I just made my first steps with CP3 and have now devised a very robust pipeline which we’re going to use a lot in the near future. Next, i am going to write an R-Script that extracts the values from the output spreadsheets of my pipeline and performs some statistical analyses (+plotting) on them. Ideally, the output would be looped through such that it all runs automatically from the point of selecting the pictures of interest. Is there a way to a) call a cellprofiler pipeline from within R or b) forward the output from within cellprofiler and execute a given Script?
Many thanks in advance!
With kind regards,