Cell Profiler Anaylst Rules

Hi all,

I have been playing around with Cell Profiler Analyst and discovered the “Rules” option within the program. I’ve played with the sample image set and clicked “Train Classifier” to discover the five rules. My question now is can I write my own rules for my own image sets? If so, how? I would just like to know more about the “Rules” function. Thanks!


The Rules are meant as an output only, and there is not a built-in functionality to manually modify/add rules. Please note that Rules here are just fancy filters that are discovered by supervised machine learning. In fact, you can copy the rules from CPAnalyst into a file and have the FilterObjects CellProfiler module read them in to apply the rules (there is a ‘Rules’ setting there). So you can follow this procedure in CellProfiler if you want to try and write a complicated object filter.

But the idea behind the Rules and the machine learning procedure in CPA is that you use this extra step in only the cases in which you cannot divine a robust or complex enough set of measurement filters in a reasonable fashion within CellProfiler (or whatever your main image analysis algorithm is), so you let the ‘machine’ learn based on your intuition and just let the rules fall out.

Hope that helps!