Works in Single Mode but not Batch Mode


Any help in finalising this pathway would be much appreciated.

I Have made some further progress on the pathway thanks to your posted batch mode setup David. Thank you.

Cellprofiler BATCH MODE FIRST ITERATION AXION PBMC 010915.cpproj (912 KB)

Getting stuck on the pathway when I run it in batch mode but not when I run it in single three set image mode.

This is the error message I get when I run this in batch mode:

Traceback (most recent call last):
File “cellprofiler\pipeline.pyc”, line 1934, in run_image_set
File “cellprofiler\modules\identifysecondaryobjects.pyc”, line 704, in run
File “cellprofiler\objects.pyc”, line 636, in add_objects
AssertionError: The object, GREEN_NUCLEI_AND_CYTOPLASM_CP, is already in the object set

Is it an error or is it my naming system?

Suspect it has to do with the naming of the files and/or the objects in the pathway but not sure why it only comes up when I try to run in batch mode.



Hi Casey,

OK, I have finally had time, and found a couple issues.
(1) Your Metadata module was not set up properly. If you are extracting metadata from filenames/folders, you should always click the little magnifying glass icon to inspect what text is being extracted. In your case, it was none. I have made some guesses at what you would like to extract, but you may want to check the names I assigned at the very least. See the attached pipeline.
(2) ExportToSpreadsheet is complaining, and I am pretty sure it’s because of underscores in some measurement names. Underscores are usually ok to use in naming objects or measurements (and certainly preferable to spaces or other ‘odd’ characters!), but they can also cause complications. Our measurement naming scheme is parsed by underscores, so that when a module like ExportToSpreadsheet is trying to be helpful and allow you to exclude measurements, it parses out the measurement names by underscores. Unfortunately, I think it is a little confused by your underscores. So, I suggest you change all of your underscores and capital letter names to upper and lower case concatenated names instead. As a first pass, you could just export ALL measurements to make sure #1 above works. And then try shorter names with say, 1 or 2 underscores until the warning goes away.

Hope that helps!
DLpipe.cppipe (37.8 KB)