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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, multilabel status and type (binary, multilabel, instance or panoptic), plus the most frequent session/user/voxel-spacing/multilabel combinations. Results can be filtered to specific runs, users, sessions, names, voxel sizes, multilabel status or segmentation type (binary and multilabel by default), and printed as a human-readable table or as JSON.

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.
--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.
--segmentation-type choice (binary | multilabel | instance | panoptic | all) — Segmentation type to summarize; 'all' for every type. Default: binary and multilabel segmentations.
--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 the project's binary and multilabel segmentations
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

# Instance or panoptic segmentations only, or every type
copick stats segmentations --config config.json --segmentation-type instance
copick stats segmentations --config config.json --segmentation-type panoptic
copick stats segmentations --config config.json --segmentation-type all

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

See also