Improving your four-dimensional image: traveling through a decade of light-sheet-based fluorescence microscopy research

Abstract

Light-sheet-based fluorescence microscopy features optical sectioning in the excitation process. This reduces phototoxicity and photobleaching by up to four orders of magnitude compared with that caused by confocal fluorescence microscopy, simplifies segmentation and quantification for three-dimensional cell biology, and supports the transition from on-demand to systematic data acquisition in developmental biology applications.

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Figure 1: LSFM in three-dimensional cell biology.
Figure 2: LSFM in insect developmental biology.

References

  1. 1

    Schneckenburger, H. et al. Light exposure and cell viability in fluorescence microscopy. J. Microsc. 245, 311–318 (2012).

    CAS  PubMed  Article  Google Scholar 

  2. 2

    Stelzer, E.H.K. Light-sheet fluorescence microscopy for quantitative biology. Nat. Methods 12, 23–26 (2015).

    CAS  PubMed  Article  Google Scholar 

  3. 3

    Resandt, R.W.W. et al. Optical fluorescence microscopy in three dimensions: microtomoscopy. J. Microsc. 138, 29–34 (1985).

    Article  Google Scholar 

  4. 4

    Cox, I.J. Scanning optical fluorescence microscopy. J. Microsc. 133, 149–154 (1984).

    CAS  PubMed  Article  Google Scholar 

  5. 5

    Huisken, J., Swoger, J., Del Bene, F., Wittbrodt, J. & Stelzer, E.H.K. Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science 305, 1007–1009 (2004).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  6. 6

    Fahrbach, F.O., Voigt, F.F., Schmid, B., Helmchen, F. & Huisken, J. Rapid 3D light-sheet microscopy with a tunable lens. Opt. Express 21, 21010–21026 (2013).

    PubMed  Article  Google Scholar 

  7. 7

    Huisken, J. & Stainier, D.Y.R. Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM). Opt. Lett. 32, 2608–2610 (2007).

    PubMed  Article  Google Scholar 

  8. 8

    Keller, P.J., Schmidt, A.D., Wittbrodt, J. & Stelzer, E.H.K. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 322, 1065–1069 (2008).

    CAS  PubMed  Article  Google Scholar 

  9. 9

    Weber, M. & Huisken, J. Light sheet microscopy for real-time developmental biology. Curr. Opin. Genet. Dev. 21, 566–572 (2011).

    CAS  PubMed  Article  Google Scholar 

  10. 10

    Keller, P.J. & Ahrens, M.B. Visualizing whole-brain activity and development at the single-cell level using light-sheet microscopy. Neuron 85, 462–483 (2015).

    CAS  PubMed  Article  Google Scholar 

  11. 11

    Royer, L.A. et al. ClearVolume: open-source live 3D visualization for light-sheet microscopy. Nat. Methods 12, 480–481 (2015).

    CAS  PubMed  Article  Google Scholar 

  12. 12

    Stegmaier, J. et al. Real-time three-dimensional cell segmentation in large-scale microscopy data of developing embryos. Dev. Cell 36, 225–240 (2016).

    CAS  PubMed  Article  Google Scholar 

  13. 13

    von Wangenheim, D. et al. Rules and self-organizing properties of post-embryonic plant organ cell division patterns. Curr. Biol. 26, 439–449 (2016).

    CAS  PubMed  Article  Google Scholar 

  14. 14

    Keller, P.J., Ahrens, M.B. & Freeman, J. Light-sheet imaging for systems neuroscience. Nat. Methods 12, 27–29 (2015).

    CAS  PubMed  Article  Google Scholar 

  15. 15

    Pampaloni, F., Chang, B.-J. & Stelzer, E.H.K. Light sheet-based fluorescence microscopy (LSFM) for the quantitative imaging of cells and tissues. Cell Tissue Res. 360, 129–141 (2015).

    CAS  PubMed  Article  Google Scholar 

  16. 16

    Amat, F. & Keller, P.J. Towards comprehensive cell lineage reconstructions in complex organisms using light-sheet microscopy. Dev. Growth Differ. 55, 563–578 (2013).

    PubMed  Article  Google Scholar 

  17. 17

    Zschenker, O., Streichert, T., Hehlgans, S. & Cordes, N. Genome-wide gene expression analysis in cancer cells reveals 3D growth to affect ECM and processes associated with cell adhesion but not DNA repair. PLoS One 7, e34279 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  18. 18

    Pampaloni, F., Reynaud, E.G. & Stelzer, E.H.K. The third dimension bridges the gap between cell culture and live tissue. Nat. Rev. Mol. Cell Biol. 8, 839–845 (2007).

