I am working with CellProfiler for the first time and attempting to identify cells on filters.
I am having some trouble either recognizing all or atleast most of the cells while excluding the filter pores. I am able to recognize cells in some pictures but unfortunately not in all. Since I have quite a few images it would be nice to just have to quickly check the results and not have to edit most of the identified cells.
What seems to be a problem so far is that cells and filter pores are being recognizes as one objects and later being discarded due to the dark pore, but I am not sure that is the actual problem.
I have attached my pipeline and some images. I hope some images show that the recognition actually works and others show the difficulties.
Thanks for helping
image_analysis_15_micron_FOV.cpproj (721.4 KB)