I am new at using CellProfiler and I am trying to quantify green and red fluorescence in the nucleus and cytoplasm of yeast cells. Having read one of the questions and answers in forum, I managed to do a decent outlining of the nucleus and this is working fine I think. However, the outlining of the outer cellular membrane is still a bit problematic, the outlined cell tends to be larger than the cell itself. I am attaching two of my images (green and red channels) and my pipeline. Could you please tell me how I could improve it, so I have a better delimitation of the cell?
Thanks a lot!
Yeast cells_Nucleus and Cytoplasm.cp (22 KB)