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copick export segmentation

core

Export segmentations to MRC, TIFF, Zarr, or EM.

Usage

copick export segmentation [OPTIONS]

Description

Selects segmentations with the --segmentation-uri filter (e.g. membrane:user1/*@10.0, in name:user/session@voxel-spacing form) and writes each label map to the chosen format under --output-dir. For MRC, TIFF, and EM 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.
--segmentation-uri text required URI to filter segmentations for export (e.g., 'membrane:user1/*@10.0').
--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 | em) required Output format for segmentations.
--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 membrane segmentations at 10A to MRC
copick export segmentation -c config.json \
    --segmentation-uri "membrane:*/*@10.0" \
    --output-dir ./output --output-format mrc

# Export segmentations to TIFF with LZW compression
copick export segmentation -c config.json \
    --segmentation-uri "membrane:user1/*@10.0" \
    --output-dir ./output --output-format tiff --compression lzw

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

See also