Advanced Object Processing


I love identify primary object, but i would like more advanced options such as;

  1. Method for drawing dividing lines as a new module. I would like to specify which image to do this. I have been using cytosol to find primary objects (since my nuclei stain overlaps with my cytosol), but i would like to see how a brightfeild image does to draw dividing lines.

  2. I would like to distinguish multiple objects and then combine them with different options. Is this possible in an easy way?

Thank you in advanced



  1. You may try:

First use ImageMath to combine or other manipulations of cytosol, nuclei and bright field images, then use the resulting ImageAfterMath for IdentifyPrimaryObjects. That way you can test which channel is best for making the dividing lines.


You may try to use cytosol channel for IdentifyPrimaryObjects, then IdentifySecondaryObjects with bright field images.

Or you may try using ilastik as explained here

  1. In general, you can try a combination of FilterObjects, RelateObjects or ReassignObjectNumbers to combine objects in multiple ways.

Hope that helps.


Hey i’m trying to limit my objects.

IdentifyPrimaryObjects has the option

Handling of objects if excessive number of objects identified

I would like this option during my FilterObjects module or a seperate module.

Currently i am identifying all objects from IdentifyPrimaryObjects. I then MeasureObjectSizeShape, and then filter the objects into different classes. I would like to limit the number of cells in each class.

Can i do this?

If not, is there a tutorial on how to start working in the python environment?


You could filter the number of objects by using FilterObjects on the ObjectNumber, but just be warned it won’t be a completely random sampling since objects are ordered based on their locations. AFAICT, there’s no way to randomly subset the objects (in CellProfiler, anyway, you certainly CP-Analyst or other downstream processing programs).

We do have a wiki detailing how to use CP as a python package but it’s currently quite minimal; the wiki articles under the ‘Contributing’ heading go into more detail.