A package for working with OMERO by ResearchIT at The Jackson Laboratory.

This repository also contains scripts that use jax-omeroutils for managing commons tasks.

In addition to the requirements in requirements.txt, due to the fact that we use omero transfer prepare, you need to have bftools. The easiest way to install that is conda install -c bioconda bftools.

Spreadsheet submission forms need to either contain columns named "dataset" and "project", or a column named "screen". Plates should be submitted with a "screen" column, and only one plate per folder is allowed (this is due to limitations on session time server-side). If multiple plates need to be submitted, they should be put in separate folders with separate submission forms.

When submitting plates, here is how this workflow behaves for different situations:

• Multiple plates in the same submission folder: the first plate will import correctly and be correctly put into the relevant screen and annotated; following plates will import correctly, but will NOT be moved to the right screen or annotated, no matter what the contents of the submission form are.
• Plate and regular images in the same submission folder, submission spreadsheet contains "project" and "dataset" columns: all will be imported correctly, but plate will not be placed in the project/dataset nor be annotated.
• Plate and regular images in the same submission folder, submission spreadsheet contains "screen" column: all be imported correctly, but regular images will not be placed in screen nor be annotated.