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copick add tiltseries

core

Add a tilt series from a stack and its acquisition metadata.

Usage

copick add tiltseries [OPTIONS] PATH

Description

Imports an MRC, TIFF or Zarr stack as a multiscale tilt series, with the nominal tilt angles, acquisition order, dose, movies and CTF fits found in a SerialEM mdoc (next to the stack by default), an angle file and a CTF file. A glob pattern imports many stacks; the run name is then taken from each file name.

Arguments

Argument Description
PATH The stack (.mrc, .st, .mrcs, .ali, .tif, .zarr) or a glob pattern.

Options

Option Type Default Description
-c, --config path — Path to the configuration file.
--run-name-prefix text "" Prefix to prepend to run names after regex extraction.
--run-regex text (.*) Regular expression to extract the run name from the filename. If not provided, will use the file name without extension. The regex should capture the run name in the first group.
--run text "" The name of the run. If not specified, will use the name of the file (stripping extension), ignored if PATH is glob pattern.
--ts-type text raw Type of the tilt series.
--file-type choice (mrc | tiff | zarr) — Format of the stack. Default: from the extension (.mrc, .st, .mrcs, .ali, .tif, .tiff, .zarr).
--pixel-size float — Pixel size in Angstrom, overriding the stack's header.
--angles file — Tilt angles in stack order: IMOD .rawtlt/.tlt or AreTomo3 _TLT.txt.
--angles-format choice (rawtlt | tlt | aretomo3-tlt) — Format of --angles. Default: from its name.
--mdoc text auto SerialEM mdoc: a path, 'auto' (the stack's sibling .mdoc or .mdoc) or 'none'.
--ctf file — Per-image CTF fits: AreTomo3 _CTF.txt, CTFFIND4 output, Warp XML or RELION tomograms.star.
--ctf-format choice (aretomo3 | ctffind4 | warp | relion) — Format of --ctf. Default: from its name.
--dose-per-tilt float — Dose of every image in e/Ų, overriding the mdoc.
--voltage float — Acceleration voltage in kV.
--cs float — Spherical aberration in mm.
--amplitude-contrast float — Amplitude contrast (e.g. 0.07).
--tilt-axis float — Tilt-axis angle in degrees, overriding the mdoc.
--handedness choice (right_handed | left_handed) — Handedness of the acquisition geometry, if known.
--section-map choice (auto | index | sorted | angle) auto How the rows of a file map to tilt-series sections: 'auto' (the file's default), 'index' (row i is section i), 'sorted' (rows in ascending angle pair with sections in ascending nominal angle) or 'angle' (nearest nominal angle).
--angle-tolerance float 1.0 Largest difference in degrees between a row's angle and the nominal angle of its section.
--sort-by-angle / --keep-order boolean flag False Store the sections in ascending nominal tilt angle, or in the stack's order.
--is-aligned boolean flag False The images are already aligned.
--pyramid-levels integer 3 Number of pyramid levels.
--chunk-size text 1,1024,1024 Chunk shape 'z,y,x'.
--dtype choice (float32 | float16 | int16 | uint16 | int8 | uint8 | keep) float32 Data type of the stored images ('keep': that of the stack).
--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

# A SerialEM stack with its mdoc (TS_01.mrc.mdoc) next to it
copick add tiltseries TS_01.mrc -c config.json --voltage 300 --cs 2.7

# An AreTomo3 output stack with its angle and CTF files
copick add tiltseries TS_01.mrc --angles TS_01_TLT.txt --ctf TS_01_CTF.txt -c config.json

# Many stacks, run names from the file names
copick add tiltseries "stacks/TS_*.st" -c config.json --run-regex "^(TS_\d+)"

See also