copick rm
core
Remove copick objects by URI.
Usage
Description
Deletes picks, meshes, segmentations, tomograms, or features that match a
copick URI. A URI may target a single object or many at once via glob (*)
wildcards or a regular expression prefixed with re:. The command operates
across every run by default, or on a single run when --run is given.
The URI shape depends on the object type: picks and meshes use
object_name:user_id/session_id; segmentations use
name:user_id/session_id@voxel_spacing; tomograms use
tomo_type@voxel_spacing; and features use tomo_type@voxel_spacing:feature_type.
Pattern-based deletions require --force as a safety measure, unless
--dry-run is used. Use --dry-run to preview exactly what would be removed
without deleting anything.
Arguments
| Argument | Description |
|---|---|
OBJECT_TYPE |
Type of object to remove (picks, mesh, segmentation, tomogram, or feature). |
URI |
Copick URI selecting the objects to remove; supports glob wildcards and re: regex patterns. |
Options
| Option | Type | Default | Description |
|---|---|---|---|
-c, --config |
path | — | Path to the configuration file. |
-r, --run |
text | — | Specific run name to operate on (default: all runs). |
--dry-run |
boolean flag | False |
Show what would be deleted without actually deleting. |
--force |
boolean flag | False |
Required for pattern-based deletions (safety measure). |
--workers, -w |
integer | 8 |
Number of parallel worker processes. |
--debug / --no-debug |
boolean flag | False |
Enable debug logging. |
Examples
# Remove a specific pick set
copick rm picks "ribosome:user1/session-001" -c config.json
# Preview deletion of test segmentations without removing them
copick rm --dry-run segmentation "membrane:*/test-*@10.0" -c config.json
# Remove all manual picks from user1 (pattern requires --force)
copick rm --force picks "ribosome:user1/manual-*" -c config.json
# Remove segmentations matching a regex pattern
copick rm --force segmentation "re:membrane:user1/session-\d+@10.0" -c config.json