copick convert fil2picks

utils

Sample picks along filaments.

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 fil2picks output — Output

Sample picks along filaments.

Usage

copick convert fil2picks [OPTIONS]

Description

Places picks along each filament at a fixed --spacing, measured along the filament's curve. Each pick's orientation has its +Z axis along the filament, in the filament's point order, and its rotation about that axis follows --roll. Every pick carries its filament's ID as its instance ID and the filament's score, and the picks are written filament by filament, in order along each one. Exported to RELION with copick export picks --filament-columns on, they carry RELION's filament conventions.

A filament's stored curve is used when it still matches the filament: the B-spline that copick convert seg2fil fitted, or control points from an editor. A filament without one is sampled along a smooth curve derived from its points. Sampling is cheap and does not change the filaments, so different spacings can be tried without tracing again.

URI Format

Filaments: object_name:user_id/session_id
Picks: object_name:user_id/session_id

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
`--spacing`	float	required	Distance between picks along a filament (unit: --length-unit). Required: no spacing suits every filament.
`--anchor`	choice (center \| start)	`center`	'center' splits the length left after the last full step evenly between both ends; 'start' places the first pick at the filament's start.
`--roll`	choice (parallel \| random)	`parallel`	Rotation of the picks about the filament axis: 'parallel' turns as little as possible along the filament (rotation-minimizing frames); 'random' is uniformly random per pick.
`--seed`	integer	—	Random seed for --roll random.
`--length-unit`	choice (angstrom \| voxel)	`angstrom`	Unit of --spacing ('voxel' needs the filaments' voxel spacing).
`--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

# Picks every 82 Å (one tubulin dimer), in the filaments' own session
copick convert fil2picks -i "microtubule:trace/1" -o "microtubule:trace/1" --spacing 82

# Every 4 nm with a random rotation about the axis
copick convert fil2picks -i "microtubule:trace/1" -o "microtubule:picks/4nm" --spacing 40 --roll random --seed 1