First, I’d like to say that the cellprofiler seems great and I am very happy that I stumbled across it!
My main interest is to use this software to track cells migrating within a tissue over time, while identifying each cells neighbours at each time point. I hope to be able to use this data to be able to see when cells exchange neighbours and make contact with a new cell.
I have been playing around with the sample data set for object tracking provided on the cellprofiler website, and I noticed that when exporting data to excel (in both the primary objects file and the object relationships file) the image objects are not consistent. For example, when objects 1-6 are tracked for the first three frames, and object 1 leaves the frame, objects 2-6 are now reported as objects 1-5 in the exported excel data. This will be an issue when extending this process to imaging tissue with ~100 cells in frame, with cells entering and exiting every few timepoints.
First, I was wondering if there is a way to ensure that the objects retain their original identity when there are objects entering and exiting the frame at every time point.
Second, if anyone has any suggestions for an efficient process to identify events of neighbour exchange outside of manually looking at the object relationships for each object at every time point and noting if a new contact was made, I would greatly appreciate it!
Thanks for your time,