Skip to content

copick convert mesh2seg

utils

Convert meshes to segmentation volumes.

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 mesh2seg Default input
Input

copick convert mesh2seg Default output
Output

Convert meshes to segmentation volumes.

copick convert mesh2seg Boundary input
Input

copick convert mesh2seg Boundary output
Output

Convert meshes to segmentation volumes.

copick convert mesh2seg Invert input
Input

copick convert mesh2seg Invert output
Output

Convert meshes to segmentation volumes.

Usage

copick convert mesh2seg [OPTIONS]

Description

Voxelize one or more meshes into a label volume on a reference tomogram grid. Two voxelization modes are supported: watertight fills the entire interior using ray casting, while boundary voxelizes only the surface with a controllable sampling density. Use --invert to fill outside the mesh instead of inside (watertight mode), and --boundary-sampling-density to tune the surface sampling in boundary mode.

Input meshes are selected by pattern: exact (membrane:user1/session1), glob (membrane:user1/session*), regex (re:membrane:user\d+/session\d+), or a bare wildcard (membrane, which expands to membrane:*/*).

URI Format

Meshes: object_name:user_id/session_id
Segmentations: name:user_id/session_id@voxel_spacing?multilabel=true

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.

Tool Options

Option Type Default Description
--mode choice (watertight | boundary) watertight Voxelization mode: 'watertight' fills the entire mesh interior, 'boundary' only voxelizes the surface.
--boundary-sampling-density float 1.0 Surface sampling density for boundary mode (samples per voxel edge length).
--invert / --no-invert boolean flag False Invert the volume (fill outside instead of inside for watertight mode).
--tomo-type, -tt text wbp Type of tomogram to use as reference.
--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.

Examples

# Convert mesh interior to segmentation (default)
copick convert mesh2seg -i "membrane:user1/manual-001" -o "membrane:mesh2seg/from-mesh-001@10.0"

# Convert mesh boundary only with high sampling density
copick convert mesh2seg --mode boundary --boundary-sampling-density 2.0 \
    -i "membrane:user1/manual-001" -o "membrane:mesh2seg/boundary-001@10.0"

# Invert watertight mesh (fill outside)
copick convert mesh2seg --invert -i "membrane:user1/manual-001" -o "membrane:mesh2seg/inverted-001@10.0"

# Convert all manual meshes using pattern matching with multilabel output
copick convert mesh2seg -i "membrane:user1/manual-.*" -o "membrane:mesh2seg/from-mesh-{input_session_id}@10.0?multilabel=true"

See also