What You Will Learn in This Chapter
Here, we report analysis and summary of research in the field of localization microscopy for optical imaging. We introduce the basic elements of super-resolved localization microscopy methods for PALM and STORM, commonly used both in vivo and in vitro, discussing the core essentials of background theory, instrumentation, and computational algorithms. We discuss the resolution limit of light microscopy and the mathematical framework for localizing fluorescent dyes in space beyond this limit, including the precision obtainable as a function of the amount of light emitted from a dye, and how it leads to a fundamental compromise between spatial and temporal precision. The properties of a “good dye” are outlined, as are the features of PALM and STORM super-resolution microscopy and adaptations that may need to be made to experimental protocols to perform localization determination. We analyze briefly some of the methods of modern super-resolved optical imaging that work through reshaping point spread functions and how they utilize aspects of localization microscopy, such as stimulated depletion (STED) methods and MINFLUX, and summarize modern methods that push localization into 3D using non-Gaussian point spread functions. We report on current methods for analyzing localization data including determination of 2D and 3D diffusion constants, molecular stoichiometries, and performing cluster analysis with cutting-edge techniques, and finally discuss how these techniques may be used to enable important insight into a range of biological processes.
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References
Wollman AJM, Nudd R, Hedlund EG, Leake MC. From animaculum to single molecules: 300 years of the light microscope. Open Biol. 2015;5(4):150019. https://doi.org/10.1098/rsob.150019.
Gelles J, Schnapp BJ, Sheetz MP. Tracking kinesin-driven movements with nanometre-scale precision. Nature. 1988;331(6155):450–3. https://doi.org/10.1038/331450a0.
Ormö M, Cubitt AB, Kallio K, Gross LA, Tsien RY, Remington SJ. Crystal structure of the Aequorea victoria green fluorescent protein. Science. 1996;273(5280):1392–5. https://doi.org/10.1126/science.273.5280.1392.
Marsh RJ, et al. Artifact-free high-density localization microscopy analysis. Nat Methods. 2018;15(9):689–92. https://doi.org/10.1038/s41592-018-0072-5.
Gustafsson MGL. Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J Microsc. 2000;198(2):82–7. https://doi.org/10.1046/j.1365-2818.2000.00710.x.
Holden SJ, Uphoff S, Kapanidis AN. DAOSTORM: an algorithm for high-density super-resolution microscopy. Nat Methods. 2011;8(4):279–80. https://doi.org/10.1038/nmeth0411-279.
Min J, et al. FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data. Sci Rep. 2014;4:4577. https://doi.org/10.1038/srep04577.
Ovesný M, Křížek P, Borkovec J, Švindrych Z, Hagen GM. ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging. Bioinformatics. 2014;30(16):2389–90. https://doi.org/10.1093/bioinformatics/btu202.
Cox S, et al. Bayesian localization microscopy reveals nanoscale podosome dynamics. Nat Methods. 2012;9(2):195–200. https://doi.org/10.1038/nmeth.1812.
Miller H, Zhou Z, Wollman AJM, Leake MC. Superresolution imaging of single DNA molecules using stochastic photoblinking of minor groove and intercalating dyes. Methods. 2015;88:81–8. https://doi.org/10.1016/j.ymeth.2015.01.010.
Karslake JD, et al. SMAUG: analyzing single-molecule tracks with nonparametric Bayesian statistics. Methods. 2020;193:16–26. https://doi.org/10.1016/j.ymeth.2020.03.008.
Rees EJ, Erdelyi M, Schierle GSK, Knight A, Kaminski CF. Elements of image processing in localization microscopy. J Opt (United Kingdom). 2013;15(9) https://doi.org/10.1088/2040-8978/15/9/094012.
Henriques R, Lelek M, Fornasiero EF, Valtorta F, Zimmer C, Mhlanga MM. QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ. Nat Methods. 2010;7(5):339–40. https://doi.org/10.1038/nmeth0510-339.
Schneider CA, Rasband WS, Eliceiri KW. NIH image to ImageJ: 25 years of image analysis. Nat Methods. 2012;9(7):671–5. https://doi.org/10.1038/nmeth.2089.
