Skip to content

copick config dataportal

core

Set up a configuration file from CZDP dataset IDs.

Usage

copick config dataportal [OPTIONS]

Description

Builds a copick configuration that reads tomograms, picks, and other annotations directly from one or more CryoET Data Portal datasets, using a local overlay directory for any new or intermediate files you create. The portal data stays read-only; everything you write lands in the overlay.

Pass --dataset-id once per dataset to combine several portal datasets into a single project.

Options

Option Type Default Description
-ds, --dataset-id integer · multiple required Dataset IDs from the CryoET Data Portal to include in the configuration
--overlay directory required Path to the local overlay directory where intermediate files will be stored or read.
--output file required Path to save the generated configuration file.
--debug / --no-debug boolean flag False Enable debug logging.

Examples

# Generate a config for a single portal dataset
copick config dataportal --dataset-id 10000 --overlay ./overlay --output config.json

# Combine several portal datasets into one project
copick config dataportal -ds 10000 -ds 10001 -ds 10002 --overlay ./overlay --output multi_config.json

See also