copick process validbox

utils

Generate valid area box meshes for tomographic reconstructions.

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.

Generate valid area box meshes for tomographic reconstructions.

Usage

copick process validbox [OPTIONS]

Description

Creates box meshes representing the valid imaging area of tomographic reconstructions. The box dimensions are derived from the tomogram voxel dimensions and can be optionally rotated around the Z-axis, which is useful when the specimen was imaged at an in-plane tilt.

The resulting slab mesh can be passed downstream to copick convert mesh2caps (to keep only the top/bottom caps) and to copick logical clippicks (to select particles inside the valid imaging volume).

URI Format

Meshes: 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).
`--tomogram, -t`	COPICK_URI	required	Tomogram URI (format: tomo_type@voxel_spacing). Example: 'wbp@10.0'

Tool Options

Option	Type	Default	Description
`--angle`	float	`0.0`	Rotation angle around Z-axis in degrees.
`--workers`	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.

Examples

# Generate validbox meshes for all runs
copick process validbox --tomogram wbp@10.0 -o "validbox"

# Generate with rotation and a specific tomogram type
copick process validbox -t imod@10.0 --angle 45.0 -o "validbox/rotated"