Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ
10.1038/ncomms10980
Crossref journal-article
Springer Science and Business Media LLC
Nature Communications (297)
Abstract

AbstractSuper-resolved structured illumination microscopy (SR-SIM) is an important tool for fluorescence microscopy. SR-SIM microscopes perform multiple image acquisitions with varying illumination patterns, and reconstruct them to a super-resolved image. In its most frequent, linear implementation, SR-SIM doubles the spatial resolution. The reconstruction is performed numerically on the acquired wide-field image data, and thus relies on a software implementation of specific SR-SIM image reconstruction algorithms. We present fairSIM, an easy-to-use plugin that provides SR-SIM reconstructions for a wide range of SR-SIM platforms directly within ImageJ. For research groups developing their own implementations of super-resolution structured illumination microscopy, fairSIM takes away the hurdle of generating yet another implementation of the reconstruction algorithm. For users of commercial microscopes, it offers an additional, in-depth analysis option for their data independent of specific operating systems. As a modular, open-source solution, fairSIM can easily be adapted, automated and extended as the field of SR-SIM progresses.

Bibliography

Müller, M., Mönkemöller, V., Hennig, S., Hübner, W., & Huser, T. (2016). Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ. Nature Communications, 7(1).

Authors 5
  1. Marcel Müller (first)
  2. Viola Mönkemöller (additional)
  3. Simon Hennig (additional)
  4. Wolfgang Hübner (additional)
  5. Thomas Huser (additional)
References 45 Referenced 287
  1. 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)
  2. 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)
  3. 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)
  4. 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)
  5. Kner, P., Chhun, B. B., Griffis, E. R., Winoto, L. & Gustafsson, M. G. L. Super-resolution video microscopy of live cells by structured illumination. Nat. Methods 6, 339–342 (2009). (10.1038/nmeth.1324) / Nat. Methods by P Kner (2009)
  6. Hirvonen, L. M., Wicker, K., Mandula, O. & Heintzmann, R. Structured illumination microscopy of a living cell. Eur. Biophys. J. 38, 807–812 (2009). (10.1007/s00249-009-0501-6) / Eur. Biophys. J. by LM Hirvonen (2009)
  7. Shao, L., Kner, P., Rego, E. H. & Gustafsson, M. G. L. Super-resolution 3D microscopy of live whole cells using structured illumination. Nat. Methods 8, 1044–1046 (2011). (10.1038/nmeth.1734) / Nat. Methods by L Shao (2011)
  8. Fiolka, R., Shao, L., Rego, E. H., Davidson, M. W. & Gustafsson, M. G. Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination. Proc. Natl Acad. Sci. USA 109, 5311–5315 (2012). (10.1073/pnas.1119262109) / Proc. Natl Acad. Sci. USA by R Fiolka (2012)
  9. 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)
  10. Sonnen, K. F., Schermelleh, L., Leonhardt, H. & Nigg, E. A. 3D-structured illumination microscopy provides novel insight into architecture of human centrosomes. Biol. Open 1, 965–976 (2012). (10.1242/bio.20122337) / Biol. Open by KF Sonnen (2012)
  11. Planchon, T. A. et al. Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination. Nat. Methods 8, 417–423 (2011). (10.1038/nmeth.1586) / Nat. Methods by TA Planchon (2011)
  12. Gao, L. et al. Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens. Cell 151, 1370–1385 (2012). (10.1016/j.cell.2012.10.008) / Cell by L Gao (2012)
  13. Mandula, O. et al. Line scan—structured illumination microscopy super-resolution imaging in thick fluorescent samples. Opt. Express 20, 24167–24174 (2012). (10.1364/OE.20.024167) / Opt. Express by O Mandula (2012)
