copick convert picks2seg

utils

Convert picks to segmentation volumes by painting spheres.

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 picks2seg output — Output

Convert picks to segmentation volumes by painting spheres.

Usage

copick convert picks2seg [OPTIONS]

Description

Paints a solid sphere of the given --radius (in physical units) at every pick location into a label segmentation, producing a dense volume from sparse point annotations. The output is sized and aligned to the reference tomogram (--tomo-type) at the voxel spacing given in the output URI.

Both input and output URIs accept regex patterns and {input_*} templating, so many pick sets can be painted in one call; runs are discovered and processed in parallel via --workers.

URI Format

Picks: object_name:user_id/session_id
Segmentations: name:user_id/session_id@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 picks URI (format: object_name:user_id/session_id). Supports glob patterns.

Tool Options

Option	Type	Default	Description
`--radius`	float	`10.0`	Radius of spheres to paint at pick locations (in angstroms).
`--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 a single pick set to a segmentation
copick convert picks2seg -i "ribosome:user1/manual-001" -o "ribosome:picks2seg/painted-001@10.0"

# Convert all manual picks using pattern matching, keeping the source session id
copick convert picks2seg -i "ribosome:user1/manual-.*" -o "ribosome:picks2seg/painted-{input_session_id}@10.0"

# Paint larger spheres against a denoised reference tomogram
copick convert picks2seg --radius 80 --tomo-type denoised \
    -i "ribosome:user1/manual-001" -o "ribosome:picks2seg/painted-001@10.0"