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.

Quantitative analysis of super-resolved structures using ASAP

Abstract

Super-resolution microscopy allows imaging of cellular structures with high throughput and detail. However, the efficient and quantitative analysis of images generated is challenging with existing tools. Here, we develop ASAP (automated structures analysis program) to enable rapid and automated detection, classification and quantification of super-resolved structures. We validate ASAP on ground truth data and demonstrate its broad applicability by analyzing images of nucleoporins, TORC1 complexes, endocytic vesicles and Bax pores.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: ASAP workflow.
Fig. 2: Analysis of simulated structures.
Fig. 3: Analysis of super-resolved nucleoporins.

Data availability

The data that support the findings of this study are available from the corresponding authors upon request.

Code availability

Updated versions and source code for ASAP can be obtained from https://github.com/jdanial/ASAP. Compliations of ASAP for Windows and MacOS are available as Supplementary Software.

References

  1. 1.

    Prouteau, M. et al. Nature 550, 265 (2017).

    Article  Google Scholar 

  2. 2.

    Salvador-Gallego, R et al. EMBO J. 35, 389–401 (2016).

  3. 3.

    Bisson-Filho, A. W. et al. Science 355, 739–743 (2017).

  4. 4.

    Betzig, E. et al. Science 313, 1642–1645 (2006).

    CAS  Article  Google Scholar 

  5. 5.

    Zhao, Z. W. et al. Proc. Natl Acad. Sci. USA 111, 681–686 (2013).

    Article  Google Scholar 

  6. 6.

    Chojnacki, J. et al. Science 338, 524–528 (2012).

    CAS  Article  Google Scholar 

  7. 7.

    Jans, D. et al. Proc. Natl Acad. Sci. USA 110, 8936–8941 (2013).

    CAS  Article  Google Scholar 

  8. 8.

    Holden, S. J. et al. Proc. Natl Acad. Sci. USA 111, 4566–4571 (2014).

    CAS  Article  Google Scholar 

  9. 9.

    Gustafsson, N. et al. Nat. Commun. 7, 12471 (2016).

    CAS  Article  Google Scholar 

  10. 10.

    Chen, B. C. et al. Sci. 346, 1257998 (2014).

  11. 11.

    Almada, P. et al. Nat. Commun. 10, 1223 (2019).

    Article  Google Scholar 

  12. 12.

    Szymborska, A. et al. Science 341, 655–658 (2013).

    CAS  Article  Google Scholar 

  13. 13.

    Grossman, E., Medalia, O. & Zwerger, M. Annu. Rev. Biophys. 41, 557–584 (2012).

    CAS  Article  Google Scholar 

  14. 14.

    Beck, M. & Hurt, E. Nat. Rev. Mol. Cell Biol. 18, 73 (2016).

    Article  Google Scholar 

  15. 15.

    Mund, M. et al. Cell 174, 884–896.e17 (2018).

    CAS  Article  Google Scholar 

  16. 16.

    Holden, S. J. et al. Proc. Natl Acad. Sci. 111, 4566–4571 (2014).

    CAS  Article  Google Scholar 

  17. 17.

    Li, D. et al. Science 349, aab3500 (2015).

    Article  Google Scholar 

Download references

Acknowledgements

We would like to thank C. Sieben and S. Manley (Ecole polytechnique fédérale de Lausanne, EPFL) for providing super-resolved images of TORC1, M. Mund and J. Ries (European Molecular Biology Laboratory, EMBL) for data sets of proteins involved in clathrin-mediated endocytosis and useful discussions, R. Salvador-Gallego (University of Colorado Boulder) for helpful discussions on the data sets of the apoptotic protein Bax, and S. Alexander and J. Ellenberg (EMBL) for super-resolved images of nucleoporins. We acknowledge a Max Planck Society (Max-Planck-Gesellschaft) postdoctoral fellowship, awarded to J.S.H.D. This work was supported by Deutsche Forschungsgemeinschaft (DFG) grant GA164/3-1 and the European Research Council (ERC) starting grant 309966 awarded to A.J.G.S.

Author information

Affiliations

Authors

Contributions

J.S.H.D. and A.J.G.S. conceived and designed the study, J.S.H.D. wrote the software and performed the analysis. J.S.H.D. and A.J.G.S. assessed performance and wrote the manuscript.

Corresponding authors

Correspondence to John S. H. Danial or Ana J. Garcia-Saez.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information: Rita Strack was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Notes 1–7

Reporting Summary

Supplementary Software

ASAP v1.0 Software

Supplementary Software Guides

User manual, description of parameters, errors and warnings messages syntax, automation script syntax, methodology and workflow.

User and Software Examples

User manual examples, description of parameters examples and automation script examples.

Supplementary Data

Supplementary source data for figures within Supplementary Notes.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Danial, J.S.H., Garcia-Saez, A.J. Quantitative analysis of super-resolved structures using ASAP. Nat Methods 16, 711–714 (2019). https://doi.org/10.1038/s41592-019-0472-1

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

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