copick process skeletonize

utils

Skeletonize segmentations in 3D using pattern matching.

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 process skeletonize input — Input

copick process skeletonize output — Output

Skeletonize segmentations in 3D using pattern matching.

Usage

copick process skeletonize [OPTIONS]

Description

Reduces each input segmentation to a 1-voxel-wide medial skeleton, exposing the centerlines of the objects it contains. Two backends are available: skimage (scikit-image 3D thinning) and distance_transform (local maxima of the Euclidean distance transform).

The input session ID is treated as a regex, so a single invocation can skeletonize many segmentations at once. This pairs naturally with the output of connected-component separation (e.g. pattern inst-.* to match inst-0, inst-1, etc.). Optional cleanup removes small objects before thinning and small skeleton pieces afterwards, and --prune-length prunes short side branches (spurs) off the skeleton. The output takes the name given in -o.

URI Format

Segmentations: name:user_id/session_id@voxel_spacing

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.
`--debug / --no-debug`	boolean flag	`False`	Enable debug logging.

Input Options

Option	Type	Default	Description
`--input, -i`	COPICK_URI	required	Input segmentation URI (format: name:user_id/session_id@voxel_spacing). Supports glob patterns. Append ?instance=true or ?panoptic=true to read those segmentation types.

Tool Options

Option	Type	Default	Description
`--method`	choice (skimage \| distance_transform)	`skimage`	Skeletonization method.
`--remove-noise / --keep-noise`	boolean flag	`True`	Remove small objects before skeletonization.
`--min-object-size`	integer	`50`	Minimum size of objects to keep during preprocessing.
`--remove-short-branches / --keep-short-branches`	boolean flag	`True`	Remove small skeleton pieces (whole connected pieces with fewer than --min-branch-length voxels). To shorten side branches of a larger skeleton, use --prune-length.
`--min-branch-length`	integer	`5`	Minimum number of voxels of a skeleton piece to keep (see --remove-short-branches).
`--prune-length`	float	—	Prune side branches (spurs) of the skeleton shorter than this (unit: --length-unit). Unset: no pruning.
`--length-unit`	choice (angstrom \| voxel)	`angstrom`	Unit of --prune-length.
`--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. Append ?instance=true or ?panoptic=true to write those segmentation types.

Examples

# Skeletonize a single segmentation (exact session match)
copick process skeletonize -i "membrane:user1/inst-0@10.0" -o "membrane:skel/skel-0@10.0"

# Skeletonize every instance matched by a session-ID pattern
copick process skeletonize -i "membrane:user1/inst-.*@10.0" \
    -o "membrane:skel/skel-{input_session_id}@10.0"

# Prune side branches shorter than 20 nm
copick process skeletonize -i "microtubule:easymode/job006@10.0" -o "microtubule:skel/job006@10.0" \
    --prune-length 200

# Use the distance-transform backend and keep short branches
copick process skeletonize --method distance_transform --keep-short-branches \
    -i "membrane:user1/inst-.*@10.0" -o "membrane:skel/skel-{input_session_id}@10.0"