copick logical picksout

utils

Filter picks to exclude those inside a reference volume.

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.

Filter picks to exclude those inside a reference volume.

Usage

copick logical picksout [OPTIONS]

Description

The reference volume can be either a watertight mesh or a segmentation (provide exactly one via --ref-mesh or --ref-seg). Each input pick is tested against the volume and only those whose coordinates fall outside it are written to the output. This is the inverse of copick logical picksin, which keeps the picks that fall inside the volume instead.

Each pick is tested at its particle centre (its location plus the shift stored in its transform). Kept picks are written unchanged and in their original order, so their orientations, instance IDs (e.g. filament IDs) and scores survive. If no pick is kept, an empty pick set is written.

URI Format

Picks: object_name:user_id/session_id
Meshes: object_name:user_id/session_id
Segmentations: name:user_id/session_id@voxel_spacing

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 picks URI (format: object_name:user_id/session_id). Supports glob patterns.

Reference Options

Option	Type	Default	Description
`--ref-mesh, -rm`	COPICK_URI	—	Reference mesh URI (format: object_name:user_id/session_id). Supports glob patterns.
`--ref-seg, -rs`	COPICK_URI	—	Reference segmentation URI (format: name:user_id/session_id@voxel_spacing). Supports glob patterns. Append ?instance=true or ?panoptic=true to use an instance or panoptic segmentation (any non-zero voxel of an instance segmentation, or of a panoptic one's label channel, counts).

Tool Options

Option	Type	Default	Description
`--workers, -w`	integer	`8`	Number of worker processes.

Output Options

Option	Type	Default	Description
`--output, -o`	COPICK_URI	required	Output picks URI. Supports smart defaults (e.g., "ribosome", "ribosome/my-session", or "/my-session"). Full format: object_name:user_id/session_id.

Examples

# Exclude picks inside a reference mesh
copick logical picksout -i "ribosome:user1/all-001" -rm "boundary:user1/boundary-001" \
    -o "ribosome:picksout/outside-001"

# Exclude picks inside a segmentation
copick logical picksout -i "ribosome:user1/all-001" -rs "mask:user1/mask-001@10.0" \
    -o "ribosome:picksout/outside-001"