tomotools

Scripts to make cryo-electron tomography a bit easier

Usage

Full options can be listed via: tomotools --help tomotools [subcommand] --help

Currently supported subcommands:

Preprocessing & Reconstruction:

• blend-montages: Blends SerialEM montages, write results to separate folder.
  • Example: tomotools blend-montages MMM*.mrc montages-blended
• preprocess: Prepare tiltseries for reconstruction.
  • Takes data directory from SerialEM or Tomo5 as input and writes the final stacks to the target directory.
  • Frames are aligned using MotionCor2 and reordered if desired. Supports GainRef conversion from dm4 to mrc and the SerialEM-generated defects.txt.
  • Example: tomotools preprocess --mcbin 1 --gainref frames/GainRef.dm4 *.mrc ts-aligned
• reconstruct: Perform batch reconstruction using AreTomo or imod.
  • Takes tiltseries and their associated mdoc files as input, automatically identified associated EVN/ODD stacks. Finds alignment using AreTomo, then applies it to EVN/ODD stacks. Alternatively, can move files and then open etomo. Reconstruction is done using imod's tilt.
  • Example: tomotools reconstruct --move --bin 4 --sirt 12 --do-evn-odd *.mrc

Denoising & Deconvolution

• cryocare-extract: Extract cryoCARE training data from EVN/ODD reconstructions.
• cryocare-train: Wrapper for cryoCARE training.
• cryocare-predict: Wrapper for cryoCARE prediction.
• deconv: Python implementation of Dimitry Tegunov's tomdeconv.m_ script.

Subtomogram Averaging Preparation

• imod2warp: Takes a list of imod directories or a file listing them and prepares everything for Warp or WarpTools.
• aretomo2warp: Takes a list of directories with AreTomo-aligned tiltseries or a file listing them and prepares everything for Warp or WarpTools.
• imod2tomotwin: Takes a list of imod directories and reconstructs for TomoTwin picking.
• aretomo2tomotwin: Takes a list of AreTomo directories and reconstructs for TomoTwin picking.
• fit-ctf: Run imod ctfplotter on a set of tiltseries and save results to their folder.
• merge-dboxes: Very beta, merges Dynamo DBoxes.
• reconstruct-3dctf: Perform reconstruction using imods ctf3d function.

Other

• semnavigator: Display SerialEM navigator files to find back you tomogram positions
• create-movie: Create a movie from a series of image files.
• update: Automatically pulls the most recent version from GitHub and runs pip install --upgrade on it.
• restore-frames: Restore SubFramePath to mdoc of tiltseries preprocessed with tomotools < 0.4.

Dependencies

tomotools depends on commands from MotionCor2 or MotionCor3, IMOD, and AreTomo 1.X or AreTomo2 for full functionality. IMOD should be in PATH. MotionCor2/3 and AreTomo2/3 can either be in PATH as MotionCor2 / MotionCor3 or AreTomo / AreTomo2 respectively, or set using the envar MOTIONCOR_EXECUTABLE or ARETOMO_EXECUTABLE.

Installation

We suggest installing tomotools into its own conda / mamba environment. If you can only access your userspace, consider using micromamba.

If you want to use the scripts interfacing with cryoCARE denoising, please install tomotools[cryocare].

Full Install via:

conda create -n tomotools python=3.8 cudatoolkit=11.0 cudnn=8.0 -c conda-forge conda activate tomotools pip install "tomotools[cryocare] @ git+https://github.com/tomotools/tomotools.git"

Minimal Install via:

conda create -n tomotools python=3.8 -c conda-forge conda activate tomotools pip install "tomotools @ git+https://github.com/tomotools/tomotools.git"

Confirm Installation:

With tomotools installed into a conda environment, you can then start tomotools with: conda activate tomotools tomotools --help

Notes on sbgrid:

If you're using an sbgrid environment, make sure to set the following in your .sbgrid.conf file:

PYTHON_X=3.8.8 (anything > 3.8 works)

Additionally, try pip --version to make sure it's correctly working. This is required for tomotools update. Else, you can add the following line to your .bashrc:

alias pip='python -m pip'

Likely, you will also need to add your local Python path to .bashrc:

export PATH="/YOURHOMEFOLDER/.local/bin:$PATH"

Feedback, Bug Reports and Contributions are always welcome!