copick convert fil2seg

utils

Paint tubes around filaments into an instance segmentation.

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.

Paint tubes around filaments into an instance segmentation.

Usage

copick convert fil2seg [OPTIONS]

Description

Each filament becomes a tube around its centreline, labelled with the filament's ID, so the result is an instance segmentation with the same IDs as the filaments and their picks. A filament's tube radius is its own radius (copick convert seg2fil records the radius of the segmentation it traced), otherwise --radius, otherwise the object's radius. Where tubes overlap, each voxel goes to the nearest centreline. The segmentation has the shape of the run's --tomo-type tomogram at the voxel spacing given in the output URI.

Useful for filaments drawn or edited by hand, or imported, that have no segmentation yet: for example as per-filament masks, or as input to copick convert seg2fil.

URI Format

Filaments: object_name:user_id/session_id
Segmentations: name:user_id/session_id@voxel_spacing?instance=true

Options

Option	Type	Default	Description
`-c, --config`	path	—	Path to the configuration file.
`--run-names, -r`	text · multiple	—	Specific run names to process (default: all runs). Repeatable; pass -r once per run.
`--debug / --no-debug`	boolean flag	`False`	Enable debug logging.

Input Options

Option	Type	Default	Description
`--input, -i`	COPICK_URI	required	Input filaments URI (format: object_name:user_id/session_id). Supports glob patterns.

Tool Options

Option	Type	Default	Description
`--radius`	float	—	Tube radius in angstroms for filaments without their own radius. Unset: the object's radius.
`--tomo-type, -tt`	text	`wbp`	Type of tomogram whose shape the segmentation takes.
`--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. Append ?instance=true or ?panoptic=true to write those segmentation types.

Examples

# Tubes of each filament's own radius, at 10 Å
copick convert fil2seg -i "microtubule:manual/1" -o "microtubule:tubes/1@10.0?instance=true"

# 125 Å tubes against a denoised tomogram
copick convert fil2seg -i "microtubule:manual/1" -o "microtubule:tubes/1@10.0?instance=true" \
    --radius 125 --tomo-type denoised