tomodrgn backproject_voxel

Purpose

Reconstruct a 3-D volume from pre-aligned 2-D tilt-series projections via weighted back projection. CTF correction is performed by phase flipping only.

Sample usage

The examples below are adapted from tomodrgn/testing/commandtest*.py, and rely on other outputs from commandtest.py to execute successfully.

# Warp v1 style inputs
tomodrgn \
    backproject_voxel \
    data/10076_classE_32_sim.star \
    --output output/00_backproject/classE_sim.mrc \
    --uninvert-data \
    --recon-dose-weight

# WarpTools style inputs
tomodrgn \
    backproject_voxel \
    data/warptools_test_4-tomos_10-ptcls_box-32_angpix-12_optimisation_set.star \
    --output output/backproject/warptools_70S_doseweight.mrc \
    --uninvert-data \
    --flip \   # note: flip is used because the handedness of this toy dataset is inverted
    --recon-dose-weight

Arguments

usage: backproject_voxel [-h] --output OUTPUT [--plot-format {png,svgz}]
                         [--source-software {auto,warp,cryosrpnt,nextpyp,cistem,warptools,relion}]
                         [--ind-ptcls PKL] [--ind-imgs IND_IMGS]
                         [--sort-ptcl-imgs {unsorted,dose_ascending,random}]
                         [--use-first-ntilts USE_FIRST_NTILTS]
                         [--use-first-nptcls USE_FIRST_NPTCLS]
                         [--uninvert-data] [--datadir DATADIR] [--lazy]
                         [--recon-tilt-weight] [--recon-dose-weight]
                         [--lowpass LOWPASS] [--flip]
                         particles

Positional Arguments

particles

Input particles_imageseries.star (if using Warp/M or NextPYP), or optimisation set star file (if using WarpTools or RELION v5)

Named Arguments

--output

Output .mrc file

--plot-format

Possible choices: png, svgz

File format with which to save plots

Default: 'png'

Particle starfile loading and filtering

--source-software

Possible choices: auto, warp, cryosrpnt, nextpyp, cistem, warptools, relion

Manually set the software used to extract particles. Default is to auto-detect.

Default: 'auto'

--ind-ptcls

Filter starfile by particles (unique rlnGroupName values) using np array pkl as indices

--ind-imgs

Filter starfile by particle images (star file rows) using np array pkl as indices

--sort-ptcl-imgs

Possible choices: unsorted, dose_ascending, random

Sort the star file images on a per-particle basis by the specified criteria

Default: 'unsorted'

--use-first-ntilts

Keep the first use_first_ntilts images of each particle in the sorted star file.Default -1 means to use all. Will drop particles with fewer than this many tilt images.

Default: -1

--use-first-nptcls

Keep the first use_first_nptcls particles in the sorted star file. Default -1 means to use all.

Default: -1

Dataset loading options

--uninvert-data

Do not invert data sign

Default: True

--datadir

Path prefix to particle stack if loading relative paths star file

--lazy

Lazy loading if full dataset is too large to fit in memory (Should copy dataset to SSD)

Default: False

Reconstruction options

--recon-tilt-weight

Weight images in fourier space by cosine(tilt_angle)

Default: False

--recon-dose-weight

Weight images in fourieri space per tilt per pixel by dose dependent amplitude attenuation

Default: False

--lowpass

Lowpass filter reconstructed volume to this resolution in Angstrom. Defaults to FSC=0.143 correlation between half-maps

--flip

Flip handedness of output volume

Default: False

Common next steps

• Backproject a different particle subset (e.g. using --ind-ptcls) to validate structural heterogeneity in a subset of particles identified by tomoDRGN’s decoder network