Tracking the area of non-circular objects over time

Hi Everybody,
This dataset is biting me in the a$$ for some time, hopfully this great community will provide insights.
I’m looking for a holisitic solution for this dataset, ideally with fiji alone.

Thanks to the helpers!

Sample image and/or code

run("Duplicate...", "duplicate");
run("Invert", "stack");
setAutoThreshold("Default dark");
//setThreshold(129, 255);
setOption("BlackBackground", true);
run("Convert to Mask", "method=Default background=Dark black");
run("Fill Holes", "stack");
run("Analyze Particles...", "display clear summarize add in_situ stack");


  • What is the image about?

This is a time series of ice crystals in grayscale RGB.
The file was then segmented with ilastik 1.3.3, pixel classification workflow to difine the crystals.
The segmentation result was exported to further analysis with fiji as .tif (filename: segm.).
What you see is the thresholded images with their detected ROIs of each image (on top of each other).

Analysis goals

  • What information are you interested in getting from this image?
    What I’m trying to achieve is the change of particle area over time.


  • What stops you from proceeding?
    fiji doesn’t do it automatically upon analayze particles.

  • What have you tried already?
    Ilastik 1.3.3 - I’m aware of the object calssification workflow, but I was asked to provide a simple macro, if possible.

  • Have you found any related forum topics?
    No, just trackmate,and I haven’t seen the paramaters I need over there.

segm.tif (2.1 MB) Braslavsky_recrystallization_test2020.tif (6.4 MB)

Hello Daniel,

I have exactly the same issue as you. Have you managed to track these crystals? Either with fiji or ilastik? I have tried both but I don’t get good results. It would be great if you could share some tips on this.


1 Like

I managed to do it only once, with Icy. Can’t reproduce it unfortunately. We can discuss further if you’d like to solve it together.

I have managed to do it with ilastik! thanks though

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Hi @Daniel_Waiger , Hi @Iago_Lopez_Grobas ,

Modifying this script you would be able to track ROIs in the roiManager. @oburri is working on it so we can reopen tracks and correct them if necessary within Trackmate interface.




Thanks, @romainGuiet,

I’ll definitely try it! Once I have the result I’ll post again with my conclusions.


Actually, I should have thought of it myself.
It totally skipped my mind.

Thanks for the eye opening feedback!