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copick convert mesh2picks

utils

Convert meshes to picks using different sampling strategies.

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 mesh2picks Default input
Input

copick convert mesh2picks Default output
Output

Convert meshes to picks using different sampling strategies.

copick convert mesh2picks Inside input
Input

copick convert mesh2picks Inside output
Output

Convert meshes to picks using different sampling strategies.

copick convert mesh2picks Outside input
Input

copick convert mesh2picks Outside output
Output

Convert meshes to picks using different sampling strategies.

copick convert mesh2picks Vertices input
Input

copick convert mesh2picks Vertices output
Output

Convert meshes to picks using different sampling strategies.

Usage

copick convert mesh2picks [OPTIONS]

Description

Samples points from copick meshes and writes them out as picks. Four sampling types are supported: inside (points within the mesh volume), surface (points on the mesh surface), outside (points outside the mesh), and vertices (the mesh vertices themselves). For surface sampling you can attach the surface normals as orientations, or request random orientations for any type.

A tomogram is required to define the volume bounds: it constrains inside/outside sampling and the --edge-dist buffer (in voxels) that keeps points away from the volume edges, and its voxel spacing sets the default --min-dist between points.

URI Format

Meshes: object_name:user_id/session_id
Picks: object_name:user_id/session_id
Tomograms: tomo_type@voxel_spacing

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 mesh URI (format: object_name:user_id/session_id). Supports glob patterns.
--tomogram, -t COPICK_URI required Tomogram URI (format: tomo_type@voxel_spacing). Example: 'wbp@10.0'

Tool Options

Option Type Default Description
--sampling-type choice (inside | surface | outside | vertices) required Type of sampling: inside (points inside mesh), surface (points on mesh surface), outside (points outside mesh), vertices (return mesh vertices).
--n-points integer 1000 Number of points to sample (ignored for 'vertices' type).
--min-dist float — Minimum distance between points (default: 2 * voxel_spacing).
--edge-dist float 32.0 Distance from volume edges in voxels.
--include-normals / --no-include-normals boolean flag False Include surface normals as orientations (surface sampling only).
--random-orientations / --no-random-orientations boolean flag False Generate random orientations for points.
--seed integer — Random seed for reproducible results.
--workers, -w integer 8 Number of worker processes.

Output Options

Option Type Default Description
--output, -o COPICK_URI required Output picks URI. Supports smart defaults (e.g., "ribosome", "ribosome/my-session", or "/my-session"). Full format: object_name:user_id/session_id.

Examples

# Convert a single mesh to picks with surface sampling
copick convert mesh2picks -i "boundary:user1/boundary-001" --tomogram wbp@10.0 \
    --sampling-type surface -o "boundary"

# Convert all boundary meshes using pattern matching, sampling inside the volume
copick convert mesh2picks -i "boundary:user1/boundary-.*" -t wbp@10.0 \
    --sampling-type inside -o "{input_session_id}"

# Return the mesh vertices directly as picks
copick convert mesh2picks -i "boundary:user1/boundary-001" -t wbp@10.0 \
    --sampling-type vertices -o "boundary-vertices"

See also