I made a few previous posts, but this captures the essence of what I need to find out. Is there a way to specify the parameters of a pipeline using command line? For example, if I have a pipeline that contains the ApplyThreshold module, can I specify that I want the Manual Threshold value to be .25 using a command in command line? If so, then I could change the value at each iteration in a system call, and thus have many iterations of CellProfiler pipelines without actually creating new pipelines manually. Thanks!
I think I’ve addressed this post here: Running a Pipeline Iteratively