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.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
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
Prouteau, M. et al. Nature 550, 265 (2017).
Salvador-Gallego, R et al. EMBO J. 35, 389–401 (2016).
Bisson-Filho, A. W. et al. Science 355, 739–743 (2017).
Betzig, E. et al. Science 313, 1642–1645 (2006).
Zhao, Z. W. et al. Proc. Natl Acad. Sci. USA 111, 681–686 (2013).
Chojnacki, J. et al. Science 338, 524–528 (2012).
Jans, D. et al. Proc. Natl Acad. Sci. USA 110, 8936–8941 (2013).
Holden, S. J. et al. Proc. Natl Acad. Sci. USA 111, 4566–4571 (2014).
Gustafsson, N. et al. Nat. Commun. 7, 12471 (2016).
Chen, B. C. et al. Sci. 346, 1257998 (2014).
Almada, P. et al. Nat. Commun. 10, 1223 (2019).
Szymborska, A. et al. Science 341, 655–658 (2013).
Grossman, E., Medalia, O. & Zwerger, M. Annu. Rev. Biophys. 41, 557–584 (2012).
Beck, M. & Hurt, E. Nat. Rev. Mol. Cell Biol. 18, 73 (2016).
Mund, M. et al. Cell 174, 884–896.e17 (2018).
Holden, S. J. et al. Proc. Natl Acad. Sci. 111, 4566–4571 (2014).
Li, D. et al. Science 349, aab3500 (2015).
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
Authors and Affiliations
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
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
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
About this article
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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41592-019-0472-1
This article is cited by
-
RegiSTORM: channel registration for multi-color stochastic optical reconstruction microscopy
BMC Bioinformatics (2023)
-
Detecting continuous structural heterogeneity in single-molecule localization microscopy data
Scientific Reports (2023)
-
Maximum-likelihood model fitting for quantitative analysis of SMLM data
Nature Methods (2023)
-
Automatic classification and segmentation of single-molecule fluorescence time traces with deep learning
Nature Communications (2020)
-
Ana J. García Sáez
Nature Methods (2019)