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Tools

Every copick CLI transform at a glance — drag a slider to wipe between the input and the result. Click a tool for full usage and options.

Convert

mesh2caps input mesh2caps output

utils

mesh2caps

Extract the top/bottom surfaces (caps) of a slab box mesh.

mesh2picks input mesh2picks output

utils

mesh2picks

Convert meshes to picks using different sampling strategies.

mesh2seg input mesh2seg output

utils

mesh2seg

Convert meshes to segmentation volumes.

picks2ellipsoid input picks2ellipsoid output

utils

picks2ellipsoid

Convert picks to ellipsoid meshes.

picks2mesh input picks2mesh output

utils

picks2mesh

Convert picks to meshes using convex hull or alpha shapes.

picks2plane input picks2plane output

utils

picks2plane

Convert picks to plane meshes.

picks2seg input picks2seg output

utils

picks2seg

Convert picks to segmentation volumes by painting spheres.

picks2slab input picks2slab output

torch

picks2slab

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

picks2sphere input picks2sphere output

utils

picks2sphere

Convert picks to sphere meshes.

picks2surface input picks2surface output

utils

picks2surface

Convert picks to 2D surface meshes.

seg2mesh input seg2mesh output

utils

seg2mesh

Convert segmentation volumes to meshes using marching cubes.

seg2picks input seg2picks output

utils

seg2picks

Convert segmentation to picks.

seg2slab input seg2slab output

torch

seg2slab

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

Process

combine input combine output

utils

combine

Combine single-label segmentations into a multilabel segmentation.

expand-labels input expand-labels output

utils

expand-labels

Expand labels in segmentations to fill holes and gaps.

filter-components input filter-components output

utils

filter-components

Filter connected components in segmentations by size.

fit-spline input fit-spline output

utils

fit-spline

Fit 3D splines to skeletons and generate oriented picks.

hull input hull output

utils

hull

Compute hull operations on meshes.

rescale input rescale output

utils

rescale

Rescale segmentations to a different voxel spacing.

separate-components input separate-components output

utils

separate-components

Separate connected components in segmentations.

skeletonize input skeletonize output

utils

skeletonize

Skeletonize segmentations in 3D using pattern matching.

split input split output

utils

split

Split multilabel segmentations into single-class masks.

thickness-filter input thickness-filter output

utils

thickness-filter

Remove thin regions from segmentations.

validbox input validbox output

utils

validbox

Generate valid area box meshes for tomographic reconstructions.

Logical

clipmesh input clipmesh output

utils

clipmesh

Limit mesh vertices within distance of a reference surface.

clippicks input clippicks output

utils

clippicks

Limit picks to those within distance of a reference surface.

clipseg input clipseg output

utils

clipseg

Limit segmentation voxels by distance to a reference.

enclosed input enclosed output

utils

enclosed

Remove enclosed components from a segmentation.

meshop input meshop output

utils

meshop

Perform boolean operations between meshes.

picksin input picksin output

utils

picksin

Filter picks to include only those inside a reference volume.

picksout input picksout output

utils

picksout

Filter picks to exclude those inside a reference volume.

segop input segop output

utils

segop

Perform boolean operations between segmentations.