Scripts to make cryo-electron tomography a bit easier
Full options can be listed via:
tomotools --help
tomotools [subcommand] --help
- blend-montages: Blends SerialEM montages, write results to separate folder.
- Example:
tomotools blend-montages MMM*.mrc montages-blended
- Example:
- batch-prepare-tiltseries: Prepare tiltseries for reconstruction.
- Takes data directory from SerialEM 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 batch-prepare-tiltseries --mcbin 1 --gainref frames/GainRef.dm4 *.mrc ts-aligned
- reconstruct: Perform batch reconstruction using AreTomo and 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. Reconstruction is done using imod's
tilt. - Example:
tomotools reconstruct --move --bin 4 --sirt 12 --do-evn-odd *.mrc
- 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. Reconstruction is done using imod's
- 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 tom_deconv.m script.
- merge-dboxes: Very beta, merges Dynamo DBoxes.
- semnavigator: Display SerialEM navigator files to find back you tomogram positions
- create-movie: Create a movie from a series of image files.
- nff-to-amiramesh
- update: Automatically pulls the most recent version from GitHub and runs
pip install --upgradeon it.
We suggest installing tomotools into its own conda / mamba environment. If you can only access your userspace, consider using micromamba.
conda create -n tomotools python=3.8 cudatoolkit=11.0 cudnn=8.0 -c conda-forge
conda activate tomotools
pip install 'git+https://github.com/MoritzWM/tomotools.git'
With tomotools installed into a conda environment, you can then start tomotools with:
conda activate tomotools
tomotools --help
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'