IdentifyPrimaryObjects identifies too many objects

cellprofiler

#1

Hi,

I am a new user.

I am trying to do nuclear foci with stains of DAPI and Green (for my protein). In the IdentifyPrimaryObjects, my pipeline identifies too many objects in the green channel. I changed Threshold strategy and it does not make any difference.

h2ax-foci-count_1.cpproj (708.2 KB)

I would like to keep the number of objects identifies same as the number of foci i can see .

I am attaching my pipeline.


#2

Hi,

Without images it’s hard to say for sure, but by picking 3 class Otsu with the center class being classified as foreground will ensure a pretty low threshold- for something like an H2AX focus, RobustBackground typically works much better. Good luck!