Make calculations across timepoints

Dear CellProfiler,

I have a set of images comprising 5 time points spanning a drug application (so that intensity of a fluorophor varies across time in response to drug), with 3 channels (nuclei, calcium, GAD). Timepoints 1 and 2 are designated “basal” and timepoints 3, 4 and 5 are designated “stimulated”. The objects are tracked through the timecourse to give them a unique ID. What I would like, for each object that I have segmented, is to be able to get the difference in intensity from the average of 1 & 2 (basal) to the average at 3, 4 and 5 (stimulated). Is there any way of doing this easily without having to go into the spreadsheet and try to manipulate the data?

Thanks so much for your time


Sorry for the slow response. To some extent, you can do this. Use Metadata to assign information like “basal” and “stimulated”. It is often easiest if you use LoadData for this since you have total control of your inputs. Since each cycle of CellProfiler only “knows” about itself (except for odd module, like TrackObjects), you will run your analysis completely. Use ExportToDatabase (sqlite is simplest) and then try our other software, CellProfiler Analyst. There are tools to plot histograms, etc that respect metadata there.

Hope that helps!