TrackMate statistics: speed calculation and track length

trackmate
Tags: #<Tag:0x00007fb8833b18c8>

#1

Hello,

I have been using TrackMate to follow the path of rats in a behavioural task. The tracking works great, however, I have some questions regarding the TrackMate statistics:

  1. With which parameters is the track speed calculated?
  2. Which units are used for the parameters? Are there standard units or does TrackMate get them from another source (e.g. general ImageJ settings)?
  3. Is there a possibility to determine the distance/track length (not the displacement)?

Thanks for the help,

Wiebke


#2

Hello @Wiebke


#3

Update: I put the link to the jar and code of the track analysis module on the TrackMate page for extensions:


#4

Hello @tinevez

Thank you very much for your help.
The traveled distance is an important parameter I needed for a proper analyses of the experiment; the extension is thus appreciated a lot.

Best,
Wiebke


#5

Hello,

I am having a problem with this file, when i install it and restart fiji, fiji no longer loads. I have to reinstall fiji but everytime I try to install the jar file it stops fiji from opening.

cheers

heather


#6

Hi @saskiSwift

What is the error message in the log?


#7

Hi,
There is no log i click to open fiji and the blue symbol comes up and then disappears and thats it.
I have reinstalled and then updated image J, and restarted, it told me to manage my update sites and add Java, which I did and now I am having the exact same problem.
thanks


#8

This looks like a Java problem on your computer. I would suggest the following:

  • Make sure you have Java 8 64-bit installed. REALLY make sure.
  • Reinstall Fiji and make sure the Java-8 update site is selected.

#9

Hi
thanks for your advice, so i have made sure Java is up to date. I have reinstalled Fiji and selected Java-8 update site. when I then restart Fiji I get the blue icon and then the program doesn’t load.

so I have reinstalled Fiji and tried trackmate with the extension (without selecting the Java-8 update site) and get this error, but is this because I need the Java-8 updates?

[ERROR] Could not instantiate fiji.plugin.trackmate.features.edge.LinearTrackEdgeStatistics
org.scijava.InstantiableException: Class not found: fiji.plugin.trackmate.features.edge.LinearTrackEdgeStatistics
	at org.scijava.plugin.PluginInfo.loadClass(PluginInfo.java:285)
	at org.scijava.plugin.PluginInfo.createInstance(PluginInfo.java:297)
	at fiji.plugin.trackmate.providers.AbstractProvider.registerModules(AbstractProvider.java:68)
	at fiji.plugin.trackmate.providers.AbstractProvider.<init>(AbstractProvider.java:25)
	at fiji.plugin.trackmate.providers.EdgeAnalyzerProvider.<init>(EdgeAnalyzerProvider.java:13)
	at fiji.plugin.trackmate.gui.TrackMateGUIController.createProviders(TrackMateGUIController.java:494)
	at fiji.plugin.trackmate.gui.TrackMateGUIController.<init>(TrackMateGUIController.java:257)
	at fiji.plugin.trackmate.TrackMatePlugIn_.run(TrackMatePlugIn_.java:67)
	at ij.IJ.runUserPlugIn(IJ.java:221)
	at ij.IJ.runPlugIn(IJ.java:185)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:662)
[ERROR] Could not instantiate fiji.plugin.trackmate.features.track.LinearTrackDescriptor
org.scijava.InstantiableException: Class not found: fiji.plugin.trackmate.features.track.LinearTrackDescriptor
	at org.scijava.plugin.PluginInfo.loadClass(PluginInfo.java:285)
	at org.scijava.plugin.PluginInfo.createInstance(PluginInfo.java:297)
	at fiji.plugin.trackmate.providers.AbstractProvider.registerModules(AbstractProvider.java:68)
	at fiji.plugin.trackmate.providers.AbstractProvider.<init>(AbstractProvider.java:25)
	at fiji.plugin.trackmate.providers.TrackAnalyzerProvider.<init>(TrackAnalyzerProvider.java:17)
	at fiji.plugin.trackmate.gui.TrackMateGUIController.createProviders(TrackMateGUIController.java:495)
	at fiji.plugin.trackmate.gui.TrackMateGUIController.<init>(TrackMateGUIController.java:257)
	at fiji.plugin.trackmate.TrackMatePlugIn_.run(TrackMatePlugIn_.java:67)
	at ij.IJ.runUserPlugIn(IJ.java:221)
	at ij.IJ.runPlugIn(IJ.java:185)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:662)

#10

I have fixed the problem, thank you for your help


#11

Good!
Can you tell us what was the problem and solution?


#12

I guess by re-downloading Fiji (with bundled Java 8). Quoting @saskiSwift’s response from a different thread: