CP 2.2 not working on Mac


as mentioned in another discussion with Beth, CellProfiler 2.2 does not on any of the machines in house. Here is a list of problems with their traceback:

Problem creating a directory

Traceback (most recent call last):
File “/Applications/CellProfiler22.app/Contents/Resources/lib/python2.7/cellprofiler/gui/pipelinecontroller.py”, line 2246, in on_analyze_images
File “/Applications/CellProfiler22.app/Contents/Resources/lib/python2.7/cellprofiler/gui/pipelinecontroller.py”, line 2258, in do_analyze_images
File “/Applications/CellProfiler22.app/Contents/Resources/lib/python2.7/cellprofiler/gui/preferencesview.py”, line 391, in check_preferences
File “os.pyc”, line 150, in makedirs
File “os.pyc”, line 150, in makedirs
File “os.pyc”, line 150, in makedirs
File “os.pyc”, line 150, in makedirs
File “os.pyc”, line 150, in makedirs
File “os.pyc”, line 150, in makedirs
File “os.pyc”, line 150, in makedirs
File “os.pyc”, line 150, in makedirs
File “os.pyc”, line 157, in makedirs
OSError: [Errno 13] Permission denied: ‘/Volumes/tds/projects’

When sending error report, an error 405 is thrown

Error when trying to run a pipeline

Traceback (most recent call last):
File “/Applications/CellProfiler22.app/Contents/Resources/lib/python2.7/cellprofiler/pipeline.py”, line 1956, in run_image_set
File “/Applications/CellProfiler22.app/Contents/Resources/lib/python2.7/cellprofiler/pipeline.py”, line 2067, in run_module
File “/Applications/CellProfiler22.app/Contents/Resources/lib/python2.7/cellprofiler/modules/saveimages.py”, line 473, in run
File “/Applications/CellProfiler22.app/Contents/Resources/lib/python2.7/cellprofiler/modules/saveimages.py”, line 517, in run_image
File “/Applications/CellProfiler22.app/Contents/Resources/lib/python2.7/cellprofiler/modules/saveimages.py”, line 709, in save_image
File “/Applications/CellProfiler22.app/Contents/Resources/lib/python2.7/cellprofiler/modules/saveimages.py”, line 827, in get_filename
File “/Applications/CellProfiler22.app/Contents/Resources/lib/python2.7/cellprofiler/measurements.py”, line 1111, in apply_metadata
File “/Applications/CellProfiler22.app/Contents/Resources/lib/python2.7/cellprofiler/measurements.py”, line 960, in get_measurement
File “/Applications/CellProfiler22.app/Contents/Resources/lib/python2.7/cellprofiler/utilities/hdf5_dict.py”, line 360, in getitem
File “/Applications/CellProfiler22.app/Contents/Resources/lib/python2.7/cellprofiler/utilities/hdf5_dict.py”, line 364, in getitem

Images were black when displayed with PlateViewer. After changing the Preferences to Log normalised display, the PlateViewer does not display anything anymore. Changing back the Preferences did not revive it.

Both the first and second errors sound like you’re trying to get CellProfiler to write to places it does not have permission to write to- can you try changing your output to a different directory (like say your desktop) and see if those errors still persist?

I’ll try to get into your PlateViewer thing today.


yes after posting I realised indeed that the first error is due to that. But that is not the case for the second one, since I was outputting to the desktop. I’ll have a look again though just make double sure.
I had a discussion with people from AstraZeneca who are evaluating deploying CP in their infrastructures and the issue of the PlateViewer was also of concern to them. Something else came up which I thought would be indeed a great improvement: it would be great to be able to change the names of the modules when you build a pipeline. It is true that sometime you have 5 IdentifyPrimaryObjects and you don’t which refer to which. If one could change the name to IdentifyNuclei and IdentifyGolgi etc it would be much more readable and easier to modify. Shall I make a new topic on the forum?


Marc Bickle, PhD
Head HT-Technology Development Studio
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
D-01307 Dresden

phone +49 351 210 2595
fax +49 351 210 1689
mail bickle@mpi-cbg.de
web: http://www.mpi-cbg.de/facilities/profiles/ht-tds.html

DRESDEN-concept Technology Platform:

The AssertionError you posted is known to pop up if you’re trying to use SaveImages with the “Same folder as image” option but on an image that’s been derived over the course of the pipeline and therefore doesn’t have a natural home- see here for more discussion but it’s on our radar. Are you by any chance doing that in your pipeline?

I doubt that being able to change the displayed names of the modules is likely to happen, but we’ve definitely experienced the difficulty of having too many modules in a pipeline and have thought about different ways we could make it easier to track which modules go with which. We have it tagged as a Feature request in the future of the project; our sorftware team is hard at work on some other improvements right now but hopefully it’s something they can get to in the near-to-medium future.