IHC staining help!


I am a graduate student that is new to Cell Profiler and having a hard time setting up a module. I am working with some tissue microarrays that have been stained with NucBlue and a aptamer attached to Alexafloursuent 546. Imaging was done using DAPI and RFP channels. The NucBlue is only used for focusing under the microscope but what I’m really trying to do is set up a module that is good at finding out which tissues in my TMA’s are specific for this aptamer/AF546.

I have been trying different things but none of them seem to give me good data. I have tried intensity and object measurements but it doesn’t seem to help! Some of the tissue staining is highly saturated and others aren’t.

I’m really needing some help setting up a module that will identify which tissues in the array have the most aptamer staining and are most intense. Please help!!!


Hi Addilynn,

If you could post a few sample images plus the pipeline you have thus far, we can take a look. Also, please describe what readout you are looking for, i.e, what quantitative value represents the result of interest.