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A 3D digital atlas of C. elegans and its application to single-cell analyses

Nature Methods volume 6, pages 667–672 (2009)Cite this article

Abstract

We built a digital nuclear atlas of the newly hatched, first larval stage (L1) of the wild-type hermaphrodite of Caenorhabditis elegans at single-cell resolution from confocal image stacks of 15 individual worms. The atlas quantifies the stereotypy of nuclear locations and provides other statistics on the spatial patterns of the 357 nuclei that could be faithfully segmented and annotated out of the 558 present at this developmental stage. We then developed an automated approach to assign cell names to each nucleus in a three-dimensional image of an L1 worm. We achieved 86% accuracy in identifying the 357 nuclei automatically. This computational method will allow high-throughput single-cell analyses of the post-embryonic worm, such as gene expression analysis, or ablation or stimulation of cells under computer control in a high-throughput functional screen.

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Figure 1: Automatic processing of a 3D image of C. elegans.
Figure 2: Statistics of nuclear positions.
Figure 3: The nuclear spatial location patterns for different cell types.
Figure 4: The AP axis graphs for different cell types derived from the atlas.
Figure 5: Nuclear sizes for different cell types.
Figure 6: Accuracies of automated segmentation and annotation of 55 image stacks.

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References

  1. Riddle, D.L., Blumenthal, T., Meyer, B.J. & Priess, J.R. C. elegans II. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 1997).

  2. Sulston, J.E., Schierenberg, E., White, J.G. & Thomson, J.N. The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol. 100, 64–119 (1983).

    Article  CAS  Google Scholar 

  3. Sulston, J.E. & Horvitz, H.R. Post-embryonic cell lineages of the nematode, Caenorhabditis elegmans. Dev. Biol. 56, 110–156 (1977).

    Article  CAS  Google Scholar 

  4. White, J.G., Southgate, E., Thomson, J.N. & Brenner, S. The structure of the nervous system of the nematode C. elegans. Philos. Trans. R. Soc. Lond. B Biol. Sci. 314, 1–340 (1986).

    Article  CAS  Google Scholar 

  5. Chen, B.L., Hall, D.H. & Chklovskii, D.B. Wiring optimization can relate neuronal structure and function. Proc. Natl. Acad. Sci. USA 103, 4723–4728 (2006).

    Article  CAS  Google Scholar 

  6. Stein, L.D. et al. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol. 1, E45 (2003).

    Article  Google Scholar 

  7. Reece-Hoyes, J.S. et al. A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biol. 6, R110 (2005).

    Article  Google Scholar 

  8. Kim, S. et al. A gene expression map for C. elegans. Science 293, 2087–2092 (2001).

    Article  CAS  Google Scholar 

  9. Wang, J. & Kim, S. Global analysis of dauer gene expression in Caenorhabditis elegans. Development 130, 1621–1634 (2003).

    Article  CAS  Google Scholar 

  10. Hall, D.H. & Altun, Z.F. C. elegans atlas. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2007).

  11. Bao, Z. et al. Automated cell lineage tracing in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 103, 2707–2712 (2006).

    Article  CAS  Google Scholar 

  12. Murray, J.I. et al. Automated analysis of embryonic gene expression with cellular resolution in C. elegans. Nat. Methods 5, 703–709 (2008).

    Article  CAS  Google Scholar 

  13. Pearson, B.J. & Doe, C.Q. Regulation of neuroblast competence in Drosophila. Nature 425, 624–628 (2003).

    Article  CAS  Google Scholar 

  14. Peng, H., Long, F., Liu, X., Kim, S. & Myers, E. Straightening Caenorhabditis elegans images. Bioinformatics 24, 234–242 (2008).

    Article  Google Scholar 

  15. Vincent, L. & Soille, P. Watersheds in digital spaces: an efficient algorithm based on immersion simulations. IEEE Trans. Pattern Anal. Mach. Intell. 13, 583–598 (1991).

    Article  Google Scholar 

  16. Beucher, S. & Meyer, F. The morphological approach to segmentation: the watershed transformation. in Mathematical Morphology in Image Processing (ed., Dougherty, E.R.) 433–482 (Marcel Dekker, New York, 1993).

    Google Scholar 

  17. Vapnik, V. The Nature of Statistical Learning Theory (Springer-Verlag, New York, 1995).

  18. Peng, H., Long, F. & Ding, C. Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans. Pattern Anal. Mach. Intell. 27, 1226–1238 (2005).

    Article  Google Scholar 

  19. Peng, H., Long, F. & Myers, G. VANO: a volume-object image annotation system. Bioinformatics 25, 695–697 (2009).

    Article  CAS  Google Scholar 

  20. Fischler, M.A. & Bolles, R.C. Random sample consensus: a paradigm for model fitting with applications to image analysis and automated cartography. Commun. ACM 24, 381–395 (1981).

    Article  Google Scholar 

  21. Cormen, T.H., Leiserson, C.E., Rivest, R.L. & Stein, C. Introduction to algorithms 2nd edn. (MIT Press and McGraw-Hill, Cambridge, Massachusetts, USA, 2001).

  22. Long, F., Peng, H., Liu, X., Kim, S. & Myers, E. Automatic recognition of cells (ARC) for 3D images of C. elegans. Lect. Notes Comput. Sci. 4955, 128–139 (2008).

    Article  Google Scholar 

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Acknowledgements

We thank A. Fire for providing reagents and advice. The work of X.L. and S.K.K. was funded by the Ellison Medical Foundation and the US National Institutes of Health. X.L. was also funded by the Larry L. Hillblom Foundation. The work of F.L., H.P. and E.M. was funded by Howard Hughes Medical Institute.

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Author notes

  1. Fuhui Long and Hanchuan Peng: These authors contributed equally to this work.

Authors and Affiliations

  1. Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA

    Fuhui Long, Hanchuan Peng & Eugene Myers

  2. Department of Developmental Biology, Stanford University Medical Center, Stanford, California, USA

    Xiao Liu & Stuart K Kim

Authors
  1. Fuhui Long
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  2. Hanchuan Peng
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  3. Xiao Liu
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  4. Stuart K Kim
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  5. Eugene Myers
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Contributions

F.L., H.P. and E.M. developed the pipeline and related algorithms, built the atlas, performed the statistical analysis and wrote the manuscript. X.L. and S.K.K. prepared the worm assays and images, manually annotated the nuclei and helped prepare the manuscript.

Corresponding author

Correspondence to Eugene Myers.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6, Supplementary Table 1 and Supplementary Note (PDF 4181 kb)

Supplementary Video 1

Three-dimensional images before and after worm body straightening, and its segmentation result. (MOV 3204 kb)

Supplementary Video 2

Three-dimensional point-cloud rendering of the nuclei of 357 cells in L1 hermaphrodites larvae. (MOV 6041 kb)

Supplementary Video 3

A tutorial movie showing how to use V3D software to view the 3D digital atlas and interactively access/edit the content of individual nuclei annotation. (MOV 8675 kb)

Supplementary Data 1

3D digital atlas of L1 represented as a point cloud. (ZIP 11 kb)

Supplementary Data 2

CellExplorer software package, which also contains the sample data set. This software package can straighten worm stacks, segment nuclei, automatically annotate nuclei names and perform related analysis. Read the README file inside this package for further instructions. (ZIP 13487 kb)

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Long, F., Peng, H., Liu, X. et al. A 3D digital atlas of C. elegans and its application to single-cell analyses. Nat Methods 6, 667–672 (2009). https://doi.org/10.1038/nmeth.1366

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