Using Identify_Primary_Object to mask well edges


Using Identify_Primary_Object to mask well edges it draws a nearly complete circle around the well edge, then fails to identify it as an object. Is there a way to make that last step and identify the object? This problem is happening on multiple wells.
E025_PipelineTest_170821_V4_Forum.cpproj (110.7 KB)



It’s because your size settings are super strict, which is what is leading to your object not getting recognized (it’s why the circle is pink and not green); if instead of 870-930 I set it to something super permissive like 100-1000 I get the well edge just fine.

(Based on this you may also want to adjust your threshold settings a bit if you need to capture the whole well edge, as it seems like it’s missing a couple of areas at the bottom).


Okay, here’s the completed pipeline, analysis spreadsheet, and image files.

I had to set up three analysis methods to get the well outlined in every case.
The results of these three analyses are then pasted into a spreadsheet and sorted by well_number.
Is there a better way to do this? I wish CellProfiler had IF/THEN.


I’ve definitely wished that too in the past- unfortunately it’d significantly complicate the software under the hood and make it unmanageably complex to maintain. Sorry! I’m glad you found a way to get your data out though.