  14. Rossberger, S. et al. Combination of structured illumination and single molecule localization microscopy in one setup. J. Opt. 15, 094003–24174 (2013). (10.1088/2040-8978/15/9/094003) / J. Opt. by S Rossberger (2013)
  15. Hamel, V. et al. Correlative multicolor 3D SIM and STORM microscopy. Biomed. Opt. Express 5, 3326–3336 (2014). (10.1364/BOE.5.003326) / Biomed. Opt. Express by V Hamel (2014)
  16. Monkemoller, V., Oie, C., Hubner, W., Huser, T. & McCourt, P. Multimodal super-resolution optical microscopy visualizes the close connection between membrane and the cytoskeleton in liver sinusoidal endothelial cell fenestrations. Sci. Rep. 5, 16279 (2015). (10.1038/srep16279) / Sci. Rep. by V Monkemoller (2015)
  17. Heintzmann, R., Jovin, T. M. & Cremer, C. Saturated patterned excitation microscopy - a concept for optical resolution improvement. J. Opt. Soc. Am. A 19, 1599–1609 (2002). (10.1364/JOSAA.19.001599) / J. Opt. Soc. Am. A by R Heintzmann (2002)
  18. Gustafsson, M. G. Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. Proc. Natl Acad. Sci. USA 102, 13081–13086 (2005). (10.1073/pnas.0406877102) / Proc. Natl Acad. Sci. USA by MG Gustafsson (2005)
  19. Rego, E. H. et al. Nonlinear structured-illumination microscopy with a photoswitchable protein reveals cellular structures at 50-nm resolution. Proc. Natl Acad. Sci. USA 109, E135–E143 (2012). (10.1073/pnas.1107547108) / Proc. Natl Acad. Sci. USA by EH Rego (2012)
  20. Li, D. et al. Extended resolution structured illumination imaging of endocytic and cytoskeletal dynamics. Science 349, aab3500 (2015). (10.1126/science.aab3500) / Science by D Li (2015)
  21. Chang, B. J., Chou, L. J., Chang, Y. C. & Chiang, S. Y. Isotropic image in structured illumination microscopy patterned with a spatial light modulator. Opt. Express 17, 14710–14721 (2009). (10.1364/OE.17.014710) / Opt. Express by BJ Chang (2009)
  22. Dan, D. et al. DMD-based LED-illumination super-resolution and optical sectioning microscopy. Sci. Rep. 3, 1116 (2013). (10.1038/srep01116) / Sci. Rep. by D Dan (2013)
  23. Lu-Walther, H. W. et al. fastSIM: a practical implementation of fast structured illumination microscopy. Methods Appl. Fluoresc. 3, 014001 (2015). (10.1088/2050-6120/3/1/014001) / Methods Appl. Fluoresc. by HW Lu-Walther (2015)
  24. Krizek, P., Lukes, T., Ovesny, M., Fliegel, K. & Hagen, G. M. SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy. Bioinformatics 32, 318–320 (2015). (10.1093/bioinformatics/btv576) / Bioinformatics by P Krizek (2015)
  25. Henriques, R. et al. QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ. Nat .Methods 7, 339–340 (2010). (10.1038/nmeth0510-339) / Nat .Methods by R Henriques (2010)
  26. Wolter, S. et al. rapidSTORM: accurate, fast open-source software for localization microscopy. Nat. Methods 9, 1040–1041 (2012). (10.1038/nmeth.2224) / Nat. Methods by S Wolter (2012)
  27. Sage, D. et al. Quantitative evaluation of software packages for single-molecule localization microscopy. Nat. Methods 12, 717–724 (2015). (10.1038/nmeth.3442) / Nat. Methods by D Sage (2015)
  28. Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012). (10.1038/nmeth.2089) / Nat. Methods by CA Schneider (2012)
  29. Schindelin, J. et al. Fiji – an open source platform for biological image analysis. Nat. Methods 9, 676–682 (2012). (10.1038/nmeth.2019) / Nat. Methods by J Schindelin (2012)
  30. Hennig, S., Monkemoller, V., Boger, C., Muller, M. & Huser, T. Nanoparticles as nonfluorescent analogues of fluorophores for optical nanoscopy. ACS Nano 9, 6196–6205 (2015). (10.1021/acsnano.5b01503) / ACS Nano by S Hennig (2015)
  31. Heintzmann, R. & Cremer, C. G. BiOS Europe'98. Proc. SPIE 3568, 185–196 (1999). (10.1117/12.336833) / Proc. SPIE by R Heintzmann (1999)
  32. Wicker, K., Mandula, O., Best, G., Fiolka, R. & Heintzmann, R. Phase optimisation for structured illumination microscopy. Opt. Express 21, 2032–2049 (2013). (10.1364/OE.21.002032) / Opt. Express by K Wicker (2013)
