I am trying to find out how to correctly setup the pipeline and export it to database. It seems that CP does not correctly relate H2AX spots to their nuclei in my setting. If I test the pipeline it looks OK - there are around 2-3 foci per nucleus (~100 nuclei and ~250 H2AX foci per image) but after analysis in CPA - it shows around 150-200 foci per nucleus. The total number of H2AX per well as calculated from several images per well seems to be correct. In export to database module it shows warning that “H2AX_spotsAll is not in 1:1 relationship with other objects …”… but I don´t know how to set it differently or if it causes the problem I am describing.
See the images and the pipeline for possible wrong setup.
Eventually, do you have by chance a model pipeline (which I can adapt to the sizes and intensities of my images) that is designed to count how many H2AX spots per nucleus exist ? I am comparing numbers in individual wells in 96 well plate.
Thank you very much.
HF_H2AX_re.cpproj (657 KB)