Skip to content

copick logical segop

utils

Perform boolean operations between 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 logical segop Default input
Input

copick logical segop Default output
Output

Perform boolean operations between segmentations.

copick logical segop Difference input
Input

copick logical segop Difference output
Output

Perform boolean operations between segmentations.

copick logical segop Intersection input
Input

copick logical segop Intersection output
Output

Perform boolean operations between segmentations.

copick logical segop Exclusion input
Input

copick logical segop Exclusion output
Output

Perform boolean operations between segmentations.

Usage

copick logical segop [OPTIONS]

Description

Combine multiple segmentations using boolean set operations. Every input is first converted to a binary mask, then combined with the chosen operation. The voxel spacing given by --voxel-spacing applies globally to all inputs and to the output.

Supported operations: union combines segmentations (logical OR) and accepts N>=1 inputs; difference subtracts the second input from the first and requires exactly 2 inputs; intersection keeps voxels common to both inputs (logical AND) and requires exactly 2 inputs; exclusion keeps voxels present in exactly one input (XOR) and requires exactly 2 inputs.

Input URIs support glob wildcards (* and ?) by default, or regular expressions when prefixed with re: (for example re:membrane:user\d+/session-\d+). When a single -i flag is given with a pattern, union expands the pattern within each run and merges every matching segmentation, which is useful for combining multiple versions or annotations within each run.

URI Format

Segmentations: name:user_id/session_id (voxel spacing supplied 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).
--input, -i COPICK_URI · multiple required Input segmentation URI (format: name:user_id/session_id@voxel_spacing). Can be specified multiple times for N-way operations. Supports glob patterns (default) or regex patterns (re: prefix).

Tool Options

Option Type Default Description
--operation, -op choice (union | difference | intersection | exclusion | concatenate) required Boolean operation to perform.
--voxel-spacing, -vs float required Voxel spacing for input and output segmentations.
--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

# Single-input union: merge all matching segmentations within each run
copick logical segop --operation union -vs 10.0 \
    -i "membrane:user*/manual-*" \
    -o "merged"

# N-way union with multiple -i flags (merge across different objects)
copick logical segop --operation union -vs 10.0 \
    -i "membrane:user1/manual-*" \
    -i "vesicle:user2/auto-*" \
    -i "ribosome:user3/pred-*" \
    -o "merged"

# N-way union with regex patterns
copick logical segop --operation union -vs 10.0 \
    -i "re:membrane:user1/manual-\d+" \
    -i "re:vesicle:user2/auto-\d+" \
    -o "merged"

# 2-way difference (exactly 2 inputs required)
copick logical segop --operation difference -vs 10.0 \
    -i "membrane:user1/manual-001" \
    -i "mask:user1/mask-001" \
    -o "membrane:segop/masked"

See also