Mortensen KI, Churchman LS, Spudich JA, Flyvbjerg H. Optimized localization analysis for single-molecule tracking and super-resolution microscopy. Nat Methods. 2010;7(5):377–81. https://doi.org/10.1038/nmeth.1447.
Thompson RE, Larson DR, Webb WW. Precise nanometer localization analysis for individual fluorescent probes. Biophys J. 2002;82(5):2775–83. https://doi.org/10.1016/S0006-3495(02)75618-X.
Wang Y, Cai E, Sheung J, Lee SH, Teng KW, Selvin PR. Fluorescence imaging with one-nanometer accuracy (fiona). J Vis Exp. 2014;91:51774. https://doi.org/10.3791/51774.
Robson A, Burrage K, Leake MC. Inferring diffusion in single live cells at the single-molecule level. Philos Trans R Soc B Biol Sci. 2013;368(1611):20120029. https://doi.org/10.1098/rstb.2012.0029.
Leake MC. Analytical tools for single-molecule fluorescence imaging in cellulo. Phys Chem Chem Phys. 2014;16(25):12635–47. https://doi.org/10.1039/c4cp00219a.
Rust MJ, Bates M, Zhuang X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods. 2006;3(10):793–5. https://doi.org/10.1038/nmeth929.
Shroff H, Galbraith CG, Galbraith JA, Betzig E. Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics. Nat Methods. 2008;5(5):417–23. https://doi.org/10.1038/nmeth.1202.
Royal Swedish Academy of Sciences. Nobel Prize in Physics press release 2018, Nobel prize press releases, 2018. [Online]. https://www.nobelprize.org/nobel_prizes/physics/laureates/1952/
Hell SW. Improvement of lateral resolution in far-field fluorescence light microscopy by using two-photon excitation with offset beams. Opt Commun. 1994;106(1–3):19–24. https://doi.org/10.1016/0030-4018(94)90050-7.
Klar TA, Jakobs S, Dyba M, Egner A, Hell SW. Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission. Proc Natl Acad Sci U S A. 2000;97(15):8206–10. https://doi.org/10.1073/pnas.97.15.8206.
Fölling J, et al. Fluorescence nanoscopy by ground-state depletion and single-molecule return. Nat Methods. 2008;5(11):943–5. https://doi.org/10.1038/nmeth.1257.
Heintzmann R, Jovin TM, Cremer C. Saturated patterned excitation microscopy—a concept for optical resolution improvement. J Opt Soc Am A. 2002;19(8):1599. https://doi.org/10.1364/josaa.19.001599.
Gustafsson MGL. Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. Proc Natl Acad Sci U S A. 2005;102(37):13081–6. https://doi.org/10.1073/pnas.0406877102.
Hofmann M, Eggeling C, Jakobs S, Hell SW. Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins. Proc Natl Acad Sci U S A. 2005;102(49):17565–9. https://doi.org/10.1073/pnas.0506010102.
Balzarotti F, et al. Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes. Science. 2017;355(6325):606–12. https://doi.org/10.1126/science.aak9913.
Zacharias DA, Violin JD, Newton AC, Tsien RY. Partitioning of lipid-modified monomeric GFPs into membrane microdomains of live cells. Science. 2002;296(5569):913–6. https://doi.org/10.1126/science.1068539.
Chalfie M, Tu Y, Euskirchen G, Ward WW, Prasher DC. Green fluorescent protein as a marker for gene expression. Science. 1994;263(5148):802–5. https://doi.org/10.1126/science.8303295.
Nagai T, Ibata K, Park ES, Kubota M, Mikoshiba K, Miyawaki A. A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications. Nat Biotechnol. 2002;20(1):87–90. https://doi.org/10.1038/nbt0102-87.
Campbell RE, et al. A monomeric red fluorescent protein. Proc Natl Acad Sci U S A. 2002;99(12):7877–82. https://doi.org/10.1073/pnas.082243699.
