Dear Team,

I am wondering whether it is possible to create a “loop” for the parameters in a CellProfiler Pipeline.

Suppose I have the following pipeline:

LoadImages

IdentifyPrimAutomatic

IdentifySecondary

SmoothOrEnhance (median filter)

I want to change three parameters: the Threshold correction factor for the primary and secondary objects, and the size of the median filter. Since I’m not sure which values will work best, I want to test all permutations of the three parameters, with Threshold correction factor going up in increments of .25 and the median filter size going up in increments of 1. However, I cannot find a way to do this in an automatic way - I must run a separate pipeline for each permutation of the parameters.

Since I am doing tests which have a large number of permutations of parameter values, I would appreciate your assistance in helping me find an automated way to change the parameters of a pipeline. Thanks for your help,

Richard