Threshold again to identify primary objects?

Hi, I am analyzing beads that have been fluorescently labeled. My step 1 is to load images, then ApplyThreshold, then IdentifyPrimaryObjects. I noticed that identifyPrimaryObjects has a threshold function. So, my question is: what should be the input image for identifyPrimaryObjects - the loaded image or the one obtained from applyThreshold?


Hi John,

The typical workflow is to use the loaded image as input into IdentifyPrimaryObjects.

Some details: IdentifyPrimaryObjects takes an image, thresholds it into foreground/background regions, then finds the objects and outputs them, whereas ApplyThreshold only performs the thresholding, and outputs the thresholded image, i.e, no object finding.

Which module is most appropriate depends on your assay but it sounds like you want the objects (i.e, beads) themselves. So you would use IdentifyPrimaryObjects rather than ApplyThreshold.