Protocol for Convolutional Neural Networks based Automated Cellular Cryo-Electron Tomograms Annotation

doi:10.1038/protex.2017.095

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Method Article

Steven J. Ludtke, Muyuan Chen, Dai Wei, Stella Y. Sun, Darius Jonasch, Cynthia Y. He, Michael F. Schmid, Wah Chiu

Steven J. Ludtke

Ludtke Lab, Baylor College of Medicine

Corresponding Author

Muyuan Chen

Ludtke Lab, Baylor College of Medicine

Dai Wei

Department of Cell Biology and Neuroscience, Center for Integrative Proteomics Research, Rutgers University, Piscataway, New Jersey USA

Stella Y. Sun

Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

Darius Jonasch

Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

Cynthia Y. He

Department of Biological Science, Centre for BioImaging Sciences, National University of Singapore, Singapore

Michael F. Schmid

Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

Wah Chiu

Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

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Cellular Electron Cryotomography (CryoET) offers the ability to look inside cells and observe macromolecules frozen in action. A primary challenge for this technique is identifying and extracting the molecular components within the crowded cellular environment. We introduce a method using convolutional neural networks to dramatically reduce the time and human effort required for subcellular annotation and feature extraction.

Keywords

Cellular Electron Cryotomography, convolutional neural network, tomogram annotation

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The authors declare no competing financial interests.

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Associated Publications

Convolutional neural networks for automated annotation of cellular cryo-electron tomograms
by Muyuan Chen, Wei Dai, Stella Y Sun, +5
Nature Methods (29 August, 2017)

An open repository of community-contributed protocols sponsored by Nature Research.

Learn more about Protocol Exchange

Method Article

Steven J. Ludtke, Muyuan Chen, Dai Wei, Stella Y. Sun, Darius Jonasch, Cynthia Y. He, Michael F. Schmid, Wah Chiu

Steven J. Ludtke

Ludtke Lab, Baylor College of Medicine

Corresponding Author

Muyuan Chen

Ludtke Lab, Baylor College of Medicine

Dai Wei

Department of Cell Biology and Neuroscience, Center for Integrative Proteomics Research, Rutgers University, Piscataway, New Jersey USA

Stella Y. Sun

Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

Darius Jonasch

Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

Cynthia Y. He

Department of Biological Science, Centre for BioImaging Sciences, National University of Singapore, Singapore

Michael F. Schmid

Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

Wah Chiu

Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

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CURRENT STATUS: Posted

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Posted 29 Aug, 2017

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Subject Areas

Computational biology and bioinformatics

Biological techniques

Mathematics and computing

DOI:

10.1038/protex.2017.095

Download PDF

The full text of this article is available to read as a PDF.

License:

This work is licensed under a CC BY 4.0 License. Read Full License

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

The authors declare no competing financial interests.

Associated Publications

Convolutional neural networks for automated annotation of cellular cryo-electron tomograms
by Muyuan Chen, Wei Dai, Stella Y Sun, +5
Nature Methods (29 August, 2017)

An open repository of community-contributed protocols sponsored by Nature Research.

Learn more about Protocol Exchange

Method Article

Steven J. Ludtke, Muyuan Chen, Dai Wei, Stella Y. Sun, Darius Jonasch, Cynthia Y. He, Michael F. Schmid, Wah Chiu

Steven J. Ludtke

Ludtke Lab, Baylor College of Medicine

Corresponding Author

Muyuan Chen

Ludtke Lab, Baylor College of Medicine

Dai Wei

Department of Cell Biology and Neuroscience, Center for Integrative Proteomics Research, Rutgers University, Piscataway, New Jersey USA

Stella Y. Sun

Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

Darius Jonasch

Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

Cynthia Y. He

Department of Biological Science, Centre for BioImaging Sciences, National University of Singapore, Singapore

Michael F. Schmid

Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

Wah Chiu

Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

DOI:

10.1038/protex.2017.095

Download PDF

License:

This work is licensed under a CC BY 4.0 License. Read Full License

Abstract

Keywords

Cellular Electron Cryotomography, convolutional neural network, tomogram annotation

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Subject Areas

Computational biology and bioinformatics

Biological techniques

Mathematics and computing

Associated Publications

Convolutional neural networks for automated annotation of cellular cryo-electron tomograms

by Muyuan Chen, Wei Dai, Stella Y Sun, +5

Nature Methods (29 August, 2017)

An open repository of community-contributed protocols sponsored by Nature Research.

Learn more about Protocol Exchange

Method Article

Steven J. Ludtke, Muyuan Chen, Dai Wei, Stella Y. Sun, Darius Jonasch, Cynthia Y. He, Michael F. Schmid, Wah Chiu

Steven J. Ludtke

Ludtke Lab, Baylor College of Medicine

Corresponding Author

Muyuan Chen

Ludtke Lab, Baylor College of Medicine

Dai Wei

Department of Cell Biology and Neuroscience, Center for Integrative Proteomics Research, Rutgers University, Piscataway, New Jersey USA

Stella Y. Sun

Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

Darius Jonasch

Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

Cynthia Y. He

Department of Biological Science, Centre for BioImaging Sciences, National University of Singapore, Singapore

Michael F. Schmid

Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

Wah Chiu

Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

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