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    Help! Why does CellProfiler say it can’t find any valid image sets?

    Beth Cimini

    Defining the input to CellProfiler can be the hardest part of getting your pipeline set up and your analysis underway.  Incoming images are configured in the first 4 modules of CellProfiler – Images, Metadata, NamesAndTypes, and Groups – which offer lots of flexibility. But it’s sometimes confusing what each one does, and it’s not always obvious which ones you need for your experiment.

    If you have mistakes in any of these modules, you may run across the dreaded errors ‘The pipeline did not identify any...

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