TrackMate Scripting: Setting Intensity Filters



I too want to write a full modelling script for my routine as has been discussed in this post by @silphe:

Currently I am stuck at the point where I want to implement a different filter, besides the QUALITY filter
that has been shown in your sample script A full example, namely the MEDIAN INTENSITY filter. I tried something similar to the way you implemented the TRACK_DISPLACEMENT filter, by calling

SpotIntensityAnalyzer however requires two arguments - which I don’t know - besides the fact that I am not entirely sure if I am actually on the right track with this approach.

Furthermore, the above mentioned discussion about how to export the .csv files stopped somewhere along the way, but i guess it should be possible by manually calling spot.getFeature as you have done to the end of Export spot, edge and track numerical features after tracking

Thanks for the help


Dear @Andome,

would you mind reverting your latest edit to your post (s.t. people find the original question) and elaborate how you have solved your issue? That way, others who might run into a similar issue can learn from your solution.



Hi @Andome,

I agree with @stelfrich, it would be helpful for others having the same problem in the future if you could quickly state how you solved the issue.
I reverted your last edit so others can still see what it was about.