Processing Tools
Transform cryoET data from the command line — convert between picks, segmentations, and meshes; process volumes and segmentations; and run spatial / boolean operations. Every tool below is a copick CLI command; click through for full usage and examples.
Convert
Convert one copick type to another.
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Extract the top/bottom surfaces (caps) of a slab box mesh.
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Convert meshes to picks using different sampling strategies.
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Convert meshes to segmentation volumes.
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Convert a copick project to nnUNet raw dataset format.
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Convert picks to ellipsoid meshes.
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Convert picks to meshes using convex hull or alpha shapes.
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Convert picks to plane meshes.
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Convert picks to segmentation volumes by painting spheres.
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Fit spline surfaces to two pick sets and create a slab mesh.
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Convert picks to sphere meshes.
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Convert picks to 2D surface meshes.
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Convert segmentation volumes to meshes using marching cubes.
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Convert segmentation to picks.
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Fit parallel planes to a segmentation and create a slab mesh.
Process
Apply processing methods to copick data.
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Band-pass filter tomograms in 3D.
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Combine single-label segmentations into a multilabel segmentation.
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Downsample tomograms via Fourier rescaling.
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Expand labels in segmentations to fill holes and gaps.
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Filter connected components in segmentations by size.
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Fit 3D splines to skeletons and generate oriented picks.
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Compute hull operations on meshes.
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Rescale segmentations to a different voxel spacing.
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Analyze connected component sizes per label in segmentations.
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Separate connected components in segmentations.
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Skeletonize segmentations in 3D using pattern matching.
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Split multilabel segmentations into single-class masks.
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Remove thin regions from segmentations.
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Generate valid area box meshes for tomographic reconstructions.
Logical
Perform logical operations on copick objects.
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Limit mesh vertices within distance of a reference surface.
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Limit picks to those within distance of a reference surface.
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Limit segmentation voxels by distance to a reference.
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Remove enclosed components from a segmentation.
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Perform boolean operations between meshes.
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Filter picks to include only those inside a reference volume.
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Filter picks to exclude those inside a reference volume.
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Perform boolean operations between segmentations.