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Custom Tilt Series Alignment Workflows

WarpTools provides wrappers around some commonly used programs for tilt series alignment IMOD and AreTomo2.

  • ts_aretomo
  • ts_etomo_fiducials
  • ts_etomo_patches

These wrappers provide fully automated solutions and are well integrated into the WarpTools processing flow.

What if you want to do something different?

Tilt Series Alignment in WarpTools

Tilt series alignment in WarpTools can be broken down into three steps

  1. generating tilt series stacks
  2. running a tilt series alignment program
  3. importing alignments

Easy as 1, 2, 3...

WarpTools provides everything you need to do each of these steps separately yourself if you want to work outside the wrappers.

Generate tilt series stacks

WarpTools has a subcommand called ts_stack which can be used to generate tilt series at a specific pixel size. Masked regions from per-tilt mask files in <processing_directory>/mask will be replaced with gaussian noise matching local image statistics which may help subsequent alignments.

WarpTools ts_stack \
--settings <settings_file> \
--angpix 10

Tilt series in .mrc format and tilt angles in the IMOD format .rawtlt file will be placed in subdirectories of <processing_directory>/tiltstack.

Run a tilt series alignment program

Any tilt series alignment program can be run inside these tilt series directories.

Import alignments

WarpTools can import alignment metadata from the IMOD format metadata files

  • .xf text files containing 2D image transformations
  • .tlt text files containing tilt angles

The IMOD xf format is specified in their documentation.

IMOD xf spec

Each linear transformation in a transform file is specified by a line with six numbers: A11 A12 A21 A22 DX DY where the coordinate (X, Y) is transformed to (X', Y') by: X' = A11 * X + A12 * Y + DX Y' = A21 * X + A22 * Y + DY

This is done with the program ts_import_alignments.