copick export tiltseries

core

Export tilt series as MRC, TIFF or Zarr stacks.

Usage

copick export tiltseries [OPTIONS]

Description

Writes each selected tilt series as '.mrc' (or .tif, .zarr) with its nominal tilt angles ('.rawtlt', '.tlt' or AreTomo3's '_TLT.txt' with acquisition order and dose) and, optionally, its CTF fits.

Options

Option	Type	Default	Description
`-c, --config`	path	—	Path to the configuration file.
`--run-names, -r`	text · multiple	—	Specific run names to process (default: all runs). Repeatable; pass -r once per run.
`--tiltseries-uri`	text	required	Tilt series to export (e.g. 'raw').
`--output-dir`	directory	required	Output directory for exported files.
`--output-format`	choice (mrc \| tiff \| zarr)	`mrc`	Format of the stack.
`--level`	integer	`0`	Pyramid level (mrc, tiff).
`--angles`	choice (rawtlt \| tlt \| aretomo3-tlt \| none)	`rawtlt`	Angle file to write next to the stack.
`--ctf-format`	choice (aretomo3 \| ctffind4 \| none)	`none`	CTF file to write next to the stack.
`--debug / --no-debug`	boolean flag	`False`	Enable debug logging.

Examples

copick export tiltseries -c config.json --tiltseries-uri raw --output-dir out --angles aretomo3-tlt \
    --ctf-format aretomo3