downloads:particletracker2d
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downloads:particletracker2d [2010/11/19 13:37] – kota | downloads:particletracker2d [2020/11/26 09:11] (current) – external edit 127.0.0.1 | ||
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- | ====== Particle Tracker (2D) Extended====== | + | ===== Particle Tracker (2D) Extended===== |
- | ~~NOTOC~~ | + | |
[{{ : | [{{ : | ||
Line 9: | Line 9: | ||
==== History ==== | ==== History ==== | ||
10-11-19 First release\\ \\ | 10-11-19 First release\\ \\ | ||
+ | |||
+ | === recent | ||
+ | {{rss> | ||
+ | |||
=== Source === | === Source === | ||
- | [[https:// | + | [[https:// |
==== Installation ==== | ==== Installation ==== | ||
- | Download [[http:// | + | 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 ==== | ==== Requires ==== | ||
ImageJ ver 1.44h or higher ([[http:// | ImageJ ver 1.44h or higher ([[http:// | ||
==== Description ==== | ==== 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:// | 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:// | ||
- | <quote> | + | |
+ | **As of Nov. 2013, there is a [[http:// | ||
+ | |||
+ | When you use this plugin, please cite: | ||
+ | |||
+ | <blockquote> | ||
**I. F. Sbalzarini and P. Koumoutsakos.**\\ | **I. F. Sbalzarini and P. Koumoutsakos.**\\ | ||
**Feature point tracking and trajectory analysis for video imaging in cell biology.** \\ | **Feature point tracking and trajectory analysis for video imaging in cell biology.** \\ | ||
J. Struct. Biol., 151(2): 182-195, 2005.\\ | J. Struct. Biol., 151(2): 182-195, 2005.\\ | ||
[[http:// | [[http:// | ||
- | </quote>\\ | + | </blockquote>\\ |
==== Work Flow ==== | ==== Work Flow ==== | ||
[{{ : | [{{ : | ||
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* You could export only a specific trajectory. First, visualize trajectories by clicking " | * 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