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SuReSim: simulating localization microscopy experiments from ground truth models


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.

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

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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.).

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Authors and Affiliations



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.

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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)

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

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