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copick convert picks2slab

torch

Fit spline surfaces to two pick sets and create a slab mesh.

Plugin command — copick-torch

This command is provided by the copick-torch plugin, not copick core. Install it to make this command available:

pip install copick-torch

See the plugin system guide for details.

copick convert picks2slab Default input
Input

copick convert picks2slab Default output
Output

Fit spline surfaces to two pick sets and create a slab mesh.

copick convert picks2slab Coupled input
Input

copick convert picks2slab Coupled output
Output

Fit spline surfaces to two pick sets and create a slab mesh.

copick convert picks2slab Parallel input
Input

copick convert picks2slab Parallel output
Output

Fit spline surfaces to two pick sets and create a slab mesh.

Usage

copick convert picks2slab [OPTIONS]

Description

Fit surfaces to two pick sets and create a closed slab mesh.

Takes two sets of picks (e.g. top-layer and bottom-layer boundary annotations) and fits surfaces to each. Three methods are available:

  • spline (default): Fits two independent cubic B-spline surfaces, one per pick set. Produces smooth, flexible surfaces that follow the curvature of the picks. The two surfaces are unconstrained relative to each other.
  • coupled: Fits one shared curved B-spline surface plus two z-offsets, so both layers share a single curvature and stay exactly parallel (constant gap). A curved-but-parallel slab; the middle ground between spline and parallel.
  • parallel: Fits two parallel planes with a shared normal vector and different offsets. Produces flat, rigid surfaces guaranteed to be parallel.

For the spline and coupled methods, --regularization adds a bending-energy (curvature) penalty: higher values flatten the fitted surface(s), which is useful to keep a deformed slab from over-curving.

The fitted surfaces are connected with side walls to form a closed, watertight slab mesh.

URI Format

Picks: object_name:user_id/session_id
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).
--input1, -i1 COPICK_URI required First input picks URI (format: object_name:user_id/session_id). Supports glob patterns.
--input2, -i2 COPICK_URI required Second input picks URI (format: object_name:user_id/session_id). Supports glob patterns.

Tool Options

Option Type Default Description
--tomogram, -t COPICK_URI required Tomogram URI (format: tomo_type@voxel_spacing). Example: 'wbp@10.0'
--method choice (spline | parallel | coupled) spline Surface fitting method: 'spline' fits two independent B-spline surfaces, 'coupled' fits one shared curved surface with two offsets (curved but exactly parallel slab), 'parallel' fits two flat parallel planes (shared normal, two offsets).
--grid-resolution integer (5, 5) B-spline knot grid resolution (rows cols). Used with --method spline and coupled.
--regularization float 0.0 Curvature (bending-energy) penalty weight for --method spline and coupled; higher = flatter. Ignored for --method parallel.
--fit-resolution integer (50, 50) Output mesh grid resolution (rows cols).
--num-iterations integer 500 Number of optimization iterations per surface.
--learning-rate float 0.1 Learning rate for Adam optimizer.
--workers, -w 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

# Fit slab with flexible spline surfaces (default)
copick convert picks2slab -c config.json \
    -i1 "top-layer:bob/1" -i2 "bottom-layer:bob/1" \
    -t "wbp@7.84" \
    -o "sample:picks2slab/0"

# Fit a curved-but-parallel slab (shared surface), gently regularized
copick convert picks2slab -c config.json \
    -i1 "top-layer:bob/1" -i2 "bottom-layer:bob/1" \
    -t "wbp@7.84" --method coupled --regularization 5 \
    -o "sample:picks2slab/0"

# Fit slab with parallel planes
copick convert picks2slab -c config.json \
    -i1 "top-layer:bob/1" -i2 "bottom-layer:bob/1" \
    -t "wbp@7.84" --method parallel \
    -o "sample:picks2slab/0"

# With custom spline and mesh resolution
copick convert picks2slab -c config.json \
    -i1 "top-layer:user1/manual" -i2 "bottom-layer:user1/manual" \
    -t "wbp@10.0" \
    --grid-resolution 7 7 --fit-resolution 100 100 \
    -o "sample:picks2slab/fitted"

See also