Error in Identify Primary Objects- Index out of range

Hi guys,
I’m getting a “Index out of range” error in Identify Primary Objects that I’ve pasted below… weirdly, it only comes up on the 3rd and 4th time I call IPO- I suspect therefore it may be an issue with the Crop modules just upstream, even though I have “remove empty rows” set to “no”. Project and images are attached, as always your help is much appreciated!

Traceback (most recent call last):
File “cellprofiler\pipeline.pyc”, line 1934, in run_image_set
File “cellprofiler\modules\identifyprimaryobjects.pyc”, line 898, in run
File “cellprofiler\modules\identify.pyc”, line 754, in threshold_image
File “cellprofiler\modules\identify.pyc”, line 872, in get_threshold
File “cellprofiler\cpmath\threshold.pyc”, line 175, in get_threshold
IndexError: index (1024) out of range (0<=index<1023) in dimension 0
TSQ1_CP21Test.cpproj (1.26 MB)

I did some more tracing, and it’s actually coming from the rescale upstream, not the crop- still a bug though. Thanks!

I was able to replicate the bug with your pipeline; I’ll file a report on it. In the meantime, the workaround is either to:

  • Use the un-rescaled image for thresholding, which we recommend anyway.
  • Specify an object for the per-object thresholding in this module, rather than “From image”.

EDIT: Filed as … ssues/1259

This issue was been resolved, and the fix will be in the next release.

Thanks so much!