Help Series

Help! I want to use CellProfiler Analyst but I ran my pipeline with ExportToSpreadsheet!

David R. Stirling

We’ve all done this before – CellProfiler Analyst needs a database file, but your CellProfiler pipeline that took days to run was set up to export spreadsheets. To make matters worse, you also need a .properties file explaining what to do with that database. Fortunately, you don’t need to re-run the entire experiment to get your data into CellProfiler Analyst. This blog post will cover how to convert a spreadsheet into a database and make a usable .properties file with which to load it into CellProfiler Analyst.

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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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Help! What are these three different modules to identify objects?

Beth Cimini

It can be confusing when you’re trying to set up your first pipeline to figure out which modules to use to generate your objects!  A helpful way to understand the difference between Identifying Primary, Secondary, and Tertiary objects:

  • Primary objects are segmented independently from any other object you’ve designated (like segmenting nuclei from your DAPI channel).
  • Secondary objects are created around a primary object, and so they usually need two pieces of information – a primary...
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