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Algorithms: ImageJ's plugins
BIG > Daniel Sage > Bio-imaging software > SpotTracker25 June 2016
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SPOTTRACKER

Description

Reference

Software

Example Movies

Applications

Conditions of use

Download

SpotTracker2D

Classic version

SpotTracker2D Extended

Extended version which offer more controls

SpotTracker2D Telomere

Special version for tracking telomeres

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

spottracker

A moving particle in a cell nucleus

spottracker

Path in red over one specific XY image

spottracker

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

These plugins consist in one single JAR file; place it into the "plugins" folder of ImageJ. Do not unzip the JAR file.

It exists three versions:

The distribution includes two plug-ins: "SpotTracker" to track a single bright particle and "SpotEnhancingFilter" to enhance a gaussian-like particle. spottracker

Test Sequence

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

Example Movies

Applications

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.