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copick sync segmentations

core

Synchronize segmentations between two Copick projects.

Usage

copick sync segmentations [OPTIONS]

Description

Copies segmentation data from a source Copick project to a target project. You can restrict the sync to specific runs, voxel spacings, segmentation names, and users, and optionally remap source names to different target names. The source may instead be one or more CryoET Data Portal datasets via --source-dataset-ids, in which case --config is ignored and a temporary dataportal configuration is created.

When specific segmentation names are requested, the matching pickable objects are created in the target project before copying (non-multilabel segmentations require the name to match a pickable object). Use --exist-ok to overwrite segmentations that already exist in the target.

Options

Option Type Default Description
-c, --config path — Path to the configuration file.
--source-dataset-ids text "" Comma-separated list of dataset IDs to use as source from CryoET Data Portal. If provided, --config will be ignored and a temporary dataportal configuration will be created.
--target-config path required Path to the target configuration file.
--source-runs text "" Comma-separated list of source run names to synchronize. If not specified, all runs will be synced.
--target-runs text "" Comma-separated mapping of source run names to target run names (e.g. 'run1:target1,run2:target2'). If not specified, source run names will be used.
--voxel-spacings text "" Comma-separated list of voxel spacings to consider for synchronization. If not specified, all voxel spacings will be synced.
--source-names text "" Comma-separated list of source segmentation names to synchronize. If not specified, all segmentations will be synced.
--target-names text "" Comma-separated mapping of source segmentation names to target names (e.g. 'seg1:target1,seg2:target2'). If not specified, source names will be used.
--source-users text "" Comma-separated list of source user IDs to synchronize. If not specified, all users will be synced.
--target-users text "" Comma-separated mapping of source user IDs to target user IDs (e.g. 'user1:target1,user2:target2'). If not specified, source user IDs will be used.
--exist-ok / --no-exist-ok boolean flag False Allow overwriting existing segmentations in the target project.
--max-workers integer 4 Maximum number of worker threads to use for synchronization.
--log / --no-log boolean flag False Enable verbose logging of the synchronization process.
--debug / --no-debug boolean flag False Enable debug logging.

Examples

# Sync all segmentations from all runs
copick sync segmentations -c source_config.json --target-config target_config.json

# Sync specific runs and voxel spacings
copick sync segmentations -c source_config.json --target-config target_config.json \
    --source-runs "run1,run2" --voxel-spacings "10.0,20.0"

# Sync specific segmentation names with name mapping
copick sync segmentations -c source_config.json --target-config target_config.json \
    --source-names "ribosome,membrane" --target-names "ribosome:ribo,membrane:mem"

See also