Ot2Rec is a Python suite which aims to automate the preprocessing and reconstruction workflow of (cryo-)electron tomographic images. This code is a product of the Artificial Intelligence & Informatics (AI&I) group at the Rosalind Franklin Institute.
Ot2Rec was developed with three aims in mind:
- Enable mixing and matching of different software tools for each stage of image processing through to tomogram reconstruction.
- User-friendly GUI to capture user input, which is kept to a minimum
- Provide framework for performance measurement and eventually automated parameter tuning for optimum reconstruction without user intervention
- Supports a wide range of plugins (MotionCor2, IMOD, AreTomo, Savu, CTFFind4, CTFSim, RedLionfish Deconvolution)
- Runs in parallel on computer clusters
- GPU operations enabled in stages where possible
- Highly modularised API
- Software architecture supports internal and serialised metadata
- Input parameters automatically updated upon running
- Supports multiple data formats (Tiff, Mrc, EER)
- Easy integration of new plugins
For questions regarding Ot2Rec, please raise an issue.
This software is licensed under the Apache License (V2). Copyright (C) 2021 Rosalind Franklin Institute.
- CUDA
- Motioncor2*
- CTFFind4*
- IMOD*
- AreTomo*
- Savu*
- miniconda
- for plugins
Ot2Rec can be obtained by cloning this repository
git clone https://github.com/rosalindfranklininstitute/Ot2Rec.git
-
You will need miniconda. If you have not yet installed miniconda yet, you can obtain it by following the instructions here.
-
(Optional, but recommended) Update miniconda
conda update conda -
Once miniconda is set up, create a virtual environment for Ot2Rec and activate the environment
conda create --name o2r conda activate o2r -
Go to the Ot2Rec folder and install Ot2Rec
cd /path/to/Ot2Rec/ python setup.py develop
Please see the tutorial on our Wiki
We welcome all contributions - you don't have to code to contribute. Please see our contributing guide to get started. If you'd like to write your own plugin, we have a guide to help.
tbc