Shaner NC, Campbell RE, Steinbach PA, Giepmans BNG, Palmer AE, Tsien RY. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat Biotechnol. 2004;22(12):1567–72. https://doi.org/10.1038/nbt1037.
Zhang G, Gurtu V, Kain SR. An enhanced green fluorescent protein allows sensitive detection of gene transfer in mammalian cells. Biochem Biophys Res Commun. 1996;227(3):707–11. https://doi.org/10.1006/bbrc.1996.1573.
Pédelacq JD, Cabantous S, Tran T, Terwilliger TC, Waldo GS. Engineering and characterization of a superfolder green fluorescent protein. Nat Biotechnol. 2006;24(1):79–88. https://doi.org/10.1038/nbt1172.
Ernst LA, Gupta RK, Mujumdar RB, Waggoner AS. Cyanine dye labeling reagents for sulfhydryl groups. Cytometry. 1989;10(1):3–10. https://doi.org/10.1002/cyto.990100103.
Invitrogen. Alexa Fluor 488 Phalloidin - Product Page. [Online]. https://www.thermofisher.com/order/catalog/product/A12379. Accessed 03 Oct 2020.
Lalande ME, Ling V, Miller RG. Hoechst 33342 dye uptake as a probe of membrane permeability changes in mammalian cells. Proc Natl Acad Sci U S A. 1981;78:363–7. https://doi.org/10.1073/pnas.78.1.363.
Grimm JB, et al. A general method to improve fluorophores for live-cell and single-molecule microscopy. Nat Methods. 2015;12(3):244–50. https://doi.org/10.1038/nmeth.3256.
Patterson GH, Lippincott-Schwartz J. A photoactivatable GFP for selective photolabeling of proteins and cells. Science. 2002;297(5588):1873–7. https://doi.org/10.1126/science.1074952.
Gunewardene MS, et al. Superresolution imaging of multiple fluorescent proteins with highly overlapping emission spectra in living cells. Biophys J. 2011;101(6):1522–8. https://doi.org/10.1016/j.bpj.2011.07.049.
Wang S, Moffitt JR, Dempsey GT, Xie XS, Zhuang X. Characterization and development of photoactivatable fluorescent proteins for single-molecule-based superresolution imaging. Proc Natl Acad Sci U S A. 2014;111(23):8452–7. https://doi.org/10.1073/pnas.1406593111.
Ando R, Hama H, Yamamoto-Hino M, Mizuno H, Miyawaki A. An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein. Proc Natl Acad Sci U S A. 2002;99(20):12651–6. https://doi.org/10.1073/pnas.202320599.
Adam V, Nienhaus K, Bourgeois D, Nienhaus GU. Structural basis of enhanced photoconversion yield in green fluorescent protein-like protein Dendra2. Biochemistry. 2009;48(22):4905–15. https://doi.org/10.1021/bi900383a.
Kapanidis AN, Lee NK, Laurence TA, Doose S, Margeat E, Weiss S. Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules. Proc Natl Acad Sci U S A. 2004;101(24):8936–41. https://doi.org/10.1073/pnas.0401690101.
Huang B, Wang W, Bates M, Zhuang X. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science. 2008;319(5864):810–3. https://doi.org/10.1126/science.1153529.
Pavani SRP, et al. Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function. Proc Natl Acad Sci U S A. 2009;106(9):2995–9. https://doi.org/10.1073/pnas.0900245106.
Wollman AJM, Hedlund EG, Shashkova S, Leake MC. Towards mapping the 3D genome through high speed single-molecule tracking of functional transcription factors in single living cells. Methods. 2020;170:82–9. https://doi.org/10.1016/j.ymeth.2019.06.021.
Lew MD, Lee SF, Badieirostami M, Moerner WE. Corkscrew point spread function for far-field three-dimensional nanoscale localization of pointlike objects. Opt Lett. 2011;36(2):202. https://doi.org/10.1364/ol.36.000202.
Andronov L, Orlov I, Lutz Y, Vonesch JL, Klaholz BP. ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy. Sci Rep. 2016;6:24084. https://doi.org/10.1038/srep24084.
