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copick convert seg2slab

torch

Fit parallel planes to a segmentation 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 seg2slab Default input
Input

copick convert seg2slab Default output
Output

Fit parallel planes to a segmentation and create a slab mesh.

copick convert seg2slab Spline input
Input

copick convert seg2slab Spline output
Output

Fit parallel planes to a segmentation and create a slab mesh.

copick convert seg2slab Parallel input
Input

copick convert seg2slab Parallel output
Output

Fit parallel planes to a segmentation and create a slab mesh.

copick convert seg2slab IoU input
Input

copick convert seg2slab IoU output
Output

Fit parallel planes to a segmentation and create a slab mesh.

Usage

copick convert seg2slab [OPTIONS]

Description

Fit a slab to a segmentation volume and create a closed slab mesh.

Extracts a single label from the segmentation and finds the largest connected component. For the 'spline'/'coupled'/'parallel' methods it then extracts top- and bottom-surface point-clouds and fits a surface with the same machinery as picks2slab (B-spline grid resolution, curvature regularization). The legacy 'iou' method instead fits two flat parallel planes directly to the binary volume by maximizing intersection-over-union. The two fitted surfaces are connected with side walls to form a closed, watertight box mesh.

URI Format

Segmentations: name:user_id/session_id@voxel_spacing
Meshes: object_name:user_id/session_id

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
--label, -l integer required Label index to extract from the segmentation.
--method choice (spline | coupled | parallel | iou) coupled Surface fitting method: 'coupled' fits one shared curved surface with two offsets (curved but exactly parallel slab); 'spline' fits two independent B-spline surfaces; 'parallel' fits two flat parallel planes to the extracted surface points; 'iou' fits two flat parallel planes directly to the binary volume via intersection-over-union (legacy).
--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 and iou.
--surface-stride integer 1 Column subsampling stride for surface-point extraction (>=1); bounds the point count on large volumes. Ignored for --method iou.
--fit-resolution integer (50, 50) Output mesh grid resolution (rows cols).
--num-iterations integer 500 Number of optimization iterations for surface fitting.
--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 a coupled (curved, parallel) slab from a segmentation
copick convert seg2slab -c config.json \
    -i "sample:postproc/largest@20.0" \
    --label 1 --method coupled --grid-resolution 5 5 --regularization 5 \
    -o "sample:seg2slab/0"

# Process specific runs with the legacy IoU flat-plane fit
copick convert seg2slab -c config.json \
    -r 14114 -r 14132 \
    -i "predictions:model/run-001@10.0" \
    --label 1 --method iou --fit-resolution 100 100 \
    -o "sample:seg2slab/fitted"

See also