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What is Ot2Rec?

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.

Initially built with the principle of least privilege, Ot2Rec works as a wrapper suite of the batch version of IMOD and takes the user through the data processing workflow with a minimal amount of human intervention required. This allows smooth transitions between processing stages, and results in overall speed-up when compared with the fully manual counterpart of the same workflow.

Features

• Preprocessing of tomographic data with MotionCor2 and ctffind
• Image reconstruction and tomogram generation with IMOD
• 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 (TIFFs / MRCs)
• Easy integration of new plugins

Contacts

For questions regarding Ot2Rec, please feel free to contact developer at neville.yee@rfi.ac.uk.

License

This software is licensed under the Apache License (V2). Copyright (C) 2021 Rosalind Franklin Institute.