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copick stats segmentations

core

Display statistics about segmentations.

Usage

copick stats segmentations [OPTIONS]

Description

Aggregates segmentation annotations across the project and reports the total number of segmentations, their distribution by user, session, name, voxel size, and multilabel status, plus the most frequent session/user/voxel-spacing/multilabel combinations. Results can be filtered to specific runs, users, sessions, names, voxel sizes, or multilabel status, and printed as a human-readable table or as JSON.

Options

Option Type Default Description
-c, --config path — Path to the configuration file.
--runs text · multiple — Specific run names to analyze. Can be specified multiple times.
--user-id text · multiple — Filter by user ID. Can be specified multiple times.
--session-id text · multiple — Filter by session ID. Can be specified multiple times.
--name text · multiple — Filter by segmentation name. Can be specified multiple times.
--voxel-size float · multiple — Filter by voxel size. Can be specified multiple times.
--multilabel / --no-multilabel boolean flag — Filter by multilabel status.
--parallel / --no-parallel boolean flag True Enable parallel processing.
--workers integer 8 Number of workers for parallel processing.
--output choice (json | table) table Output format.
--debug / --no-debug boolean flag False Enable debug logging.

Examples

# Summarize every segmentation in the project
copick stats segmentations --config config.json

# Filter by name and voxel size
copick stats segmentations --config config.json --name membrane --voxel-size 10.0

# Restrict to multilabel segmentations only
copick stats segmentations --config config.json --multilabel

# Run in parallel and emit JSON
copick stats segmentations --config config.json --parallel --output json

See also