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.

With an output URI ending in ?panoptic=true, the result is a panoptic segmentation instead: the inputs fill its label channel (regions without instances, such as membranes), and the instance segmentations given with --instances add their objects' labels and their instance IDs. An instance ID is kept where its object's label won.

URI Format

Segmentations: name:user_id/session_id@voxel_spacing
Use glob/regex patterns to match multiple segmentations per run.
Panoptic output: append ?panoptic=true to the output URI

Options

Option	Type	Default	Description
`-c, --config`	path	—	Path to the configuration file.
`--run-names, -r`	text · multiple	—	Specific run names to process (default: all runs). Repeatable; pass -r once per run.
`--debug / --no-debug`	boolean flag	`False`	Enable debug logging.

Input Options

Option	Type	Default	Description
`--input, -i`	COPICK_URI	required	Input segmentation URI (format: name:user_id/session_id@voxel_spacing). Supports glob patterns. Append ?instance=true or ?panoptic=true to read those segmentation types.
`--instances`	text	—	Instance segmentations to add to a panoptic output (-o ...?panoptic=true), e.g. "microtubule:trace/1@10.0" (patterns allowed; ?instance=true is implied). Each one adds its object's label and its instance IDs.
`--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. Append ?instance=true or ?panoptic=true to write those segmentation types.

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"

# Membranes as regions plus microtubule instances, as one panoptic segmentation
copick process combine -i "membrane:data-portal/*@10.0" --instances "microtubule:trace/1@10.0" \
    -o "cell:combine/0@10.0?panoptic=true"