    CAS  PubMed  Article  Google Scholar 

  19. 19

    Kao, J. et al. Molecular profiling of breast cancer cell lines defines relevant tumor models and provides a resource for cancer gene discovery. PLoS One 4, e6146 (2009).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  20. 20

    Rakha, E.A. et al. Breast cancer prognostic classification in the molecular era: the role of histological grade. Breast Cancer Res. 12, 207 (2010).

    PubMed  PubMed Central  Article  Google Scholar 

  21. 21

    Azaripour, A. et al. A survey of clearing techniques for 3D imaging of tissues with special reference to connective tissue. Prog. Histochem. Cytochem. 51, 9–23 (2016).

    PubMed  Article  Google Scholar 

  22. 22

    Dodt, H.-U. et al. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat. Methods 4, 331–336 (2007).

    CAS  PubMed  Article  Google Scholar 

  23. 23

    Sanger, F. & Coulson, A.R. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J. Mol. Biol. 94, 441–448 (1975).

    CAS  Article  PubMed  Google Scholar 

  24. 24

    Ankeny, R.A. Sequencing the genome from nematode to human: changing methods, changing science. Endeavour 27, 87–92 (2003).

    CAS  PubMed  Article  Google Scholar 

  25. 25

    Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).

    CAS  PubMed  Article  Google Scholar 

  26. 26

    Preibisch, S., Saalfeld, S., Schindelin, J. & Tomancak, P. Software for bead-based registration of selective plane illumination microscopy data. Nat. Methods 7, 418–419 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  27. 27

    Preibisch, S. et al. Efficient Bayesian-based multiview deconvolution. Nat. Methods 11, 645–648 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  28. 28

    Pandey, A. & Lewitter, F. Nucleotide sequence databases: a gold mine for biologists. Trends Biochem. Sci. 24, 276–280 (1999).

    CAS  PubMed  Article  Google Scholar 

  29. 29

    Keller, P.J. et al. Fast, high-contrast imaging of animal development with scanned light sheet–based structured-illumination microscopy. Nat. Methods 7, 637–642 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  30. 30

    Tomer, R., Khairy, K., Amat, F. & Keller, P.J. Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nat. Methods 9, 755–763 (2012).

    CAS  PubMed  Article  Google Scholar 

  31. 31

    Krzic, U., Gunther, S., Saunders, T.E., Streichan, S.J. & Hufnagel, L. Multiview light-sheet microscope for rapid in toto imaging. Nat. Methods 9, 730–733 (2012).

    CAS  PubMed  Article  Google Scholar 

  32. 32

    Chhetri, R.K. et al. Whole-animal functional and developmental imaging with isotropic spatial resolution. Nat. Methods 12, 1171–1178 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  33. 33

    Strobl, F. & Stelzer, E.H.K. Non-invasive long-term fluorescence live imaging of Tribolium castaneum embryos. Development 141, 2331–2338 (2014).

    CAS  PubMed  Article  Google Scholar 

  34. 34

    Strobl, F., Schmitz, A. & Stelzer, E.H.K. Live imaging of Tribolium castaneum embryonic development using light-sheet-based fluorescence microscopy. Nat. Protoc. 10, 1486–1507 (2015).

    CAS  PubMed  Article  Google Scholar 

  35. 35

    Strobl, F. & Stelzer, E.H. Long-term fluorescence live imaging of Tribolium castaneum embryos: principles, resources, scientific challenges and the comparative approach. Curr. Opin. Insect Sci. 18, 17–26 (2016).

    PubMed  Article  Google Scholar 

  36. 36

    Siegal, M.L. & Bergman, A. Waddington's canalization revisited: developmental stability and evolution. Proc. Natl. Acad. Sci. USA 99, 10528–10532 (2002).

    CAS  PubMed  Article  Google Scholar 

  37. 37

    Heffer, A. & Pick, L. Conservation and variation in Hox genes: how insect models pioneered the evo-devo field. Annu. Rev. Entomol. 58, 161–179 (2013).

    CAS  PubMed  Article  Google Scholar 

  38. 38

    Stelzer, E.H.K., Enders, S., Huisken, J., Lindek, S. & Swoger, J.H. Microscope with a viewing direction perpendicular to the illumination direction. US patent 7554725 B2 (2009).

  39. 39

    Reynaud, E.G., Peychl, J., Huisken, J. & Tomancak, P. Guide to light-sheet microscopy for adventurous biologists. Nat. Methods 12, 30–34 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  40. 40

    Taormina, M.J. et al. Investigating bacterial-animal symbioses with light sheet microscopy. Biol. Bull. 223, 7–20 (2012).

