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

Nature Methods volume 14, pages 983–985 (2017)Cite this article

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Abstract

Cellular electron cryotomography offers researchers the ability to observe macromolecules frozen in action in situ, but a primary challenge with this technique is identifying molecular components within the crowded cellular environment. We introduce a method that uses neural networks to dramatically reduce the time and human effort required for subcellular annotation and feature extraction. Subsequent subtomogram classification and averaging yield in situ structures of molecular components of interest. The method is available in the EMAN2.2 software package.

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Figure 1: Workflow of automated tomogram annotation using a PC12 cell as an example.
Figure 2: Results from automated tomogram annotation.

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Electron Microscopy Data Bank

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Electron Microscopy Data Bank

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Acknowledgements

We gratefully acknowledge support of NIH grants (R01GM080139, P01NS092525, P41GM103832), Ovarian Cancer Research Fund and Singapore Ministry of Education. Molecular graphics and analyses performed with UCSF ChimeraX, developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco.

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Author notes

  1. Wei Dai

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

Authors and Affiliations

  1. Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, USA

    Muyuan Chen

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

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

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

    Cynthia Y He

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Contributions

M.C. designed the protocol. W.D., S.Y.S. and C.Y.H. provided the test data sets. M.C. and D.J. tested and refined the protocol. M.C., W.D., S.Y.S., M.F.S., W.C. and S.J.L. wrote the paper and provided suggestions during development.

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Correspondence to Steven J Ludtke.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Missing wedge artifact in CryoET.

a. Slice view of a tomogram in the X-Y, Y-Z and X-Z plane. b. Fourier Transform of projection of the same tomogram in X-Y, Y-Z and X-Z plane.

Supplementary Figure 2 Convolutional neural network structure.

Supplementary Figure 3 Reusability of trained neural network.

a-d. Annotation of ribosomes in a tomogram of cyanobacteria taken with a Zernike phase plate using different CNNs. a. Ribosomes annotated by a CNN trained on 5 positive and 50 negative samples from the same tomogram (89% correct). b. Using a CNN trained on 5 positive and 50 negative samples from another ZPP tomogram (86% correct). c. Using a CNN trained on 5 positive and 50 negative samples from a non ZPP tomogram (78% correct). d. Using a CNN trained on 10 positive and 100 negative samples from the tomogram in a (91.3% correct). e-h. Annotation of microtubules in two tomograms (I and II) of PC12 cells using two CNNs. CNN A is trained on 5 positive and 50 negative samples from tomogram I. CNN B is trained on 5 positive and 50 negative samples from tomogram II. e. Microtubules in tomogram I annotated by CNN A. f. Microtubules in tomogram II annotated by CNN A. g. Microtubules in tomogram I annotated by CNN B. h. Microtubules in tomogram II annotated by CNN B.

Supplementary Figure 4 Comparison of raw tomogram slices and corresponding automatic annotation in Fig 2.

a. A slice of the Cyanobacteria tomogram in Fig2. b. 3D view of the tomogram annotation of a. c. A slice of the Trypanosome tomogram in Fig2. d. 3D view of the tomogram annotation of c. e. A slice of the platelet tomogram in Fig2. f. 3D view of the tomogram annotation of e.

Supplementary Figure 5 Impact of training inaccuracy on CNN annotations.

a. One of the training samples of microtubules of PC12 cell used in Fig.1b. b. Corresponding manual annotation with a minor error marked by the red arrow. c. Annotation of the patch using a CNN trained on the sample with incorrect annotation and all the other positive and negative samples with correct manual annotation used in Fig.1b. Note the error is fixed in the annotation. d. A slice view of the tomogram. e. Annotation of the slice using the CNN in c.

Supplementary Figure 6 Removal of high contrast artifact.

a. Volume rendering of a region of the tomogram shown in Fig 1. b. Annotation of double membrane in the tomogram using the same CNN used in Fig 1. Note the carbon edge is falsely recognized as double membrane. c. Automatic annotation of carbon edge using a CNN. d. Removal of carbon edge from double membrane annotation in b.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 and Supplementary Table 1.

Life Sciences Reporting Summary

Supplementary Protocol

Supplementary Protocol.

Workflow of automated tomogram annotation

Demonstration of tomogram annotation workflow with our software package, using a PC12 cell tomogram as an example. The process includes selection of training set, annotation of the tomogram, and subtomogram averaging results.

Annotation of the PC12 cell tomogram

Movie showing the PC12 cell tomogram used in the figure and its annotation, including volume rendering and slice view of the input tomogram, and a 3D view of annotated features.

Annotation of the human platelet cell tomogram

Movie showing the human platelet cell tomogram used in the figure and its annotation, including volume rendering and slice view of the input tomogram, and a 3D view of annotated features.

Annotation of the African Trypanosomes cell tomogram

Movie showing the African Trypanosomes cell tomogram used in the figure and its annotation, including volume rendering and slice view of the input tomogram, and a 3D view of annotated features.

Annotation of the Cyanobacteria cell tomogram

Movie showing the Cyanobacteria cell tomogram used in the figure and its annotation, including volume rendering and slice view of the input tomogram, and a 3D view of annotated features.

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Chen, M., Dai, W., Sun, S. et al. Convolutional neural networks for automated annotation of cellular cryo-electron tomograms. Nat Methods 14, 983–985 (2017). https://doi.org/10.1038/nmeth.4405

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