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.
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.