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copick add tomograms-dynamo

core

Add tomograms from a Dynamo tomolist file.

Usage

copick add tomograms-dynamo [OPTIONS]

Description

Reads a Dynamo tomolist (a 2-column TSV of tomogram index and MRC path) and imports each listed tomogram into its own run. Run names are taken from the MRC filenames unless --index-map supplies an explicit index-to-run mapping. The file format is inferred from the extension unless --file-type is given, and a multiscale pyramid is computed by default.

Options

Option Type Default Description
-c, --config path — Path to the configuration file.
--tomolist path required Path to Dynamo tomolist file (2-column TSV: index, MRC path).
--index-map path — Path to CSV/TSV mapping tomogram index to run name. If not provided, run names are extracted from filenames.
--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 in the tomogram header.
--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 from a Dynamo tomolist (run names from MRC filenames)
copick add tomograms-dynamo -c config.json --tomolist tomograms.doc

# Import with custom run names from an index map
copick add tomograms-dynamo -c config.json --tomolist tomograms.doc \
    --index-map run_mapping.csv

See also