I am trying to create a pipeline for many plates using cellprofiler4.0. The planned solution is:
1, create a loadfile.csv containing all the images that need to be processed, with ‘Metadata_Plate’, ‘Metadata_Well’, ‘Metadata_Field’, and imagename and imagepath metadata for all channels.
2. Using LoadData module to load the loadata.csv.
3. create the image analysis pipelines.
4.using ExportToSpreadsheet module to save results. I set Output file location as /mypath/output/Plate, the Plate is added using ctrl+rightmouse and select metadata from the list.
5. Using the CreateBatchFiles to create Batch_data.h5 file.
6. Run the pipeline using cellprofiler -p Batch_data.h5 -c -r
So the expected result would be each plate result is saving in a separate folder. However, I only got a single folder, named as \g<Plate>, and it looks like the plate value is not passed to the folder name setting.
Is there anything wrong in this setting? thank you very much.