See the docs http://cytominer-database.readthedocs.io/en/latest/reference/ingest.html
which documents the expected structure for the CSV files
I rearranged your files
ingest_config.ini by deleting the line
object = analysis_Per_objects_ER.csv
because that is actually just the CSV file for the Cells compartment
and then ran
cytominer-database ingest --no-munge -c plate_a/ingest_config.ini plate_a/ sqlite:///plate_a.sqlite
This gives me a file
plate_a.sqlite with an image table with 753 rows and an object table with 66295 rows.
Although this works, I’d recommend a few changes to the way you are creating the CSV files in ExportToSpreadsheet
First do this so that each object (e.g. Cell, Nuclei, etc.) has a separate CSV file (not sure whether this is already the case for you)
Combine these object measurements with those of the previous object?:No
Add a prefix to file names?:No
so that the CSV files are named e.g.