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copick add picks-dynamo

core

Add picks from Dynamo table files containing multiple tomograms.

Usage

copick add picks-dynamo [OPTIONS] PATH

Description

Imports particle picks from one or more Dynamo table files, where a single file can hold picks from many tomograms (the tomogram index is read from column 20). Provide exactly one of --index-map (a 2-column CSV/TSV mapping tomogram index to run name, e.g. 1,TS_001) or --tomolist (a Dynamo tomolist whose run names come from the MRC filenames) to map indices to copick runs. A voxel size is required to convert coordinates.

Arguments

Argument Description
PATH Path to the Dynamo table file (.tbl) or a glob pattern.

Options

Option Type Default Description
-c, --config path — Path to the configuration file.
--object-name text required Name of the pickable object (must exist in config).
--session-id text 1 Session ID for the annotation.
--user-id text copick User ID for the annotation.
--voxel-size float required Voxel size in Angstrom (required for coordinate conversion).
--index-map path — Path to a CSV/TSV file mapping tomogram index to run name. Mutually exclusive with --tomolist.
--tomolist path — Path to a Dynamo tomolist file (2-column TSV: index, MRC path). Run names are extracted from MRC filenames. Mutually exclusive with --index-map.
--max-workers integer 4 Maximum number of worker threads.
--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 using an index map
copick add picks-dynamo particles.tbl -c config.json --object-name ribosome \
    --voxel-size 10.0 --index-map tomo_mapping.csv

# Import using a Dynamo tomolist (run names from MRC filenames)
copick add picks-dynamo particles.tbl -c config.json --object-name ribosome \
    --voxel-size 10.0 --tomolist tomograms.doc

# Import multiple files via a glob pattern
copick add picks-dynamo "*.tbl" -c config.json --object-name ribosome \
    --voxel-size 10.0 --index-map tomo_mapping.csv

See also