IdentifyPrimaryObjects problem: python error or CP error?

I am running r10996 on a Windows x64, 10 GB RAM.

During my IdentifyPrimaryObjects step, I check the ‘Discard objects touching the border of the image’ box. Running my pipeline (so far only includes LoadImages, ApplyThreshold, RescaleIntensity and IdentifyPrimaryObjects) causes this error:

Traceback (most recent call last): File "cellprofiler\pipeline.pyc", line 309, in run File "cellprofiler\modules\identifyprimaryobjects.pyc", line 722, in run File "cellprofiler\modules\identifyprimaryobjects.pyc", line 1118, in filter_on_border File "scipy\sparse\coo.pyc", line 177, in __init__ File "scipy\sparse\coo.pyc", line 213, in _check ValueError: negative row index found

If I uncheck that box, IdentifyPrimaryObjects will continue until it hits this error:

Traceback (most recent call last): File "cellprofiler\pipeline.pyc", line 309, in run File "cellprofiler\modules\identifyprimaryobjects.pyc", line 732, in run File "cellprofiler\cpmath\cpmorphology.pyc", line 427, in relabel IndexError: index -850 out of bounds 0<=index<31839

I’m uploading my pipeline FYI. I don’t know how to check my version of python, the version I have installed is (I believe) whatever was bundled with the CP installation package.

Thanks in advance,
DualChannelHypertrophy.cp (5.81 KB)

Hi Jason,

Can you upload your image too? This does sound like a bug.


Sure thing. My image is too large to be uploaded here, but I have it hosted here: (66 MB)


Hi Jason,

We fixed that bug in revision 11047; it happens when you generate more than 32K worth of objects, which I don’t think you intend to do anyway! I think it would be best if you downsample your image (you can do this in CP and save off the result, or simply use photoshop or imageJ to do so, then run the pipeline I’ve attached. I’ve also uploaded a downsampled version of your image so you can reproduce my result.


DualChannelHypertrophy.cp (4.87 KB)

Hi Kate,

Thanks for looking into this for me. I’m having 2 issues:

  • I can’t seem to download the downsampled image you uploaded (no hyperlink)
  • When I load your pipeline into the Python CP 2.0 (r10977), I get a dialog box of errors for each module in your pipeline.

Any thoughts on what might be causing this? When I load my original pipeline, I don’t get these errors.

Thanks again for your help,

Apologies, the correct formats are attached now.

DualChannelHypertrophy.cp (4.7 KB)