I have been trying for some time to create a pipeline that identifies H2B-GFP stained cell nuclei, and no matter how I preprocess my pipeline, I cannot get accurate counts. I am much closer than I was a few months ago, but I am really having trouble removing false positives and further narrowing down the accuracy of my analysis pipeline.
I also cannot get Cell Profiler Analyst to launch because creating rules to identify the cells from noise seems like it would be one of the best approaches, but when I load a properties file into CPA, it closes. Not sure if anyone might be able to provide some guidance there too.
I can’t attach the pipeline to this post, so here is a dropbox link to download it: https://www.dropbox.com/s/11zqkekg1heg3mc/TumorColonies_SDK_I7_test11_low_W1_MCF7_ctrl_A.cppipe?dl=0
I have also attached the original cropped image (green) and then the image converted to grey and change in contrast using a log contrast transform from matlab.
Any help on revising the pipeline would be very much appreciated! Thanks so much!