Filter by Intensity

cp3
filterintensity

#1

Hi CP team,

I’ve been reading previous posts and also the help section (?) to understand how the filter object works. I’m interested in filtering by intensity but I am a bit confused and wondering if you can explain a bit more or have an example to illustrate?

I want to use this in my co-culture imaging assay to eliminate the false positive stained cells. (The CTRL are on either side of the plates i.e col 2 & 23 in a 384well plate) A draft of my pipeline is as below and it would be great if you can comment on it and if I should include any other steps?

-ColorToGray
-Morph
-MaskImage
-IdentifyPrimaryObjects
-ShrinkToObjectCenter
-IdentifySecondaryObjects
-MeasureObjectIntensity
-MeasureObjectSizeShape
-MeasureTexture
-MeasureGranularity
-FilterObjects
-ExporttoExpreadsheet

Do I also need to have another pipeline setup to calculate my CTRL intensity first? or can I have them together in one & how?

Many thanks,
Shu-Oi


#2

Hi,

Filtered objects don’t retain their “parents” measurements (aka if you measure the Size/Shape of “Nuclei” and then filter to “GFPPosNuclei”, “GFPPosNuclei” will NOT have any Size/Shape measurements associated), so I would move FilterObjects up to right after MeasureObjectIntensity; if you need intensity measurements of the filtered objects, you can then add a second MeasureObjectIntensity after the filtration step. Other than that it seems reasonable!