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
- generating tilt series stacks
- running a tilt series alignment program
- 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
.