copick logical enclosed

utils

Remove enclosed components from a 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.

Remove enclosed components from a segmentation.

Usage

copick logical enclosed [OPTIONS]

Description

This command identifies connected components in the first segmentation (inner) that are completely surrounded by the second segmentation (outer), and removes them from the inner segmentation. Useful for cleaning up noise, artifacts, or unwanted fragments that are trapped inside a larger structure.

Components are filtered geometrically: each is dilated by --margin voxels and kept only if it is fully contained within the outer segmentation. Optional --min-size/--max-size bounds (in cubic angstroms) restrict which components are considered for removal.

Algorithm:

1. Label connected components in the inner segmentation (input1)
2. Dilate each component by the specified margin
3. Check if the dilated component is fully contained within the outer segmentation (input2)
4. If enclosed (and within size limits), remove the component from the inner segmentation
5. Output cleaned version of the inner segmentation

URI Format

Segmentations: name:user_id/session_id (voxel spacing specified via --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, -r`	text · multiple	—	Specific run names to process (default: all runs).
`--input1, -i1`	COPICK_URI	required	First input segmentation URI (format: name:user_id/session_id@voxel_spacing). Supports glob patterns.
`--input2, -i2`	COPICK_URI	required	Second input segmentation URI (format: name:user_id/session_id@voxel_spacing). Supports glob patterns.

Tool Options

Option	Type	Default	Description
`--voxel-spacing, -vs`	float	required	Voxel spacing for input and output segmentations.
`--margin, -m`	integer	`1`	Number of voxels to dilate when checking if components are enclosed.
`--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 consider (optional).
`--max-size`	float	—	Maximum component volume in cubic angstroms (Å³) to consider (optional).
`--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

# Remove small vesicle fragments that are enclosed by membrane
copick logical enclosed -vs 10.0 -i1 "vesicle:user1/auto-001" -i2 "membrane:user1/manual-001" \
    -o "vesicle-clean:enclosed/0"

# Remove noise fragments with size filtering (volumes in Å³)
copick logical enclosed -vs 10.0 -i1 "fragments:user1/.*" -i2 "cell:user1/.*" \
    -o "cleaned:enclosed/0" --min-size 1000 --max-size 100000 --margin 2