CLI reference

--db is a global option and goes before the subcommand, e.g. cellview --db /path/to.duckdb projects.

cellview: CellView: manage and explore single-cell measurement data.

Inspect

Browse what is already in the database.

projects: List all projects with experiment counts.
project: Show experiments and plates for project ID.
experiment: Show plates, channels and variables for experiment ID.
plate: Show summary, conditions and measurements for plate ID.

Import and export

import: Import data from a CSV file, an OMERO plate, or a screen.
export: Export the measurements for plate ID.

Explore

Interactive notebooks and their templates.

explore: Launch a Jupyter notebook for interactive data exploration.
template: Manage analysis notebook templates.

Maintain

Edit metadata, delete plates, remove orphaned records.

edit: Edit project or experiment metadata.
delete: Delete data from the database.
clean: Clean up orphaned records in the database.