TrackMate FAQ

Revision as of 01:56, 19 June 2017 by JeanYvesTinevez (talk | contribs) (TrackMate FAQ: customized track look.)

TrackMate FAQ.

This list of frequently asked questions is compiled from several questions we have seen several times on the ImageJ forum. It will be updated as questions appear there.


Exporting TrakMate overlay to a movie.

In TrackMate after completing tracking, is there any way to export/save a movie with all tracks and moving spots (exactly as it appears after using the TrackMate)?


If you keep clicking on the Next button on the GUI, you will reach the last panel of the GUI, which collects miscellaneous actions.

One of them is called Capture TrackMate overlay and does what you need. It generates a RGB stack with the tracks burned-in. After that you have to export the stack to AVI and you are done.

Careful: the frame capture is simple and brutal. If you have something that passes over the TrackMate viewer while the capture is going on, it will be captured in the final movie.


Customizing the look of tracks during movie export.

I am aware of Capture TrackMate overlay function but it only provides the final picture of the track(s) overlayed on the moving particle. I'm interested in showing that the tracks are (or a single track) being formed as the particles move.


The overlay capture abides to the display settings you set in the Display Settings GUI panel. By changing the Track display mode' here, you can get what you need. For instance choosing the Show local tracks, backward will generate a "dragon tail" aspect for the tracks in the movie.



Various java.lang.NoClassDefFoundErrors upon execution.

These errors may popup when you try to launch TrackMate, or plot features. A stack trace will show in the console and the second line will resemble this:

Exception in thread "TrackMate plot spot features thread" java.lang.NoClassDefFoundError: 
com/itextpdf/text/DocumentException
	at fiji.plugin.trackmate.features.SpotFeatureGrapher.render(SpotFeatureGrapher.java:115)
	at fiji.plugin.trackmate.gui.GrapherPanel.plotSpotFeatures(GrapherPanel.java:189)
	at fiji.plugin.trackmate.gui.GrapherPanel.access$100(GrapherPanel.java 
...

This kind of error is caused when a Java class is missing in your installation. In most cases, this happens because your Fiji installation did not update properly. Possible solutions are

  • Update Fiji.
  • Check if you have the Jave8 update site in the Fiji Updater
  • Finally, if nothing works, rather than digging in your Fiji installation in details, just install Java 8 and re-download a fresh Fiji application.