Primary objects and background subtraction

cellprofiler

#1

Hello, I’m still aquiring familiarity with CP.
I would like to identify only nuclei that have a determinated average intensity.
Using the SubtractBackground+ApplyThreshold and then IdentifyPrimAutomatic module is very easy to discard nuclei belove a selected pixel value, but I’m not able to eliminate nuclei that have an intensity obove a chosen pixel value.
Then, could be useful to combine ApplyThreshold and PrimAutomatic modules to keep only the nuclei within a selected range of average intensity?
…And how can I remove out-of-focus nuclei, that appears blurred but nevertheless they have an good nuclear intensity.
I hope my questions are clear, thank a lot.
Bye
Luigi


#2

Luigi…after you have identified the nuclei using the IdentifyPrimAutomatic module, use the MeasureObjectIntensity module on the channel that you want to filter the nuclei by, then use the FilterObjectByMeasurement module. This module lets you set both a lower and upper limit for the object intensity. Read the help file for the module for the details.