I am having trouble counting the foci of cells stained with cy3 and dap. I am trying to count the number of foci in the nuclei of each cell and the cytoplasm of each cell. I am trying to get a count of total specks per cell but also specifically just the nuclei and just the cytoplasm. I tried to base my pipeline off of the speckle example using similar modules: identify primary objects, enhance/ suppress features, mask image, identify primary objects, measure object intensity, measure object intensity, relate objects, export to spreadsheet.
The foci are not being quantified properly and I do not know what else I should add to the pipeline in order to get an accurate count. any help is appreciated! thanks