API Reference

Pipeline

Running a plate through the analysis pipeline.

loops.plate_loop()

Main loop to process a plate.

plate_dataset.PlateDataset

Manages the creation and retrieval of OMERO datasets associated with screening plates.

Metadata

Plate layout, channel names and channel roles.

metadata_parser.MetadataParser

Parses and manages channel and well metadata for an OMERO plate.

metadata_parser.resolve_channel_roles()

Resolve channel role assignments (nucleus / cell) from channel names.

Configuration

Environment files and logging setup.

config.set_env_vars()

Loads environment variables from configuration files or the environment.

config.configure_logging()

Configure the global loguru logger for an application entry point.