TomoBEAR

The general description

TomoBEAR can assist you in large-scale processing of the tomographic data acquired on the electron microscope starting from the raw tilt series, possibly dose fractionated, containing fiducials or fiducial-less or already assembled tilt stacks up to sample volume 3D reconstruction and even further - to the sub-nanometer EM map of the biological structure of interest.

TomoBEAR is designed to operate in an automated manner minimizing user intervention where that is possible. The pipeline consists of over 20 different modules which integrate the original code of widely used cryo-ET/StA processing tools (e.g. IMOD, Dynamo, MotionCor2, AreTomo, GCTF/CTFFIN4), including the modern neural network tools (e.g. IsoNet, crYOLO), as well as our developments, including our StA framework called SUSAN, in a single workflow.

Since the number of the TomoBEAR parameters is huge, to help users cope with that we have carefully designed a predefined set of defaults which were chosen based on several different cryo-ET datasets, including standard cryo-ET benchmarks. A description of all modules and corresponding default values is given on the Modules page.

The execution can be sequential as well as CPU/GPU-parallelized and suitable for both standalone workstations and high-performance computing (HPC) clusters.

Publication

Implementation details and benchmarks may be found in our preprint:
Balyschew N, Yushkevich A, Mikirtumov V, Sanchez RM, Sprink T, Kudryashev M. Streamlined Structure Determination by Cryo-Electron Tomography and Subtomogram Averaging using TomoBEAR. [Preprint] 2023. bioRxiv doi: 10.1101/2023.01.10.523437

Quick start (tutorial)

We have prepared a range of short (8-12 min) video tutorials explaining setup, usage and example output of the TomoBEAR to help you get started with TomoBEAR based on the ribosome tutorial:

• Video 1: how to get the latest TomoBEAR version and configure TomoBEAR and its dependencies;
• Video 2: description of the project configuration file and the pipeline execution;
• Video 3: additional configuration file parameters description, TomoBEAR-IMOD-TomoBEAR loop for checking tilt series alignment results and fiducials refinement (if needed);
• Video 4: checking on further intermediate results (alignment, CTF-correction, reconstruction, template matching).

Documentation

Detailed information on the installation, setup and usage as well as tutorials and example results can be found in the corresponding wiki.

Downloads. Releases

TomoBEAR releases are available at the Releases page.

If you want to clone a specific TomoBEAR version, please refer to the Setup > Get source code and binary > Clone specific version section on the wiki page Installation and Setup.

Licensing

This work is licensed under multiple licenses:

• The source code (MATLAB, Python, Bash, etc.) and the accompanying material are licensed under GPL3.
• The modified MATLAB source code of the Dynamo package (dynamo/) is licensed under GPL2.
• The documentation (wiki/), TomoBEAR logo and accompanying images (images/), as well as configuration files (configurations/), are licensed under CC-BY-4.0.

Citation policies

If you use TomoBEAR or its parts in your research, please cite TomoBEAR along with all external software packages which you have used under TomoBEAR.

The TomoBEAR modules dependencies on third-party software are listed on the page Modules and the list of the corresponding references to cite is located on the page External Software.

TomoBEAR as a FAIR software

The TomoBEAR project meets the conditions of the FAIR and FAIR4RS principles:

• TomoBEAR source code is fully deposited on the publicly accessible repository GitHub (https://github.com/KudryashevLab/TomoBEAR), is versioned and described with rich metadata (e.g. information on installation, usage and troubleshooting, citation, licensing and releases);
• TomoBEAR is licensed under the open source GNU General Public License version 3 and the corresponding GitHub repository contains information about its development;
• The release version of TomoBEAR was deposited on the open research data repository Zenodo (https://zenodo.org/record/8221247) and is accessible by search machines;
• TomoBEAR operates and exchanges data with other software using standard cryo-ET input and output file types like TIF, MRC, EER, XF, TBL, STAR, etc.;
• TomoBEAR code includes cryo-ET domain-relevant dependencies to other software, which are listed for each module along with the tested software versions on the page External Software;
• TomoBEAR project has open communication channels for users and contributors (such as dedicated GitHub pages Issues and Discussions as well as direct communication with developers by e-mail) and TomoBEAR GitHub repository contains detailed information for contributors (see CONTRIBUTING.md).

Feedback

In case of any questions, issues or suggestions you may interact with us in one of the following ways:

• open an issue/bug report, feature request or post a question using Issue Tracker;
• write an e-mail to Misha Kudryashev or Artsemi Yushkevich;
• start a discussion in Discussions;

Contribution

If you wish to contribute, please, fork this repository and make a pull request back with your changes and a short description. For further details on contribution, please read our contribution guidelines on the GitHub repository.