Tracking changes in size of individual particles

Hello all,

I am a new Fiji user and I would like some help to improve the following methods after chatting with @VolkerH.

I am trying to monitor how single cells increase in size over time. To do so, I took time-lapse mic photos with bright-field. I now have to analyse hyperstacks in Fiji.

My (very simple) cell-by-cell method is the following:

  • identify a cell to analyse (among the many) playing the time-loop in Fiji
  • draw a square around the square
  • check the specific time-frame of interest (in this example from 1 to 37)
  • play the following script:
run("Set Scale...", "distance=432 known=150 pixel=1 unit=um global");
makeRectangle(584, 727, 56, 54);
run("Duplicate...", "duplicate channels=1-3 frames=1-5");
run("Flatten", "stack");
run("Enhance Contrast...", "saturated=0.3");
run("Subtract Background...", "rolling=100 light separate"); 
run("Analyze Particles...", "size=10-400 circularity=0.2-1.00 show=[Overlay Masks] exclude include summarize in_situ stack");

(Short) example of my time-lapse images attached.

Thanks in advanced

ExampleTimeLapse-3.tif (5.6 MB)


Have you ever considered using TrackMate to do this analysis? In the examples listed… they even say " TrackMate can also be used for basic track analysis. …estimated diameter of a C.elegans cell as it divides over time."

Perhaps it’s worth taking a look? Then at least you are dealing with a more automated workflow…