neumann, F. Hediger, S.M. Gasser, M. Unser, "Automatic Tracking of Individual Fluorescence Particles: Application to the Study of Chromosome Dynamics," IEEE Transactions on Image Processing, vol. 14, no. 9, pp. 1372-1383, September 2005.

Software

ImageJ prerequirements

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 SpotTracker2D_.jar, the ImageJ's plugin. The plugin consists in one single JAR file; place it into the "plugins" folder of ImageJ. Do not unzip the JAR file.

This distribution includes two plug-ins for the public-domain ImageJ software:

• SpotTracker: plug-in to track a single bright particle
• SpotEnhancingFilter: plug-in to enhance a gaussian-like particle.

Manual

The manual of the software is avalaible on the Help... button of the plugin.

Test Sequence

A image sequence is available at: Sequence2D.zip (418 Kb).

Example Movies

• Time Coherence: Speed up a movie of a particle (3.8 Mb)
• Example 1: Natural data - Movie of fluorescent particle (6.2 Mb)
• Example 2: Synthetic data - Movie of particle over strong noise (4.9 Mb)

Applications

Example of application

• Frank Neumann, "A study of chromatin mobility by live fluorescence microscopy in Saccharomyces cerevisiae", University of Geneva, Ph.D Thesis. 2004.
• David A Drubin¹, Arman M. Garakani and Pamela A, Silver, "Motion as a phenotype: the use of live-cell imaging and machine visual screening to characterize transcription-dependent chromosome dynamics", BMC Cell Biology, April 2006. ¹Harvard Medical School and Department of Cancer Biology, Boston, MA, USA.

Special distribution

SpotTracker is used to track the movement of chromosomal loci within nuclei of budding yeast cells. The data are provided by the research group of Prof. Susan Gasser with the Departement of Molecular Biology, Unversity of Geneva. For this purpose we have a specific distribution including a module for the nucleus alignment to compensate the natural movement of the cells. It also include a graphical user interface.

More info: Gasser special distribution of the SpotTracker

Conditions of use

You'll be free to use this software for research purposes, but you must not transmit and distribute it without our consent. In addition, you undertake to include a citation whenever you present or publish results that are based on it. EPFL makes no warranties of any kind on this software and shall in no event be liable for damages of any kind in connection with the use and exploitation of this technology.