I have never used CellProfiler before, but I need to create a pipeline to automate my analysis.
Here is what I have:
- a 3D timelapse of immune cell infiltration into spheroids which I have max projected to create a 2D timelapse
Here is what I want to do:
- I want to count the immune cells infiltrating my spheroids over time. In each 2D timelapse there are multiple spheroids in an image and there are immune cells evenly distributed throughout the matrix which with time infiltrate the spheroids. So I need the end readout to be: there are x number of immune cells (or total area of immune cells) in spheroid 1 in timelapse 1 at timepoint 1, 2, 3, etc. and so on for all of the spheroids in all of my timelapses.
So far my pipeline goes as follows:
ID primary object (spheroid)
ID primary object (immune cells)
Relate objects (parent objects are spheroids and children objects are immune cells)
Now for the questions:
- Is cellprofiler unable to process timelapses as a unit? Because I’ve had to load my movies timepoint by timepoint
- Because each individual timepoint of the same movie is processed separately, when CP segments my spheroids and labels them in each image spheroid 1 at timepoint 1 may not be the same spheroid as spheroid 1 at timepoint 2 and I need continuity for me to record the number of immune cells within the same spheroid over time. So I assume that in order to keep the spheroids labelled the same from one timepoint to the next I need to track them (even though they aren’t moving tracking would tell CP that spheroid 1 in one image is still the same spheroid at a different timepoint of the same movie). How do I track my spheroids? Or if there is an alternative solution to this problem.
Thank you so much for your help!