Problem to initialize Pipeline

Hi,

I have a problem to initialize my pipeline. The LoadImages module should load two muti-page tiff files, but is never goes that far. Here is the error message:

Failed to initialie pipeline.

Traceback (most recent call last):
File “cellprofiler\gui\pipelinecontroller.pyc”, line 713, in on_analyze_images
File “cellprofiler\pipeline.pyc”, line 1064, in run_with_yield
File “cellprofiler\pipeline.pyc”, line 1033, in group
File “cellprofiler\pipeline.pyc”, line 1321, in get_groupings
File “cellprofiler\modules\loadimages.pyc”, line 2277, in get_groupings
KeyError: Exc_340nm

Any suggestions what to do?

Cheers, Sebi

Hi Sebi,

Could you post your pipeline so we could take a look? Also, it is possible to post the two multi-frame tiffs as well, or are they too big?
-Mark

Hi,

no problem. Meanwhile I figured out a work-around, so one pipeline is NOK (the one producing the error) the other one works, but it is not really clear to me why. The 2 Multi-Page TIFF have both 21 pages (21 Time Frames).

Cheers, Sebi
Ratio340_380_complete_OK.cp (7.53 KB)
Ratio340_380_complete_NOK.cp (7.22 KB)



Hi Sebi,

This issue is indeed a bug, but has since been fixed in our source code and not yet released. It good to hear that your figured out a workaround in the meantime!

Regards,
-Mark

Hi Mark/Sebi

I’m getting the same error

[quote]Traceback (most recent call last):
File “cellprofiler\gui\pipelinecontroller.pyc”, line 713, in on_analyze_images
File “cellprofiler\pipeline.pyc”, line 1064, in run_with_yield
File “cellprofiler\pipeline.pyc”, line 1033, in group
File “cellprofiler\pipeline.pyc”, line 1321, in get_groupings
File “cellprofiler\modules\loadimages.pyc”, line 2278, in get_groupings
KeyError: DNA[/quote]

The pipeline was running fine, and I was tweaking the thresholding in identifyPrimaryObjects, when it stopped working. Restarted the whole system and reverted to old pipeline, problem persisted.
I’m not sure I can see what the workaround is doing though, but selecting ‘group images by metadata’ got the pipeline running again which is good

Cheers,
Paul
Multi_Topography_Multi_Cell_01.cp (9.43 KB)