AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction
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...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Journal of Structural Biology: X |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2590152422000095 |
| _version_ | 1811298228219412480 |
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| author | Shawn Zheng Georg Wolff Garrett Greenan Zhen Chen Frank G.A. Faas Montserrat Bárcena Abraham J. Koster Yifan Cheng David A. Agard |
| author_facet | Shawn Zheng Georg Wolff Garrett Greenan Zhen Chen Frank G.A. Faas Montserrat Bárcena Abraham J. Koster Yifan Cheng David A. Agard |
| author_sort | Shawn Zheng |
| collection | DOAJ |
| description | 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). |
| first_indexed | 2024-04-13T06:16:23Z |
| format | Article |
| id | doaj.art-8cf7635fbb844f1d9b77ae94bc3a04d3 |
| institution | Directory Open Access Journal |
| issn | 2590-1524 |
| language | English |
| last_indexed | 2024-04-13T06:16:23Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Structural Biology: X |
| spelling | doaj.art-8cf7635fbb844f1d9b77ae94bc3a04d32022-12-22T02:58:48ZengElsevierJournal of Structural Biology: X2590-15242022-01-016100068AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstructionShawn Zheng0Georg Wolff1Garrett Greenan2Zhen Chen3Frank G.A. Faas4Montserrat Bárcena5Abraham J. Koster6Yifan Cheng7David A. Agard8Dept. Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, USASection Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, NetherlandsDept. Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USADept. Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USASection Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, NetherlandsSection Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, NetherlandsSection Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, NetherlandsDept. Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, USA; Corresponding authors at: Dept. Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA.Dept. Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA; Corresponding authors at: Dept. Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA.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).http://www.sciencedirect.com/science/article/pii/S2590152422000095Electron tomographyTomographic alignmentMarker-free alignmentTomographic reconstructionLocal beam-induced motionGPU acceleration |
| spellingShingle | Shawn Zheng Georg Wolff Garrett Greenan Zhen Chen Frank G.A. Faas Montserrat Bárcena Abraham J. Koster Yifan Cheng David A. Agard AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction Journal of Structural Biology: X Electron tomography Tomographic alignment Marker-free alignment Tomographic reconstruction Local beam-induced motion GPU acceleration |
| title | AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction |
| title_full | AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction |
| title_fullStr | AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction |
| title_full_unstemmed | AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction |
| title_short | AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction |
| title_sort | aretomo an integrated software package for automated marker free motion corrected cryo electron tomographic alignment and reconstruction |
| topic | Electron tomography Tomographic alignment Marker-free alignment Tomographic reconstruction Local beam-induced motion GPU acceleration |
| url | http://www.sciencedirect.com/science/article/pii/S2590152422000095 |
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