copick process thickness-filter

utils

Remove thin regions from 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 thickness-filter input — Input

copick process thickness-filter output — Output

Remove thin regions from segmentations.

Usage

copick process thickness-filter [OPTIONS]

Description

Remove thin regions from segmentations based on inscribed sphere diameter.

This command identifies thin sheet-like artifacts in a segmentation and removes them. A region is kept only if it contains at least one voxel whose largest inscribed sphere has a diameter >= min-thickness. The algorithm computes the Euclidean distance transform, thresholds to find thick cores, dilates them back, and intersects with the original mask.

For multilabel segmentations, each label is filtered independently.

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, -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
`--min-thickness, -t`	float	required	Minimum thickness (diameter) of structures to keep. Unit set by --thickness-unit.
`--thickness-unit`	choice (angstrom \| voxel)	`angstrom`	Unit for --min-thickness: 'angstrom' for Å, 'voxel' for voxel diameters.
`--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 membrane regions thinner than 50 Å
copick process thickness-filter -i "membrane:user1/auto-001@10.0" -o "membrane_thick" --min-thickness 50.0

# Filter by voxel diameters instead of angstroms
copick process thickness-filter -i "membrane:user1/auto-001@10.0" -o "membrane_thick" --min-thickness 5 --thickness-unit voxel

# Process specific runs with regex pattern
copick process thickness-filter -i "membrane:user1/.*@10.0" -o "membrane_thick" --min-thickness 40.0 -r run001 -r run002