Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Brief Communication
  • Published:

SuReSim: simulating localization microscopy experiments from ground truth models

Nature Methods volume 13, pages 319–321 (2016)Cite this article

Subjects

Abstract

Super-resolution fluorescence microscopy has become a widely used tool in many areas of research. However, designing and validating super-resolution experiments to address a research question in a technically feasible and scientifically rigorous manner remains a fundamental challenge. We developed SuReSim, a software tool that simulates localization data of arbitrary three-dimensional structures represented by ground truth models, allowing users to systematically explore how changing experimental parameters can affect potential imaging outcomes.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Simulation of 3D localization microscopy data and validation with experimental measurements.
Figure 2: Two alternative workflows of the SuReSim algorithm.

Similar content being viewed by others

References

  1. Dani, A., Huang, B., Bergan, J., Dulac, C. & Zhuang, X. Neuron 68, 843–856 (2010).

    Article  CAS  Google Scholar 

  2. Xu, K., Zhong, G. & Zhuang, X. Science 339, 452–456 (2013).

    Article  CAS  Google Scholar 

  3. Xu, K., Babcock, H.P. & Zhuang, X. Nat. Methods 9, 185–188 (2012).

    Article  Google Scholar 

  4. Endesfelder, U. & Heilemann, M. Nat. Methods 11, 235–238 (2014).

    Article  CAS  Google Scholar 

  5. Nieuwenhuizen, R.P. et al. Nat. Methods 10, 557–562 (2013).

    Article  CAS  Google Scholar 

  6. Banterle, N., Bui, K.H., Lemke, E.A. & Beck, M. J. Struct. Biol. 183, 363–367 (2013).

    Article  CAS  Google Scholar 

  7. Deschout, H. et al. Nat. Methods 11, 253–266 (2014).

    Article  Google Scholar 

  8. Endesfelder, U., Malkusch, S., Fricke, F. & Heilemann, M. Histochem. Cell Biol. 141, 629–638 (2014).

    Article  Google Scholar 

  9. Takamori, S. et al. Cell 127, 831–846 (2006).

    Article  CAS  Google Scholar 

  10. Horstmann, H., Korber, C., Satzler, K., Aydin, D. & Kuner, T. PLoS ONE 7, e35172 (2012).

    Article  CAS  Google Scholar 

  11. Weber, K., Rathke, P.C. & Osborn, M. Proc. Natl. Acad. Sci. USA 75, 1820–1824 (1978).

    Article  CAS  Google Scholar 

  12. Kremer, J.R., Mastronarde, D.N. & McIntosh, J.R. J. Struct. Biol. 116, 71–76 (1996).

    Article  CAS  Google Scholar 

  13. Dempsey, G.T., Vaughan, J.C., Chen, K.H., Bates, M. & Zhuang, X. Nat. Methods 8, 1027–1036 (2011).

    Article  CAS  Google Scholar 

  14. Buchwalow, I., Samoilova, V., Boecker, W. & Tiemann, M. Sci. Rep. 1, 28 (2011).

    Article  Google Scholar 

  15. Deschout, H. et al. Nat. Methods 11, 253–266 (2014).

    Article  CAS  Google Scholar 

  16. Nieuwenhuizen, R.P. et al. Nat. Methods 10, 557–562 (2013).

    Article  CAS  Google Scholar 

  17. Sage, D. et al. Nat. Methods 12, 717–724 (2015).

    Article  CAS  Google Scholar 

  18. Huang, B., Jones, S.A., Brandenburg, B. & Zhuang, X. Nat. Methods 5, 1047–1052 (2008).

    Article  CAS  Google Scholar 

  19. Finan, K., Raulf, A. & Heilemann, M. Angew. Chem. Int. Ed. Engl. 54, 12049–12052 (2015).

    Article  CAS  Google Scholar 

  20. Früh, S.M., Schoen, I., Ries, J. & Vogel, V. Nat. Commun. 6, 7275 (2015).

    Article  Google Scholar 

  21. Heilemann, M. et al. Angew. Chem. Int. Edn. Engl. 47, 6172–6176 (2008).

    Article  CAS  Google Scholar 

  22. Edelstein, A., Amodaj, N., Hoover, K., Vale, R. & Stuurman, N. Computer Control of Microscopes Using μManager (John Wiley & Sons, 2010).

  23. Wolter, S. et al. Nat. Methods 9, 1040–1041 (2012).

    Article  CAS  Google Scholar 

  24. Ovesný, M., Krizek, P., Borkovec, J., Svindrych, Z. & Hagen, G.M. Bioinformatics 30, 2389–2390 (2014).

    Article  Google Scholar 

Download references

Acknowledgements

We thank I. Schön and S. Früh (Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland) for providing the experimental SMLM data on fibronectin fibers, M. Cyrklaff (Centre for Infectious Diseases, Parasitology, Heidelberg, Germany) for the F-actin model data on erythrocytes, S. Srismith and M. Lanzer (Centre for Infectious Diseases, Parasitology, Heidelberg, Germany) for providing materials for erythrocyte stainings, and D. Mastronarde (Laboratory for Three-dimensional Fine Structure, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA) and J. McIntosh for providing various electron-tomographic models of organelles. We thank B. Rieger and R. Nieuwenhuizen for discussions, M. Scheurer for help with rewriting the software in Java, and C. Kocksch and M. Kaiser for excellent technical assistance. This work was supported by the German Science Foundation through the CellNetworks Cluster of Excellence (EXC 81 to T.K.) and the Cluster of Excellence Macromolecular Complexes (EXC 115 to M.H.).

Author information

Author notes

  1. Varun Venkataramani and Frank Herrmannsdörfer: These authors contributed equally to this work.

Authors and Affiliations

  1. Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany

    Varun Venkataramani, Frank Herrmannsdörfer, Mike Heilemann & Thomas Kuner

  2. Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany

    Mike Heilemann

Authors
  1. Varun Venkataramani
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Frank Herrmannsdörfer
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mike Heilemann
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Thomas Kuner
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

V.V., F.H. and T.K. conceived the project and designed the software. F.H. and V.V. programmed the software and designed, performed and analyzed experiments. M.H. and T.K. supervised the project and designed experiments. F.H., V.V., M.H. and T.K. wrote the manuscript.

Corresponding authors

Correspondence to Mike Heilemann or Thomas Kuner.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–18, Supplementary Tables 1–8 and Supplementary Notes 1–3 (PDF 9039 kb)

Supplementary Software

SuReSim Software (ZIP 128199 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Venkataramani, V., Herrmannsdörfer, F., Heilemann, M. et al. SuReSim: simulating localization microscopy experiments from ground truth models. Nat Methods 13, 319–321 (2016). https://doi.org/10.1038/nmeth.3775

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmeth.3775

This article is cited by

Search

Advanced search

Quick links

Nature Briefing AI and Robotics

Sign up for the Nature Briefing: AI and Robotics newsletter — what matters in AI and robotics research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: AI and Robotics