Excluding non-nuclear Foci




I have image files, which have 2 channels (nuclear: Blue and protein: Green). I want count foci and measure intensity of only the Green inside Blue.

What module I should use to filter? I have looked at examples and the speckle count pipeline, but it is not entirely clear to me.

Thanks in advance.


The module that should help you do that is “RelateObjects”. After you segment Blue and Green channels you can set objects in the Blue channel as Parent and objects in the Green channel as Child. I am assuming you are measuring intensities of the Green by using “MeasureObjectIntensity” module. In the produced spreadsheet you should find the Green channel objects linked to the Blue channel objects.
Best, VC