Problems from running multiple pipelines


Hi, everybody,

I am facing a problem when I tried to run multiple pipelines in a serial manner.

The problem is that when the computer finished each pipeline, a reminder box popped up saying that the output file has already existed and asking if a default output file name could be used. I can not figure out a way to set the name for the output file in each individual pipeline because it seems the output file is not a parameter that is saved in an individual pipeline. So when finishing each pipeline, a ‘yes’ button has to be clicked, prohibiting ‘silently’ running multiple pipelines.

Is there a way to inhibit the reminder and let the computer choose a default file name automatically?

Thank you,



Hi Paradise,

If your pipelines are in the same directory, and apparently they are, then currently you must clicking the dialog. One simple workaround, however, is to place your pipelines in separate directories, and they will output to their respective directories without the offending dialog. Or you can modify the code in Cellprofiler.m, if you use the developer’s version.

I agree that this, and other dialogs can be annoying. We are discussing strategies to minimize user interaction, if so desired.