copick process combine

utils

Combine single-label segmentations into a multilabel segmentation.

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.

Combine single-label segmentations into a multilabel segmentation.

Usage

copick process combine [OPTIONS]

Description

This is the inverse of copick process split. It takes multiple binary/single-label segmentations (matched by a pattern) and merges them into a single multilabel volume. Each input segmentation's name is looked up in the copick config to determine its integer label value.

When multiple inputs overlap, the lowest label value wins. This resolution is deterministic and reproducible, and overlapping voxels are logged as warnings.

URI Format

Segmentations: name:user_id/session_id@voxel_spacing
Use glob/regex patterns to match multiple segmentations per run.

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, -r`	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.
`--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

# Combine all segmentations from a split operation
copick process combine -i "*:split/*@20" -o "multilabel:combine/0"

# Combine a specific user's segmentations using regex
copick process combine -i "re:.*:napari/manual@20" -o "combined:combine/0"

# Combine for specific runs
copick process combine -r run1 -r run2 -i "*:user1/session@10.0" -o "labels:combine/0"