copick process

Apply processing methods to copick data.

Usage

copick process [OPTIONS] COMMAND [ARGS]...

Description

Commands in this group apply image-processing operations, such as filtering, denoising, or intensity transforms, to copick tomograms and related entities. Subcommands are contributed by installed plugins.

Commands

Command	Description
`bandpass`	Band-pass filter tomograms in 3D.
`combine`	Combine single-label segmentations into a multilabel segmentation.
`downsample`	Downsample tomograms via Fourier rescaling.
`expand-labels`	Expand labels in segmentations to fill holes and gaps.
`filter-components`	Filter connected components in segmentations by size.
`fit-spline`	Fit 3D splines to skeletons and generate oriented picks.
`hull`	Compute hull operations on meshes.
`rescale`	Rescale segmentations to a different voxel spacing.
`seg-stats`	Analyze connected component sizes per label in segmentations.
`separate-components`	Separate connected components in segmentations.
`skeletonize`	Skeletonize segmentations in 3D using pattern matching.
`split`	Split multilabel segmentations into single-class masks.
`thickness-filter`	Remove thin regions from segmentations.
`validbox`	Generate valid area box meshes for tomographic reconstructions.