AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction

Creators: Zheng, Shawn; Wolff, Georg; Greenan, Garrett; Chen, Zhen; Faas, Frank G.A.; Bárcena, Montserrat; Koster, Abraham J.; Cheng, Yifan; Agard, David A.

Abstract

AreTomo, an abbreviation for Alignment and Reconstruction for Electron Tomography, is a GPU accelerated software package that fully automates motion-corrected marker-free tomographic alignment and reconstruction in a single package. By correcting in-plane rotation, translation, and importantly, the local motion resulting from beam-induced motion from tilt to tilt, AreTomo can produce tomograms with sufficient accuracy to be directly used for subtomogram averaging. Another major application is the on-the-fly reconstruction of tomograms in parallel with tilt series collection to provide users with real-time feedback of sample quality allowing users to make any necessary adjustments of collection parameters. Here, the multiple alignment algorithms implemented in AreTomo are described and the local motions measured on a typical tilt series are analyzed. The residual local motion after correction for global motion was found in the range of ± 80 Å, indicating that the accurate correction of local motion is critical for high-resolution cryo-electron tomography (cryoET).

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Acknowledgement

The authors are thankful to Dr. J. Lefman and G. Thomas-Collignon for support and discussion of code optimization. NVIDIA Corporate kindly and generously provided two NVIDIA Quadro GP100 cards and two NVIDIA Quadro GV100 cards. Y.C. is an investigator of Howard Hughes Medical Institute. This work was supported by NIH grants R35GM118099 (DAA) and 1R35GM140847 (YC) as well as NIH S10 equipment grants 1S10OD026881, 1S10OD020054, and 1S10OD021741. We thank David Bulkley, Glenn Gilbert and Matt Harington for their invaluable support of the UCSF cryoEM facility.

The authors are grateful to Prof. Eric Snijder for his critical support of our virology research at Leiden University Medical Center. The data on virus-infected samples were collected at the Netherlands Centre for Electron Nanoscopy (NeCEN) made possible through financial support from the Dutch Roadmap Grant NEMI (NWO grant 184.034.014).

Code Availability

AreTomo can be downloaded from https://msg.ucsf.edu/software and is free for academic use and its source code is available on request directed to the corresponding authors.

Conflict of Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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