copick process separate-components

utils

Separate connected components in segmentations.

Plugin command — copick-utils

This command is provided by the copick-utils plugin, not copick core. Install it to make this command available:

pip install copick-utils

See the plugin system guide for details.

copick process separate-components input — Input

copick process separate-components output — Output

Separate connected components in segmentations.

Usage

copick process separate-components [OPTIONS]

Description

Connected-component analysis splits a segmentation into individual segmentations, one per connected region. Connectivity can be face (6-connected), face-edge (18-connected), or all (26-connected), and components smaller than --min-size (in cubic angstroms) are dropped.

For multilabel segmentations the analysis is performed on each label separately. Output segmentations use the {instance_id} placeholder for auto-numbering (e.g. inst-0, inst-1).

URI Format

Segmentations: name:user_id/session_id@voxel_spacing

Options

Option	Type	Default	Description
`-c, --config`	path	—	Path to the configuration file.
`--debug / --no-debug`	boolean flag	`False`	Enable debug logging.

Input Options

Option	Type	Default	Description
`--run-names`	text · multiple	—	Specific run names to process (default: all runs).
`--input, -i`	COPICK_URI	required	Input segmentation URI (format: name:user_id/session_id@voxel_spacing). Supports glob patterns.

Tool Options

Option	Type	Default	Description
`--connectivity, -cn`	choice (face \| face-edge \| all)	`all`	Connectivity for connected components (face=6-connected, face-edge=18-connected, all=26-connected).
`--min-size`	float	—	Minimum component volume in cubic angstroms (Å³) to keep (optional).
`--multilabel / --binary`	boolean flag	`True`	Process as multilabel segmentation (analyze each label separately).
`--workers, -w`	integer	`8`	Number of worker processes.

Output Options

Option	Type	Default	Description
`--output, -o`	COPICK_URI	required	Output segmentation URI. Supports smart defaults (e.g., "membrane", "membrane/my-session", or "/my-session"). Full format: object_name:user_id/session_id@voxel_spacing.

Examples

# Separate components with smart defaults (auto user_id and session template)
copick process separate-components -i "membrane:user1/manual-001@10.0" -o "{instance_id}"

# Custom session prefix
copick process separate-components -i "membrane:user1/manual-001@10.0" \
    -o "membrane:components/inst-{instance_id}"

# Full URI specification
copick process separate-components -i "membrane:user1/manual-001@10.0" \
    -o "membrane:components/comp-{instance_id}@10.0"