copick convert picks2surface

utils

Convert picks to 2D surface meshes.

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 convert picks2surface input — Input

copick convert picks2surface output — Output

Convert picks to 2D surface meshes.

Usage

copick convert picks2surface [OPTIONS]

Description

Fit an open 2D surface (a sheet-like membrane) through a set of point picks and write it as a mesh. This is useful for reconstructing membranes or other laminar structures sampled by individual particle picks.

Three surface-fitting methods are supported via --surface-method: delaunay (Delaunay triangulation of the points), rbf (radial-basis-function interpolation onto a regular grid), and grid (gridded surface at --grid-resolution). Optional clustering can split the picks into separate instances first; with --individual-meshes each cluster is written to its own mesh using the {instance_id} placeholder in the output session id.

URI Format

Picks: object_name:user_id/session_id
Meshes: object_name:user_id/session_id

Options

Option	Type	Default	Description
`-c, --config`	path	—	Path to the configuration file.
`--debug / --no-debug`	boolean flag	`False`	Enable debug logging.

Input Options

Option	Type	Default	Description
`--run-names, -r`	text · multiple	—	Specific run names to process (default: all runs).
`--input, -i`	COPICK_URI	required	Input picks URI (format: object_name:user_id/session_id). Supports glob patterns.

Tool Options

Option	Type	Default	Description
`--surface-method`	choice (delaunay \| rbf \| grid)	`delaunay`	Surface fitting method.
`--grid-resolution`	integer	`50`	Resolution for grid-based surface methods.
`--use-clustering, -cl / --no-use-clustering`	boolean flag	`False`	Cluster points before mesh creation.
`--clustering-method`	choice (dbscan \| kmeans)	`dbscan`	Clustering method.
`--clustering-eps`	float	`1.0`	DBSCAN eps parameter - maximum distance between points in a cluster (in angstroms).
`--clustering-min-samples`	integer	`3`	DBSCAN min_samples parameter.
`--clustering-n-clusters`	integer	`1`	K-means n_clusters parameter.
`--all-clusters, -mm / --largest-cluster-only`	boolean flag	`True`	Use all clusters (True) or only the largest cluster (False).
`--workers, -w`	integer	`8`	Number of worker processes.

Output Options

Option	Type	Default	Description
`--output, -o`	COPICK_URI	required	Output mesh URI. Supports smart defaults (e.g., "membrane", "membrane/my-session", or "/my-session"). Full format: object_name:user_id/session_id.
`--individual-meshes, -im / --no-individual-meshes`	boolean flag	`False`	Create individual meshes for each instance (enables {instance_id} placeholder).

Examples

# Convert single pick set to single surface mesh
copick convert picks2surface -i "membrane:user1/manual-001" -o "membrane:picks2surface/surface-001"

# Create individual surface meshes from clusters
copick convert picks2surface --individual-meshes \
    -i "membrane:user1/manual-001" -o "membrane:picks2surface/surface-{instance_id}"

# Convert all manual picks using pattern matching
copick convert picks2surface -i "membrane:user1/manual-.*" -o "membrane:picks2surface/surface-{input_session_id}"