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copick add alignment

core

Add an alignment of a tilt series from AreTomo3, Warp, RELION or IMOD files.

Usage

copick add alignment [OPTIONS] PATH

Description

Converts the tool's per-image tilt, rotation and shift to copick's CETS frame, mapping the tool's rows to the sections of the tilt series (by default AreTomo3 by ascending angle, Warp and RELION by nominal angle, IMOD by index). Only rigid alignments are stored; local ones need --rigid-only (AreTomo3) or --allow-varying-grids (Warp).

Arguments

Argument Description
PATH AreTomo3 .aln, Warp tilt-series .xml, RELION tomograms.star, or IMOD basename / .xf.

Options

Option Type Default Description
-c, --config path — Path to the configuration file.
--run text required The run.
--format choice (aretomo3 | warp | relion | imod) required Format of PATH.
--ts-type text raw The tilt series the alignment aligns.
--name text — Name of the alignment. Default: the format.
--tomo-name text — RELION: the tomogram, if the file lists several.
--reference-tomogram text — The tomogram ('tomo_type@voxel_size') the tool reconstructed with this alignment; it becomes the reference volume and is linked.
--volume-size text — Size 'x,y,z' of the tool's reconstruction in pixels of the aligned stack, overriding the files.
--thickness integer — Thickness of the tool's reconstruction in pixels (AreTomo3 -VolZ), overriding the files.
--native-pixel-size float — Pixel size of the stack the tool aligned, if not that of the tilt series (e.g. a binned stack).
--link-tomogram text · multiple — A tomogram ('tomo_type@voxel_size') reconstructed with this alignment. Repeatable.
--preferred boolean flag False Prefer this alignment over the tilt series' others.
--ctf file — CTF fits to store on the tilt series (e.g. the AreTomo3 _CTF.txt).
--ctf-format choice (aretomo3 | ctffind4 | warp | relion) — Format of --ctf. Default: from its name.
--tlt file — AreTomo3 _TLT.txt whose acquisition order and dose to store on the tilt series.
--update-tilt-series / --no-update-tilt-series boolean flag True Store --ctf and --tlt on the tilt series (writable tilt series only).
--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.
--assume-frame choice (half | floor) — IMOD only: centre convention (N/2 or floor(N/2)) for odd image or volume sizes.
--rigid-only boolean flag False Import the rigid part of a local (patch) AreTomo3 alignment; the local part is lost.
--allow-varying-grids boolean flag False Warp only: drop spatially varying deformation grids; only the rigid part is kept.
--overwrite / --no-overwrite boolean flag False Replace an existing alignment.
--debug / --no-debug boolean flag False Enable debug logging.

Examples

# An AreTomo3 alignment with its CTF fits; the reconstruction is linked
copick add alignment TS_01.aln --format aretomo3 --run TS_01 --ctf TS_01_CTF.txt \
    --tlt TS_01_TLT.txt --reference-tomogram aretomo3@7.7 -c config.json

# A RELION 5 alignment
copick add alignment tomograms.star --format relion --run TS_01 --tomo-name TS_01 -c config.json

See also