2D+t (3D+t) tracking of nuclei and spot counting within nuclei feasible in cell profiler


after looking through the webpages I am still not sure wether this is feasible: i have timelapse images and want to track nuclei and the number of spots/speckles in those identified nuclei over time (and their descriptors intensity, shape; etc), starting in 2D but ideally in 3D.
ideally then track the tiny spots within the nuclei…
before I download and install yet another software(was using icy before) is this feasible?
if yes it would be great to be able to use also CP analyst (we have tons of movies)

Any experts in France (paris region or Toulouse) that I could bug??


You can definitely track cells and their speckles in 2D but not 3D unfortunately at this time.

CP Analyst can do its supervised machine learning (aka phenotype classification) on 2D slices only. It might get a bit tricky to do the book keeping but fundamentally you can process each slice individually in CPA and merge with metrics from CellProfiler.

I’m not aware of a user friendly, robust alternative that can process 3D+ time.

There’s TrackMate in Fiji otherwise there are commercial solutions like Arivis Vision4D.

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OK I’ll give it a try for 2D + t (and try the machine learning on the side). I like the possibility of looking at the data with CP Analyst as enables me to delay llearning matlab :slight_smile: and still get my data out in a usable format.
I guess 3D would be more a t by t and linking it post-processing.
one software to rule them all…

thanks! I contacted the man him self (Jean Yves), luckily I am in Paris to look at this with MaMut et TrackMate.

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