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SMAP: a modular super-resolution microscopy analysis platform for SMLM data

Nature Methods volume 17, pages 870–872 (2020)Cite this article

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To the Editor — Tools for analyzing single-molecule localization microscopy (SMLM) data have grown extensively over the past decade. We present a modular Super-resolution Microscopy Analysis Platform (SMAP) that integrates all steps of data analysis.

SMLM, such as PALM1, STORM2 or DNA-PAINT3, achieves super-resolution imaging with nanometer resolution and can provide structural insights into cell biological questions. Reconstruction of super-resolved images from the raw data of blinking fluorophores requires extensive data analysis. Free software solutions for this task exist (for example, QuickPALM4, RapidSTORM5, Localizer6, ThunderSTORM7 or Picasso8), but often lack continual development and cannot easily be extended with additional algorithms. Commercial software is usually bundled with a specific microscope and lacks flexibility and transparency concerning the underlying algorithms. This limited functionality hinders advanced quantitative analysis to extract biological insights, motivating many research groups to develop custom solutions (for example, ~100 programs participated in SMLM software challenges9). Such continual ‘reinvention of the wheel’ slows progress and is a waste of limited developer resources for image analysis software. Building more complex analysis pipelines requires the user to chain a variety of different programs, regularly with cumbersome data conversion steps in between. Thus, even expert SMLM users would greatly profit from an open-source SMLM software platform that integrates all steps of data analysis and that is easy to use and extend.

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Fig. 1: Overview of SMAP.

Code availability

The source code can be found at http://www.github.com/jries/SMAP. A standalone version for PC or Mac is available as Supplementary Software. The standalone version, as well as documentation, test data and updated versions, can be downloaded at http://www.rieslab.de.

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Acknowledgements

We thank I. Schön, E. Klotzsch, all members of the Ries group and specifically J. Deschamps, M. Mund, U. Matti, P. Hoess Y.L. Wu, S. Liu, T. Deguchi and R. Diekmann for extensive testing of the software and contributions to the manuscript and software. This work was supported by the European Research Council (ERC CoG-724489) and the European Molecular Biology Laboratory.

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Authors and Affiliations

  1. Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany

    Jonas Ries

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  1. Jonas Ries
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Correspondence to Jonas Ries.

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The author declares no competing interests.

Additional information

Editorial note: This article has been peer reviewed.

Supplementary information

Supplementary Table (download XLSX )

List of plugins currently provided with SMAP

Supplementary Software (download ZIP )

Compiled standalone versions of SMAP for PC and Mac

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Ries, J. SMAP: a modular super-resolution microscopy analysis platform for SMLM data. Nat Methods 17, 870–872 (2020). https://doi.org/10.1038/s41592-020-0938-1

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