  33. O'Holleran, K. & Shaw, M. Optimized approaches for optical sectioning and resolution enhancement in 2D structured illumination microscopy. Biomed. Opt. Express 5, 2580–2590 (2014). (10.1364/BOE.5.002580) / Biomed. Opt. Express by K O'Holleran (2014)
  34. Shaw, M., Zajiczek, L. & O'Holleran, K. High speed structured illumination microscopy in optically thick samples. Methods 88, 11–19 (2015). (10.1016/j.ymeth.2015.03.020) / Methods by M Shaw (2015)
  35. Svistounov, D. et al. The relationship between Fenestrations, sieve plates and rafts in liver sinusoidal endothelial cells. PLoS ONE 7, e46134 (2012). (10.1371/journal.pone.0046134) / PLoS ONE by D Svistounov (2012)
  36. Svistounov, D. et al. The relationship between Fenestrations, sieve plates and rafts in liver sinusoidal endothelial cells. PLoS ONE 7, e46134 (2012). (10.1371/journal.pone.0046134) / PLoS ONE by D Svistounov (2012)
  37. Cogger, V. C. et al. Three-dimensional structured illumination microscopy of liver sinusoidal endothelial cell fenestrations. J. Struct. Biol. 171, 382–388 (2010). (10.1016/j.jsb.2010.06.001) / J. Struct. Biol. by VC Cogger (2010)
  38. Monkemoller, V. et al. Imaging fenestrations in liver sinusoidal endothelial cells by optical localization microscopy. Phys. Chem. Chem. Phys. 16, 12576–12581 (2014). (10.1039/C4CP01574F) / Phys. Chem. Chem. Phys. by V Monkemoller (2014)
  39. Wicker, K. Non-iterative determination of pattern phase in structured illumination microscopy using auto-correlations in Fourier space. Opt. Express 21, 24692–24701 (2013). (10.1364/OE.21.024692) / Opt. Express by K Wicker (2013)
  40. Shroff, S. A., Fienup, J. R. & Williams, D. R. Lateral superresolution using a posteriori phase shift estimation for a moving object: experimental results. J. Opt. Soc. Am. A 27, 1770–1782 (2010). (10.1364/JOSAA.27.001770) / J. Opt. Soc. Am. A by SA Shroff (2010)
  41. Shroff, S. A., Fienup, J. R. & Williams, D. R. Phase-shift estimation in sinusoidally illuminated images for lateral superresolution. J. Opt. Soc. Am. A 26, 413–424 (2009). (10.1364/JOSAA.26.000413) / J. Opt. Soc. Am. A by SA Shroff (2009)
  42. Chu, K. et al. Image reconstruction for structured-illumination microscopy with low signal level. Opt. Express 22, 8687–8702 (2014). (10.1364/OE.22.008687) / Opt. Express by K Chu (2014)
  43. Ayuk, R. et al. Structured illumination fluorescence microscopy with distorted excitations using a filtered blind-SIM algorithm. Opt. Lett. 38, 4723–4726 (2013). (10.1364/OL.38.004723) / Opt. Lett. by R Ayuk (2013)
  44. Mudry, E. et al. Structured illumination microscopy using unknown speckle patterns. Nat. Photon. 6, 312–315 (2012). (10.1038/nphoton.2012.83) / Nat. Photon. by E Mudry (2012)
  45. Jost, A. et al. Optical sectioning and high resolution in single-slice structured illumination microscopy by thick slice blind-SIM reconstruction. PLoS ONE 10, e0132174 (2015). (10.1371/journal.pone.0132174) / PLoS ONE by A Jost (2015)
Dates
Type When
Created 9 years, 5 months ago (March 21, 2016, 6:09 a.m.)
Deposited 2 years ago (Aug. 17, 2023, 4:40 a.m.)
Indexed 1 month ago (July 27, 2025, 3:49 a.m.)
Issued 9 years, 5 months ago (March 21, 2016)
Published 9 years, 5 months ago (March 21, 2016)
Published Online 9 years, 5 months ago (March 21, 2016)
Funders 0

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@article{M_ller_2016, title={Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ}, volume={7}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/ncomms10980}, DOI={10.1038/ncomms10980}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Müller, Marcel and Mönkemöller, Viola and Hennig, Simon and Hübner, Wolfgang and Huser, Thomas}, year={2016}, month=mar }