Random crash in IdentifyPrimaryObjects module

Hi CP developers,

I am experiencing random crashes when trying to segment DAPI stained nuclei in some images but not others. The traceback error message is listed below. The IdentifyPrimaryObject module works for the first 4 images but crashes on the 5th then it will work for another couple images. Does anyone know what could be causing this issue? I have never seen it before. I am using CP 10997 version.

Traceback (most recent call last):
File “cellprofiler\pipeline.pyc”, line 309, in run
File “cellprofiler\modules\identifyprimaryobjects.pyc”, line 804, in run
File “cellprofiler\objects.pyc”, line 233, in set_unedited_segmented
File “cellprofiler\objects.pyc”, line 504, in check_consistency

I think I found the bug. The IdentifyPrimaryObject module is unstable if you define the size of the smoothing filter to be 0. It works for some images but not all. When the setting is changed to any value above 0 it works with all image cases. I don’t know exactly why this happens but at least there is a workaround.


I gave this a shot with the images you sent, but didn’t produce the error. It may be that I set my IDPrimObjs settings naively, other than setting the smoothing filter to 0. Could you upload your pipeline?