downloads:particletracker2d
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downloads:particletracker2d [2013/11/08 11:47] – [Installation] kota | downloads:particletracker2d [2017/06/07 01:04] – changed github user name kota | ||
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+ | ===== Particle Tracker (2D) Extended===== | ||
+ | [{{ : | ||
+ | |||
+ | ==== Author ==== | ||
+ | Kota Miura\\ | ||
+ | Centre for Molecular and Cellualr Imaging (CMCI), EMBL Heidelberg\\ | ||
+ | miura at embl dot de Tel: +49 6221 387 404\\ \\ | ||
+ | ==== History ==== | ||
+ | 10-11-19 First release\\ \\ | ||
+ | |||
+ | === recent | ||
+ | {{rss> | ||
+ | |||
+ | === Source === | ||
+ | [[https:// | ||
+ | |||
+ | ==== Installation ==== | ||
+ | Download [[https:// | ||
+ | |||
+ | By [Help > Refresh Menu] or by re-launching ImageJ, you will find new menu items under **[Plugins > Particle Tracker Classic > | ||
+ | |||
+ | (following not working at the moment 20131107) | ||
+ | If you are using Fiji: Instead of installing manually, you could also set automatic download & updates by registering our update site. | ||
+ | < | ||
+ | http:// | ||
+ | </ | ||
+ | For managing update site, [[http:// | ||
+ | ==== Requires ==== | ||
+ | ImageJ ver 1.44h or higher ([[http:// | ||
+ | ==== Description ==== | ||
+ | ParticleTracker plugin written by Guy Levy (Computational Biophysics Lab, ETH Zurich) added with interactive export of segmentation and tracking results to ImageJ results table. [[http:// | ||
+ | |||
+ | **As of Nov. 2013, there is a [[http:// | ||
+ | |||
+ | When you use this plugin, please cite: | ||
+ | |||
+ | < | ||
+ | **I. F. Sbalzarini and P. Koumoutsakos.**\\ | ||
+ | **Feature point tracking and trajectory analysis for video imaging in cell biology.** \\ | ||
+ | J. Struct. Biol., 151(2): 182-195, 2005.\\ | ||
+ | [[http:// | ||
+ | </ | ||
+ | ==== Work Flow ==== | ||
+ | [{{ : | ||
+ | [{{ : | ||
+ | [{{ : | ||
+ | [{{ : | ||
+ | |||
+ | * 1. **Segmentation and Tracking ** | ||
+ | * Follow instructions in [[https:// | ||
+ | |||
+ | * 2. **Transferring all trajectory data** | ||
+ | * In the ParticleTracking Results window (see Fig.1), click "All Trajectory to Table" button. All trajectory data will be then transferred to the results table of ImageJ, which then could be directly accessed using ImageJ macro and other scripting languages (Fig. 3). | ||
+ | |||
+ | * 3. **Transferring all segmented particle data** | ||
+ | * Similarly, | ||
+ | |||
+ | * 4. **Transferring Specific Trajectory data** | ||
+ | * You could export only a specific trajectory. First, visualize trajectories by clicking " | ||
+ | |||
+ | ==== Application: | ||
+ | |||
+ | Tracking results should be analyzed... and the best convenient way is to analyze the tracked data statistically using R. | ||
+ | |||
+ | A tutorial that was given in EMBO cell biology course is on of such. If you are interested, follow the link below: | ||
+ | |||
+ | * [[documents: | ||
+ | |||
+ | ==== IJ Macro and Scripting ==== | ||
+ | |||
+ | If you want to use ParticleTracker silently (not perfectly but) then you could write a javascript that does this. Then this script can be directly executed, or called from your ImageJ macro by | ||
+ | |||
+ | < | ||
+ | jsstr = File.openAsString(" | ||
+ | eval(" | ||
+ | </ | ||
+ | |||
+ | <sxh javascript> | ||
+ | // javascript to be called from macro. Does the particle tracking by particle tracker plugin. | ||
+ | // | ||
+ | // works only with the plugin downloadable from | ||
+ | // http:// | ||
+ | // | ||
+ | // Usage: modify line 7 to 11 to set your parameter. | ||
+ | // this JS could be called from ImageJ macro by: | ||
+ | // jsstr = File.openAsString("< | ||
+ | // | ||
+ | // | ||
+ | // Kota Miura (miura@embl.de), | ||
+ | // lastupdate: 20110825 | ||
+ | rad = 3; | ||
+ | coff = 3; | ||
+ | ptl = 0.10000; | ||
+ | lik = 2 | ||
+ | disp = 10; | ||
+ | |||
+ | importClass(Packages.java.lang.Thread); | ||
+ | importClass(Packages.ij.Macro); | ||
+ | imp = IJ.getImage(); | ||
+ | |||
+ | // set macro options in the current thread | ||
+ | options = " | ||
+ | " link=" + lik + " displacement=" | ||
+ | thread = Thread.currentThread(); | ||
+ | original_name = thread.getName(); | ||
+ | thread.setName(" | ||
+ | Macro.setOptions(Thread.currentThread(), | ||
+ | |||
+ | // run the tracker | ||
+ | pt = IJ.runPlugIn(imp, | ||
+ | pt.transferTrajectoriesToResultTable(); | ||
+ | |||
+ | // try killing the particle tracker results window | ||
+ | frames = WindowManager.getNonImageWindows(); | ||
+ | IJ.log(frames.length); | ||
+ | for (var i = 0; i < frames.length; | ||
+ | IJ.log(frames[i].getTitle()); | ||
+ | if (frames[i].getTitle() == " | ||
+ | } | ||
+ | </ | ||
+ | https:// | ||
+ | |||
+ | You could test this by directly executing the script by | ||
+ | |||
+ | < | ||
+ | jsstr =File.openUrlAsString(" | ||
+ | eval(" | ||
+ | </ |
downloads/particletracker2d.txt · Last modified: 2020/11/26 09:11 by 127.0.0.1