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

Journal of Structural Biology X, vol. 6, pp. 100068

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).

Authors 9

1. Shawn Q. Zheng

   Howard Hughes Medical Institute · University of California, San Francisco

   Affiliation as printed

   Dept. Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA

   Howard Hughes Medical Institute, USA

2. Georg Wolff Aachen Section Electron Microscopy Department of Cell and Chemical Biology

   Leiden University Medical Center

   Affiliation as printed

   Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, Netherlands

3. Garrett A. Greenan

   University of California, San Francisco

   Affiliation as printed

   Dept. Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA

4. Zhen Chen

   University of California, San Francisco

   Affiliation as printed

   Dept. Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA

5. Frank G. A. Faas Aachen Section Electron Microscopy Department of Cell and Chemical Biology

   Leiden University Medical Center

   Affiliation as printed

   Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, Netherlands

6. Montserrat Bárcena Aachen Section Electron Microscopy Department of Cell and Chemical Biology

   Leiden University Medical Center

   Affiliation as printed

   Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, Netherlands

7. Abraham J. Koster Aachen Section Electron Microscopy Department of Cell and Chemical Biology

   Leiden University Medical Center

   Affiliation as printed

   Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, Netherlands

8. Yifan Cheng corresponding

   Howard Hughes Medical Institute · University of California, San Francisco

   Affiliation as printed

   Dept. Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA

   Howard Hughes Medical Institute, USA

9. David A. Agard corresponding

   University of California, San Francisco

   Affiliation as printed

   Dept. Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA