Subfolder export with lsm files

Dear CellProfiler community,

I have a pipeline I’ve built based on a couple of the example pipelines available on the site. I have 4 folders pertaining to varying conditions, each with 5 lsm files made up of 54 images of a time course with 3 channels. I’m tracking these cells for nuclear translocations. Firstly, I had a pipeline that could save an image (SaveImages) and export to Excel (ExportToSpreadsheet) that worked fine if I did it as a single lsm file at a time.

I’ve since expanded to copy the example available named “Object Tracking and Metadata Management” that has 3 specimens output in separate folders containing the images desired and Excel spreadsheets. I’ve copied the aspects of this pipeline as closely as possible. So far, the subfolders are made and my images are saved, but no Excel spreadsheets are saved based on the lsm files being tracked. The time it takes for the pipeline to execute correlates with the files being tracked, but they simply aren’t being saved.

The differences I have to the Object Tracking example:

  1. For the metadata extraction method I have to use “Extract from image file headers” as opposed to “Extract from file/folder names” otherwise I get an error saying “Sorry, your pipeline doesn’t produce any valid image sets as currently configured. Check your Input module settings…”
  2. In ExportToSpreadsheet I have additional ‘Data to export’ with secondary and tertiary objects, not just primary.

Any help here would be hugely appreciated! I’ve been fumbling with it for days now.

Could you post your current pipeline, plus a sample LSM image, so we can take a look?
P.S. You might need to use Dropbox or some such; our forum attachments don’t seem to be working right this moment…