I am a graduate student doing yeast high-content screening in collaboration with the labs of Brenda Andrews and Charlie Boone. We have been using both CP1 and CP2 to identify images of yeast cells, where our goal is to identify mutants with abnormal DNA damage foci, as well as abnormally formed nuclei.
I have a problem that I need your help with. We have performed a large number of screens using CP version 1 (identifying DNA damage foci), and are now performing screens of those same images using CP2 (identifying abnormal nuclei). I would like to establish a correspondence between the cells identified in our CP1 screens with those in our CP2 screens, to see if there is any interaction between the two phenotypes. Both the CP1 and CP2 pipelines used the IdentifyPrimaryAutomatic module to segment and identify cells. We tried running the attached CP2 pipeline on a test image, and then compared the object.CSV file to one produced from the CP1 pipeline for the same image, but the cell locations did not match. By this I mean the object locations (X,Y) do not seem to match.
- 2011_08_22_ver10415_IPANuclei_ISACells_IPACellsStringent_Relate_SaveImages.cp (15.9 KB)
- 2011_05_03_ver5811_IPANuclei_ISACells_SaveImages.mat (3.52 KB)
- cp1_version_5811_Object.csv (13.9 KB)
cp2_version_10415_Object.csv (20.1 KB)
What I’d like to do is find out how to map (X,Y) coordinates for CP1 IdentifyPrimaryAutomatic into (X,Y) coordinates for CP2 IdentifyPrimaryAutomatic. Could you suggest how I might do this? I would like to avoid having to re-screen all our data using CP2 if at all possible, as we are trying to wrap this project up.
Thanks in advance for any help you can provide. Please let me know if you need any more information,