    PubMed  PubMed Central  Article  Google Scholar 

  41. 41

    Rath, M., Grolig, F., Haueisen, J. & Imhof, S. Combining microtomy and confocal laser scanning microscopy for structural analyses of plant-fungus associations. Mycorrhiza 24, 293–300 (2014).

    PubMed  Article  Google Scholar 

  42. 42

    Fahrbach, F.O. & Rohrbach, A. A line scanned light-sheet microscope with phase shaped self-reconstructing beams. Opt. Express 18, 24229–24244 (2010).

    PubMed  Article  Google Scholar 

  43. 43

    Vettenburg, T. et al. Light-sheet microscopy using an Airy beam. Nat. Methods 11, 541–544 (2014).

    CAS  PubMed  Article  Google Scholar 

  44. 44

    Chen, B.-C. et al. Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science 346, 1257998 (2014).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  45. 45

    Pitrone, P.G. et al. OpenSPIM: an open-access light-sheet microscopy platform. Nat. Methods 10, 598–599 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  46. 46

    Wu, J., Li, J. & Chan, R.K.Y. A light sheet based high throughput 3D-imaging flow cytometer for phytoplankton analysis. Opt. Express 21, 14474–14480 (2013).

    CAS  PubMed  Article  Google Scholar 

  47. 47

    Swoger, J., Verveer, P., Greger, K., Huisken, J. & Stelzer, E.H.K. Multi-view image fusion improves resolution in three-dimensional microscopy. Opt. Express 15, 8029–8042 (2007).

    PubMed  PubMed Central  Article  Google Scholar 

  48. 48

    Verveer, P.J. et al. High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy. Nat. Methods 4, 311–313 (2007).

    CAS  Article  PubMed  Google Scholar 

  49. 49

    Wohland, T., Shi, X., Sankaran, J. & Stelzer, E.H.K. Single plane illumination fluorescence correlation spectroscopy (SPIM-FCS) probes inhomogeneous three-dimensional environments. Opt. Express 18, 10627–10641 (2010).

    CAS  PubMed  Article  Google Scholar 

  50. 50

    Friedrich, M., Gan, Q., Ermolayev, V. & Harms, G.S. STED-SPIM: stimulated emission depletion improves sheet illumination microscopy resolution. Biophys. J. 100, L43–L45 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  51. 51

    Silvestri, L., Bria, A., Sacconi, L., Iannello, G. & Pavone, F.S. Confocal light sheet microscopy: micron-scale neuroanatomy of the entire mouse brain. Opt. Express 20, 20582–20598 (2012).

    CAS  PubMed  Article  Google Scholar 

  52. 52

    Truong, T.V., Supatto, W., Koos, D.S., Choi, J.M. & Fraser, S.E. Deep and fast live imaging with two-photon scanned light-sheet microscopy. Nat. Methods 8, 757–760 (2011).

    CAS  PubMed  Article  Google Scholar 

  53. 53

    Bassi, A., Schmid, B. & Huisken, J. Optical tomography complements light sheet microscopy for in toto imaging of zebrafish development. Development 142, 1016–1020 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  54. 54

    Hoyer, P. et al. Breaking the diffraction limit of light-sheet fluorescence microscopy by RESOLFT. Proc. Natl. Acad. Sci. USA 113, 3442–3446 (2016).

    CAS  PubMed  Article  Google Scholar 

  55. 55

    Jahr, W., Schmid, B., Schmied, C., Fahrbach, F.O. & Huisken, J. Hyperspectral light sheet microscopy. Nat. Commun. 6, 7990 (2015).

    PubMed  PubMed Central  Article  Google Scholar 

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Acknowledgements

We thank K. Hötte (Goethe Universität, Frankfurt am Main, Germany) for the T47D spheroid images, S. Fischer for helpful comments on the manuscript, M.F. Schetelig (Justus-Liebig-Universität, Gießen, Germany) for the Ceratitis line, and T. Mito (Tokushima University, Tokushima, Japan) for the Gryllus line. The research was supported by funding from the Cluster of Excellence–Frankfurt am Main for Macromolecular Complexes (CEF-MC II, EXC 115; speaker: V. Dötsch) granted in part to E.H.K.S. at the Buchmann Institute for Molecular Life Sciences (BMLS; director: E. Schleiff) at the Johann Wolfgang Goethe Universität–Frankfurt am Main by the Deutsche Forschungsgemeinschaft (DFG).

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F.S., A.S., and E.H.K.S. wrote the manuscript. F.S. and A.S. prepared the display items.

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Correspondence to Ernst H K Stelzer.

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Strobl, F., Schmitz, A. & Stelzer, E. Improving your four-dimensional image: traveling through a decade of light-sheet-based fluorescence microscopy research. Nat Protoc 12, 1103–1109 (2017). https://doi.org/10.1038/nprot.2017.028

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