Hi all! I’m new to CellProfiler analyst so apologies if this has been asked before.
We’re currently trying to implement the Cell Painting assay in our lab. I took images with a Perkin Elmer Opera Phenix and exported the images for further analysis with the published pipelines for QC and illumination correction.
Following the protocol, after running the QC of the images, the data is loaded into CPA to generate the appropriate gates to select in-focus images as described 2011 Bray workflow. It’s at this stage where i encounter the following problems:
1. Fetch images error:
When i try to load the images into the Image Gallery the following error appears:
An error occurred in the program: DBException: ERROR: Database query failed for connection "MainThread" and failed to reconnect Query was: "SELECT * FROM None LIMIT 1" First exception was: no such table: None Second exception was: ERROR: Database query failed for connection "MainThread" Query was: "SELECT * FROM None LIMIT 1" Exception was: no such table: None
My first thought is this has something to do with the MySQL database generated by the QC pipeline. Because i don’t have a dedicated MySQL database for my experiments, i set up the MySQL/CSV option in the QC pipeline generating a .db file (sqlite type).
2. Plate viewer error:
This one is probably the easiest to address and the error message is pretty self-explanatory:
AssertionError: Well "r01c01" did not match well naming format "A01"
The Phenix names the images in the following way: r08c04f15p01-ch5sk1fk1fl1.tiff, where rXX and cXX are the row and column for a particular well (e.g. row 08, column 04). Because CPA expects the AXX format it’s not loading my images.
i’ve been having a look at the CPA documentation and across the forum but i have not been able to find a way to solve these errors. If anyone has any insight on how to solve i would very much appreciate it.
Thank you in advance!!!