An IMOD wrapper for performing patch-based tilt-series alignment. This wrapper will continue being developed as and when I feel a certain functionality is needed. Also note that I am developing this against Warp/Relion/M pipeline. If I start using Relion 5.0 or < I might try to develop for it as well. However, dont hold your breath.
git clone https://github.com/shahpnmlab/automateImod.git
conda create -n automateImod python=3.10 -y
conda activate automateImod
cd automateImod
pip install -e .
Also verify that IMOD is installed in your user account and installed and in your $PATH; which 3dmodshould
tell you the path to your 3dmod executable.
Verify if the package has been installed using the following command
automateImod --help
You should see -
Usage: automateImod [OPTIONS] COMMAND [ARGS]...
Options:
--install-completion [bash|zsh|fish|powershell|pwsh]
Install completion for the specified shell.
--show-completion [bash|zsh|fish|powershell|pwsh]
Show completion for the specified shell, to
copy it or customize the installation.
--help Show this message and exit.
Commands:
align-tilts Perform patch-based tilt series tracking using...
reconstruct-tomograms Reconstruct tomograms using IMOD of aligned tilt...
update-warp-xml Read in the log file generated by align-tilts...
Before staring to use the program make sure that the expected directory structure is followed, which is -
/PATH/TO/IMOD/TS_BASENAME/TS_BASENAME.{mrc,st}
TS_BASENAME.rawtlt
/PATH/TO/MDOCS/TS_BASENAME.mdoc
Note that the script cannot handle TS_BASENAME.mrc.mdoc files. In order to make things work, rename the mdoc file as indicated above. And NO, i will not modify my script to handle badly named mdoc files.
The main sub-command that you will want to run is the align-tilts command
automateImod align-tilts --help
Usage: automateImod align-tilts [OPTIONS]
Perform patch-based tilt series tracking using IMOD routines
Options:
--ts-data-path PATH directory containing tilt series data [required]
--ts-mdoc-path PATH directory containing the tilt series mdoc file
--ts-basename TEXT tilt series_basename e.g. Position_1 [required]
--ts-tilt-axis TEXT tilt axis value [required]
--ts-bin TEXT bin value to reduce the tilt series size by.
[required]
--ts-patch-size TEXT Size of patches to perform patch_tracking [required]
--help Show this message and exit.
To align multiple series, run it as a bash for loop, by looping over folders within which the tilt-series data
resides.
The mdoc file will be read to identify problematic tilt-frames and logged to text file in the imod processing directory.
The update-wrp-xml command can then be issued to disable tilts with large shifts.
automateImod update-warp-xml --help
Usage: automateImod update-warp-xml [OPTIONS]
Read in the log file generated by align-tilts and disable tilts with large
shifts.
Options:
--ts-xml-path TEXT Path to Warp processing results [required]
--ts-basename TEXT Basename of the tilt series [required]
--ts-log-path TEXT Path to imod processing directory [required]
--help Show this message and exit.
You can briefly review the results of your aligned tilt-series by reconstructing tomograms by running -
Usage: automateImod reconstruct-tomograms [OPTIONS]
Options:
--ts-data-path PATH directory containing tilt series data [required]
--ts-basename TEXT tilt series_basename e.g. Position_ [required]
--ts-extension TEXT does the TS end with an st or mrc extension? [default:
mrc]
--tomo-bin TEXT binned tomogram size [required]
--help Show this message and exit.
- Introduced a dark tilt detection routine to remove these tilts even before performing coarse alignments.
- Automatic detection of tilt series extension.
- Updates warp xml files by changing the <frame>.xml to <frame>.xml.bkp
- Support Relion 5.0 star files at some point.
- The automateImod.marker file has the wrong tilt indices.