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copick add tomograms-relion

core

Add tomograms from a RELION tomograms.star file.

Usage

copick add tomograms-relion [OPTIONS]

Description

Reads a RELION tomograms.star file and imports each reconstruction into its own run, with run names taken from the _rlnTomoName column. Voxel sizes are read from the star file unless overridden with --voxel-size, and --base-dir sets the RELION project root used to resolve relative paths in the file. Use --half to choose which reconstruction half to import. A multiscale pyramid is computed by default.

Options

Option Type Default Description
-c, --config path — Path to the configuration file.
--tomograms-star path required Path to RELION tomograms.star file.
--base-dir directory required RELION project root directory for resolving relative paths in the STAR file.
--half choice (half1 | half2) half1 Which reconstruction half to import (half1 or half2).
--tomo-type text wbp The name of the tomogram (e.g. wbp).
--file-type choice (mrc | zarr | tiff | em) — The file type of the tomogram. Will guess type based on extension if omitted.
--voxel-size float — Voxel size in Angstrom. Overrides voxel size from the star file.
--chunk-size text 256,256,256 Chunk size for the output Zarr file.
--pyramid-levels integer 3 Number of pyramid levels (each level corresponds to downscaling by factor two).
--create-pyramid / --no-create-pyramid boolean flag True Compute the multiscale pyramid.
--max-workers integer 4 Maximum number of worker threads.
--flip text — Flip (reverse) volume along specified axes. Comma-separated axis indices, e.g., '0' to flip Z, '0,2' to flip Z and X. Default: no flipping.
--transpose text — Transpose volume axes. Specify target axis order, e.g., '2,1,0' to reverse all axes, '0,2,1' to swap Y and X. Default: no transposition.
--overwrite / --no-overwrite boolean flag False Overwrite the object if it exists.
--create / --no-create boolean flag True Create the object if it does not exist.
--debug / --no-debug boolean flag False Enable debug logging.

Examples

# Import the half1 reconstructions (default)
copick add tomograms-relion -c config.json --tomograms-star tomograms.star \
    --base-dir /path/to/relion_project

# Import the half2 reconstructions instead
copick add tomograms-relion -c config.json --tomograms-star tomograms.star \
    --base-dir /path/to/relion_project --half half2

See also