Track Analysis .jar breaks my Trackmate script

Sample image and/or code

(MW.txt (6.3 KB)).

Background

  • I am working on tracking cell migration with TrackMate and I would like to put together a script to run the analysis. I have minimal experience with coding and have been working on editing the script found at “Scripting TrackMate - ImageJ” (attached).

Analysis goals

In the log output of the script I would like to be able to generate the values calculated using the “Track Analysis” .jar file.

Challenges

The first line of the error in the Fiji console shows:
Exception in thread “Linear track analysis thread 1”

In the Fiji macro window the errors starts with:
UnicodeEncodeError: ‘ascii’ codec can’t encode characters in position 2368-2369: ordinal not in range(128)

  • The overlay tracks are still generated for my original image, but the statistics are not added to the log window. Once I delete that .jar file the script works again. I have also noticed that even when using the TrackMate plugin user interface, when trying to get the Track Analysis outputs I first get a Fiji console error, but if I recalculate the tracks by just going back to that step one more time, I am able to get the results (i.e. confinement ratio, linearity, etc.).

Thank you for all of your help, I appreciate any guidance you may have!

Liam

Hello

It is a problem we get numerous times.

The link to the jar on the TrackMate page gives a faulty version. But we cannot change it because the webpage is readonly for now.

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Critical errors can still be fixed with pull requests to imagej-net-static, see this post:

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Thanks Jan!

I did not know that, and I just pushed a PR to fix the link:

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