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copick config filesystem

core

Set up a configuration file for a local project.

Usage

copick config filesystem [OPTIONS]

Description

Generates a copick configuration for a project stored on a local (or fsspec-accessible) overlay directory. Pickable objects can be declared up front with --objects name,is_particle,[radius],[pdb_id] (repeat the flag per object); particle objects may carry a radius and PDB id, while segmentation-style objects use is_particle=False.

Object names may not contain underscores. Objects are assigned sequential integer labels starting at 1 in the order given.

Options

Option Type Default Description
--overlay-root directory required Overlay root path.
--objects text · multiple — List of desired objects in the format: name,is_particle,[radius],[pdb_id]. Repeat this option for multiple objects.
--config file config.json Path to the output JSON configuration file.
--proj-name text project Name of the project configuration.
--proj-description text Config Project for SessionXXa Description of the project configuration.
--debug / --no-debug boolean flag False Enable debug logging.

Examples

# Minimal config with no objects
copick config filesystem --overlay-root /mnt/project --config config.json

# Config with a membrane segmentation and an apoferritin particle
copick config filesystem \
    --config config.json \
    --overlay-root /mnt/24sep24a/run002 \
    --objects membrane,False --objects apoferritin,True,60,4V1W \
    --proj-name 24sep24a --proj-description "Synaptic Vesicles collected on 24sep24"

See also