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copick export tomogram

core

Export tomograms to external formats (MRC, TIFF, Zarr).

Usage

copick export tomogram [OPTIONS]

Description

Selects tomograms with the --tomogram-uri filter (e.g. wbp@10.0 or *@*, in tomo-type@voxel-spacing form) and writes each one to the chosen format under --output-dir. For MRC and TIFF the --level pyramid level is exported and TIFF supports --compression; for Zarr, --copy-all-levels writes the full multiscale pyramid. Restrict the export to specific runs with --run-names.

Options

Option Type Default Description
-c, --config path — Path to the configuration file.
--tomogram-uri text required URI to filter tomograms for export (e.g., 'wbp@10.0' or '@').
--run-names text "" Comma-separated list of run names to export. If not specified, exports from all runs.
--output-dir directory required Output directory for exported files.
--output-format choice (mrc | tiff | zarr) required Output format for tomograms.
--copy-all-levels / --level-only boolean flag True Copy all pyramid levels for Zarr output.
--compression choice (lzw | zlib | jpeg | none) — Compression method for TIFF output.
--level integer 0 Pyramid level to export (for MRC and TIFF).
--max-workers integer 4 Maximum number of worker threads.
--debug / --no-debug boolean flag False Enable debug logging.

Examples

# Export all wbp tomograms at 10A to MRC
copick export tomogram -c config.json --tomogram-uri "wbp@10.0" \
    --output-dir ./output --output-format mrc

# Export tomograms to TIFF with LZW compression
copick export tomogram -c config.json --tomogram-uri "wbp@10.0" \
    --output-dir ./output --output-format tiff --compression lzw

# Export to Zarr, copying the full multiscale pyramid
copick export tomogram -c config.json --tomogram-uri "*@*" \
    --output-dir ./output --output-format zarr --copy-all-levels

See also