# omero_screen

> High-content image analysis pipeline for data stored in OMERO

## Docs

### API Reference

#### Pipeline
> Running a plate through the analysis pipeline.

- [loops.plate_loop](https://hocheggerlab.github.io/omero-screen/reference/loops.plate_loop.html)
- [plate_dataset.PlateDataset](https://hocheggerlab.github.io/omero-screen/reference/plate_dataset.PlateDataset.html)

#### Metadata
> Plate layout, channel names and channel roles.

- [metadata_parser.MetadataParser](https://hocheggerlab.github.io/omero-screen/reference/metadata_parser.MetadataParser.html)
- [metadata_parser.resolve_channel_roles](https://hocheggerlab.github.io/omero-screen/reference/metadata_parser.resolve_channel_roles.html)

#### Configuration
> Environment files and logging setup.

- [config.set_env_vars](https://hocheggerlab.github.io/omero-screen/reference/config.set_env_vars.html)
- [config.configure_logging](https://hocheggerlab.github.io/omero-screen/reference/config.configure_logging.html)