DOI: 10.1038/srep15915. SIMcheck: a Toolbox for Successful Super-resolution Structured Illumination Microscopy

SIMcheck: a Toolbox for Successful Super-resolution Structured Illumination Microscopy

10.1038/srep15915

Crossref journal-article

Springer Science and Business Media LLC

Scientific Reports (297)

Abstract

AbstractThree-dimensional structured illumination microscopy (3D-SIM) is a versatile and accessible method for super-resolution fluorescence imaging, but generating high-quality data is challenging, particularly for non-specialist users. We present SIMcheck, a suite of ImageJ plugins enabling users to identify and avoid common problems with 3D-SIM data and assess resolution and data quality through objective control parameters. Additionally, SIMcheck provides advanced calibration tools and utilities for common image processing tasks. This open-source software is applicable to all commercial and custom platforms and will promote routine application of super-resolution SIM imaging in cell biology.

Bibliography

Ball, G., Demmerle, J., Kaufmann, R., Davis, I., Dobbie, I. M., & Schermelleh, L. (2015). SIMcheck: a Toolbox for Successful Super-resolution Structured Illumination Microscopy. Scientific Reports, 5(1).

Authors 6

Graeme Ball (first)
Justin Demmerle (additional)
Rainer Kaufmann (additional)
Ilan Davis (additional)
Ian M. Dobbie (additional)
Lothar Schermelleh (additional)

References 20 Referenced 266

Hell, S. W. Far-field optical nanoscopy. Science 316, 1153–1158 (2007). (10.1126/science.1137395) / Science by SW Hell (2007)
Huang, B., Babcock, H. & Zhuang, X. Breaking the Diffraction Barrier: Super-Resolution Imaging of Cells. Cell 143, 1047–1058 (2010). (10.1016/j.cell.2010.12.002) / Cell by B Huang (2010)
Schermelleh, L., Heintzmann, R. & Leonhardt, H. A guide to super-resolution fluorescence microscopy. J Cell Biol 190, 165–175 (2010). (10.1083/jcb.201002018) / J Cell Biol by L Schermelleh (2010)
Zhang, J., Campbell, R. E., Ting, A. Y. & Tsien, R. Y. Creating new fluorescent probes for cell biology. Nat Rev Mol Cell Biol 3, 906–918 (2002). (10.1038/nrm976) / Nat Rev Mol Cell Biol by J Zhang (2002)
Heintzmann, R. & Cremer, C. Laterally modulated excitation microscopy: improvement of resolution by using a diffraction grating. in Proc SPIE (Bigio, I. J. et al.) 3568, 185–196 (SPIE, 1999). (10.1117/12.336833) / Proc SPIE (Bigio, I. J. et al.) by R Heintzmann (1999)
Gustafsson, M. G. Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J Microsc 198, 82–87 (2000). (10.1046/j.1365-2818.2000.00710.x) / J Microsc by MG Gustafsson (2000)
Gustafsson, M. G. L. et al. Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination. Biophys J 94, 4957–4970 (2008). (10.1529/biophysj.107.120345) / Biophys J by MGL Gustafsson (2008)
Schermelleh, L. et al. Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science 320, 1332–1336 (2008). (10.1126/science.1156947) / Science by L Schermelleh (2008)
Weil, T. T. et al. Drosophila patterning is established by differential association of mRNAs with P bodies. Nat Cell Biol 14, 1305–1313 (2012). (10.1038/ncb2627) / Nat Cell Biol by TT Weil (2012)
Lesterlin, C., Ball, G., Schermelleh, L. & Sherratt, D. J. RecA bundles mediate homology pairing between distant sisters during DNA break repair. Nature 506, 249–253 (2014). (10.1038/nature12868) / Nature by C Lesterlin (2014)
Burnette, D. T. et al. A contractile and counterbalancing adhesion system controls the 3D shape of crawling cells. J Cell Biol 205, 83–96 (2014). (10.1083/jcb.201311104) / J Cell Biol by DT Burnette (2014)
Smeets, D. et al. Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci. Epigenetics Chromatin 7, 8 (2014). (10.1186/1756-8935-7-8) / Epigenetics Chromatin by D Smeets (2014)
Rego, E. H. & Shao, L. Practical structured illumination microscopy. Methods Mol Biol 1251, 175–192 (2015). (10.1007/978-1-4939-2080-8_10) / Methods Mol Biol by EH Rego (2015)
Engel, U. Structured illumination superresolution imaging of the cytoskeleton. Methods Cell Biol 123, 315–333 (2014). (10.1016/B978-0-12-420138-5.00017-3) / Methods Cell Biol by U Engel (2014)
Turnbull, L. et al. Super-resolution imaging of the cytokinetic Z ring in live bacteria using fast 3D-structured illumination microscopy (f3D-SIM). J Vis Exp 51469 (2014). doi: 10.3791/51469. (10.3791/51469)
Editorial. Seeing in super-resolution. Nat Meth 11, 1183 (2014). (10.1038/nmeth.3206)
Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat Meth 9 6, 71–675 (2012). (10.1038/nmeth.2089) / Nat Meth by CA Schneider (2012)
Demmerle, J., Wegel, E., Schermelleh, L. & Dobbie, I. M. Assessing resolution in super-resolution imaging. Methods doi: 10.1016/j.ymeth.2015.07.001 (2015). (10.1016/j.ymeth.2015.07.001)
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat Meth 9, 676–682 (2012). (10.1038/nmeth.2019) / Nat Meth by J Schindelin (2012)
Anscombe, F. J. The transformation of Poisson, binomial and negative-binomial data. Biometrika 35, 246–254 (1948). (10.1093/biomet/35.3-4.246) / Biometrika by FJ Anscombe (1948)

Dates

Type	When
Created	9 years, 9 months ago (Nov. 3, 2015, 5:05 a.m.)
Deposited	2 years, 7 months ago (Jan. 5, 2023, 8:47 a.m.)
Indexed	3 weeks, 3 days ago (July 30, 2025, 10:46 a.m.)
Issued	9 years, 9 months ago (Nov. 3, 2015)
Published	9 years, 9 months ago (Nov. 3, 2015)
Published Online	9 years, 9 months ago (Nov. 3, 2015)

Funders 0

None

BibTeX

@article{Ball_2015, title={SIMcheck: a Toolbox for Successful Super-resolution Structured Illumination Microscopy}, volume={5}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/srep15915}, DOI={10.1038/srep15915}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Ball, Graeme and Demmerle, Justin and Kaufmann, Rainer and Davis, Ilan and Dobbie, Ian M. and Schermelleh, Lothar}, year={2015}, month=nov }

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