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Quantitative mapping and minimization of super-resolution optical imaging artifacts

Nature Methods 15, 263–266 (2018) | Download Citation

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Abstract

Super-resolution microscopy depends on steps that can contribute to the formation of image artifacts, leading to misinterpretation of biological information. We present NanoJ-SQUIRREL, an ImageJ-based analytical approach that provides quantitative assessment of super-resolution image quality. By comparing diffraction-limited images and super-resolution equivalents of the same acquisition volume, this approach generates a quantitative map of super-resolution defects and can guide researchers in optimizing imaging parameters.

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Acknowledgements

We thank A. Knight (Holistx Ltd.) and S. Holden (Newcastle University) for critical reading of the manuscript; J. Ries (European Laboratory for Molecular Biology, Heidelberg) for provision of customized MATLAB software and critical reading of the manuscript; K. Tosheva (University College London) for critical reading of the manuscript and beta testing of the software; and B. Baum (University College London) for reagents. Many of the look-up tables used here are based on the open-source repository of D. Williamson at King′s College London. This work was funded by grants from the UK Biotechnology and Biological Sciences Research Council (BB/M022374/1; BB/P027431/1; BB/R000697/1) (R.H. and P.M.P.), MRC Programme Grant (MC_UU12018/7) (J.M.), the European Research Council (649101–UbiProPox) (J.M.), the UK Medical Research Council (MR/K015826/1) (R.H. and J.M.), the Wellcome Trust (203276/Z/16/Z) (S.C. and R.H.) and the Centre National de la Recherche Scientifique (CNRS ATIP-AVENIR program AO2016) (C.L.). D.A. is presently a Marie Curie fellow (Marie Sklodowska-Curie grant agreement No 750673). C.J. funded by a Commonwealth scholarship, funded by the UK government.

Author information

Affiliations

  1. MRC–Laboratory for Molecular Cell Biology, University College London, London, UK.

    • Siân Culley
    • , David Albrecht
    • , Caron Jacobs
    • , Pedro Matos Pereira
    • , Jason Mercer
    •  & Ricardo Henriques

  2. Department of Cell and Developmental Biology, University College London, London, UK.

    • Siân Culley
    • , Caron Jacobs
    • , Pedro Matos Pereira
    •  & Ricardo Henriques

  3. The Francis Crick Institute, London, UK.

    • Siân Culley
    • , Pedro Matos Pereira
    •  & Ricardo Henriques

  4. Aix Marseille Université, CNRS, INP UMR7051, Marseille, France.

    • Christophe Leterrier

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Contributions

S.C. and R.H. devised the conceptual framework and derived theoretical results. S.C., D.A., C.L., J.M., and R.H. planned experiments. S.C. and R.H. wrote the algorithm. Simulations were done by S.C. Experimental data sets were acquired by S.C. (Fig. 1), D.A. (Fig. 2; Supplementary Notes 4 and 7), C.J. (Fig. 2 and Supplementary Note 9), P.M.P. (Fig. 3), and C.L. (Supplementary Notes 5, 10, and 11). Data were analyzed by S.C. and D.A.; and C.L., J.M., and R.H. provided research advice. The paper was written by S.C., D.A., J.M., and R.H. with editing contributions from all the authors.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Christophe Leterrier or Jason Mercer or Ricardo Henriques.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Notes 1–11

  2. 2.

    Life Sciences Reporting Summary

Zip files

  1. 1.

    Supplementary Software

    Binaries, source code and user manual for NanoJ-SQUIRREL

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DOI

https://doi.org/10.1038/nmeth.4605

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