copick process split

utils

Split multilabel segmentations into single-class masks.

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.

Split multilabel segmentations into single-class masks.

Usage

copick process split [OPTIONS]

Description

This command takes a multilabel segmentation and creates separate binary segmentations for each label value. Each output segmentation is named after the corresponding PickableObject (as defined in the copick config) and uses the same session ID as the input.

By default the object name for each label value is resolved from the pickable-objects config. Pass --labels with an explicit 'name:value,...' map when the segmentation's label values do not match the config object labels; only the listed values are then split. The input URI must name an exact segmentation (no wildcards) and include a voxel spacing.

URI Format

    Segmentations: name:user_id/session_id@voxel_spacing

Label-to-Object Mapping:

    The tool looks up each label value in the pickable_objects configuration
    and uses the object name for the output segmentation:
    - Label 1 (ribosome) → ribosome:split/session-001@10.0
    - Label 2 (membrane) → membrane:split/session-001@10.0
    - Label 3 (proteasome) → proteasome:split/session-001@10.0

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.

Tool Options

Option	Type	Default	Description
`--labels`	text	—	Explicit label map 'name:value,...' (e.g. 'sample:1,vacuum:2'). When set, outputs are named by this map and only the listed label values are split. Use when the segmentation's label values do not match the config object labels. Default: resolve names from the pickable-objects config.
`--workers, -w`	integer	`8`	Number of worker processes.

Output Options

Option	Type	Default	Description
`--output-user-id`	text	`split`	User ID for output segmentations.

Examples

# Split multilabel segmentation (outputs named by pickable objects)
copick process split -i "predictions:model/run-001@10.0"

# Split with custom output user ID
copick process split -i "classes:annotator/manual@10.0" --output-user-id "per-class"

# Process specific runs only
copick process split -i "labels:curator/manual@10.0" --run-names TS_001 --run-names TS_002

# Split only specific label values with an explicit name:value map
copick process split -i "predictions:model/run-001@10.0" --labels "sample:1,vacuum:2"