Hey everyone, I am new to CellProfiler (version 3.1.8) and I have set 2 channels- one as DAPI and the other as Alexa 488 and found the intensities for the cytoplasm (488), which was my secondary object, and the nuclei (DAPI), which was my primary object. I ran everything and it came out normal but I was wondering if there is a way to isolate and analyze the intensity of only the nuclei from the Alexa488 because it stains differently from the DAPI. Open to any ideas!
Welcome to the forum.
Sounds like you are basically there! Once you have your objects you can measure them in what ever channel you want. In your MeasureObjectIntensity module you need both images (DAPI and 488) listed to be measured and then your two objects as well (Cytoplasm and Nuclei). If you do that you’ll be able to find both objects have been measured for each channel.
@lmurphy oh it was that simple! I fixed it and it worked great, thank you so much!