I am calculating fluorescent intensity of labeled beads. I am using CellProfiler to ApplyThreshold, IdentifyPrimaryObjects (beads), MeasureImageIntensity, and MeasureObjectIntensity, then export the data for both the beads and the image. I have attached the pipeline and a sample of the values I get.
For the image data, I do not understand what the columns total_intensity for beads and threshold report, and why are the values so different. And, also, the final threshold values are so low - I don’t know what that means.
For the bead data, the intensity_integrated for beads is a whole number whereas the intensity_integrated for threshold is a fraction. Are these reporting similar things?
Is my pipeline correct? In the end, I want to be able to get the intensity values of beads across images, also get an integrated (total) intensity value for each image.
I will appreciate any help.
particles.cp (8.53 KB)