Cellprofiler batch processing to generate individual files

In cellprofiler, when I use the ExportToSpreadsheet module, how do I generate a separate Excel file for each folder when there are multiple folders?

Hi @day0,

You can try using “CreateBatchFiles” module at the end of the pipeline. For more details check below thread,

Hope this helps,



In general, if you want your output to go into different folders, you want to use ExportToSpreadsheet “Output File Location Setting” setting on either “DefaultInputFolder Sub-folder” or “DefaultOutputFolder Sub-folder”; either then allows you to right-click/ctl-click in the box and use a piece of metadata (such as what the input folder was) to separate out your output.

For this to work, though, you need to make sure that whatever factor you want to split the files based on is identified as a piece of metadata in the Metadata module!