Describing shape of objects in a 2D+t timelapse


The timelapse attached is a 2D+time image of some objects growing in the horizontal direction (darker than the background).

Analysis goals

I am interested in getting how the shape (aspect ratio) and size of every object changes with time.


My understanding is that I need to use the pixel classification and then track these objects. The pixel classification workflow works perfectly, the main problem comes with tracking. The step of ‘threshold and size filter’ works fine. I skip the ‘division detection step’ because my objects don’t divide, they just change shape.
I think one of the main problems comes from the ‘object count classification’. It is not clear to me what I have to do here. I want to describe the change in shape of all my objects in the image. They are not different to each other. So basically I just put all of them as ‘1 object’ and none of them as ‘false detection’. Even if I put all of them as different objects, things don’t improve.
Once I track using automatic tracking, the main problem I have is that in some cases the algorithm passes the track from a specific object to the neighboring object. I played with the parameters quite a lot and this keeps happening. Often the track in object A, instead of just disappearing at certain frame, goes to another object B in the image.
I also tried ‘tracking with learning’ but the option to change the parameters is grayed out (even though I have installed Gurobi 8.1.1). So this is not an option.

Any help? I am open to using FIJI or Matlab if you think there is a better workflow that I could use there.
Fused_subtracted_cut-1.tif (4.0 MB)

You need to fix the link to the image.

sorry, I hope now it’s solved