Running a pipeline

When I set up a pipeline it works in the test mode but then won’t run when I do the actual analysis. The bar at the bottom just says ‘processing: 0 out of 2 images completed’ and stays like that indefinitely.

Can you post the pipeline, plus a sample image, so we can test things out? Also, are you using Windows or Mac?

I’ve got it working now when I use a computer that has Windows 7. It still won’t work with Windows 8 except in Test mode. However the problem in Windows7 is that it crashes after doing a few images.
I have also run it using the very old version of CellProfiler on my ancient computer and that works but is obviously very slow.

Also, is there a way of listing the filename in the final spreadsheet?

I attach the pipeline.
spheroid2.cpproj (74.4 KB)

Hi Frances,
Could you post a couple of sample images as well, for testing?

Picture attached

Hmm, I seemed to have no problem in running it under Windows 7 (my own PC) or Windows 8.1 (using a virtual machine; see screenshot).

What error does running under Windows 7 produce?

I’ll check Windows 7 tomorrow morning. In the meantime I have attached a screenshot of what happens when I use windows 8. The program gets to that stage and then stays like that until I stop it.

It appears that you are using version 2.1.0, at least on the 8.1 machine. Perhaps you might try upgrading to 2.1.1 (which is what I used for this test)?


I’ve attached a couple of screenshots. I uninstalled the older version of Cellprofiler from the Windows 8 computer and installed the latest version but the program still wouldn’t run with.
The windows 7 computer gives a different problem in that it crashes all the time and I have a screenshot of that. I currently just run a few images at a time in the hope that I can get some data exported before it crashes but this is obviously not a solution.


I’m wondering if it could be some sort of network communication issue - for instance your firewall is blocking it. If you have the correct privileges, the first time you run CellProfiler 2.1 or later, Windows should display a dialog asking whether to allow CellProfiler to have network access. This is needed for CellProfiler to communicate with its workers in analysis mode. You can check to see if CellProfiler has this access by doing the following:

  • open the control panel
  • choose Windows Firewall
  • click on “Advanced Settings” to bring up “Windows Firewall with Advanced Security”
  • select “Inbound Rules” on the list on the left
  • look on the Inbound Rules list for CellProfiler - it should have a green checkmark to the left.

I would first try and see if you can analyze the example pipeline from the welcome screen - that would help us figure out whether it was something specific to your pipeline or a more general problem.