copick process rescale

utils

Rescale segmentations to a different voxel spacing.

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.

Rescale segmentations to a different voxel spacing.

Usage

copick process rescale [OPTIONS]

Description

Resamples segmentation data using nearest-neighbor interpolation (default) to preserve label integrity. Supports both upscaling (finer spacing) and downscaling (coarser spacing). When --tomo-type is provided, the output shape is matched to an existing tomogram at the target spacing for exact alignment.

URI Format

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 segmentation URI (format: name:user_id/session_id@voxel_spacing). Supports glob patterns.

Tool Options

Option	Type	Default	Description
`--target-voxel-spacing, -tvs`	float	—	Target voxel spacing in angstroms. If omitted, derived from output URI @voxel_spacing.
`--tomo-type, -tt`	text	—	Tomogram type to use as shape reference at target spacing (e.g. 'wbp'). When provided, output shape matches the tomogram exactly.
`--order`	choice (0 \| 1)	`0`	Interpolation order: 0=nearest-neighbor (labels), 1=linear (float data).
`--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

# Upscale: 10 angstrom -> 5 angstrom
copick process rescale -i "membrane:user1/auto@10.0" -o "membrane:rescale/0@5.0"

# Downscale: 5 angstrom -> 20 angstrom
copick process rescale -i "membrane:user1/manual@5.0" -o "membrane:rescale/0@20.0"

# Match tomogram shape exactly
copick process rescale -i "membrane:user1/auto@10.0" -o "membrane:rescale/0@5.0" --tomo-type wbp

# Explicit target spacing (when output URI uses smart defaults)
copick process rescale -i "membrane:user1/auto@10.0" -o "membrane_rescaled" --target-voxel-spacing 5.0

# Rescale specific runs
copick process rescale -i "organelle:pred/auto@10.0" -o "organelle:rescale/0@7.5" -r run1 -r run2

# Linear interpolation (for non-label float data)
copick process rescale -i "density:user1/auto@10.0" -o "density:rescale/0@5.0" --order 1