Ester M, Kriegel H-P, Sander J, Xu X. A density-based algorithm for discovering clusters in large spatial databases with noise. In: Proceedings of the 2nd international conference on knowledge discovery and data mining, vol. 96. New York: ACM Digital Library; 1996. p. 226–31.
Kiskowski MA, Hancock JF, Kenworthy AK. On the use of Ripley’s K-function and its derivatives to analyze domain size. Biophys J. 2009;97(4):1095–103. https://doi.org/10.1016/j.bpj.2009.05.039.
Getis A, Franklin J. Second-order neighborhood analysis of mapped point patterns. Ecology. 1987;68(3):473–7. https://doi.org/10.2307/1938452.
Lopes FB, et al. Membrane nanoclusters of FcγRI segregate from inhibitory SIRPα upon activation of human macrophages. J Cell Biol. 2017;216(4):1123–41. https://doi.org/10.1083/jcb.201608094.
Khater IM, Nabi IR, Hamarneh G. A review of super-resolution single-molecule localization microscopy cluster analysis and quantification methods. Patterns. 2020;1(3):100038. https://doi.org/10.1016/j.patter.2020.100038.
Griffié J, et al. 3D Bayesian cluster analysis of super-resolution data reveals LAT recruitment to the T cell synapse. Sci Rep. 2017;7(1):4077. https://doi.org/10.1038/s41598-017-04450-w.
Williamson DJ, et al. Machine learning for cluster analysis of localization microscopy data. Nat Commun. 2020;11(1):1493. https://doi.org/10.1038/s41467-020-15293-x.
Hyman AA, Weber CA, Jülicher F. Liquid-liquid phase separation in biology. Annu Rev Cell Dev Biol. 2014;30(1):39–58. https://doi.org/10.1146/annurev-cellbio-100913-013325.
Dresser L, et al. Amyloid-β oligomerization monitored by single-molecule stepwise photobleaching. Methods. 2020;193:80–95. https://doi.org/10.1016/j.ymeth.2020.06.007.
Leake MC, Wilson D, Bullard B, Simmons RM, Bubb MR. The elasticity of single kettin molecules using a two-bead laser-tweezers assay. FEBS Lett. 2003;535(1–3):55–60. https://doi.org/10.1016/S0014-5793(02)03857-7.
Yan X, Hoek TA, Vale RD, Tanenbaum ME. Dynamics of translation of single mRNA molecules in vivo. Cell. 2016;165(4):976–89. https://doi.org/10.1016/j.cell.2016.04.034.
Syeda AH, et al. Single-molecule live cell imaging of Rep reveals the dynamic interplay between an accessory replicative helicase and the replisome. Nucleic Acids Res. 2019;47(12):6287–98. https://doi.org/10.1093/nar/gkz298.
Wooten M, Li Y, Snedeker J, Nizami ZF, Gall JG, Chen X. Superresolution imaging of chromatin fibers to visualize epigenetic information on replicative DNA. Nat Protoc. 2020;15(3):1188–208. https://doi.org/10.1038/s41596-019-0283-y.
Xu K, Zhong G, Zhuang X. Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons. Science. 2013;339(6118):452–6. https://doi.org/10.1126/science.1232251.
Xu K, Babcock HP, Zhuang X. Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton. Nat Methods. 2012;9(2):185–8. https://doi.org/10.1038/nmeth.1841.
Pan L, et al. Hypotonic stress induces fast, reversible degradation of the vimentin cytoskeleton via intracellular calcium release. Adv Sci. 2019;6(18):1900865. https://doi.org/10.1002/advs.201900865.
Bálint Š, Vilanova IV, Álvarez ÁS, Lakadamyali M. Correlative live-cell and superresolution microscopy reveals cargo transport dynamics at microtubule intersections. Proc Natl Acad Sci U S A. 2013;110(9):3375–80. https://doi.org/10.1073/pnas.1219206110.
Wollman AJM, et al. Critical roles for EGFR and EGFR-HER2 clusters in EGF binding of SW620 human carcinoma cells. J R Soc Interface. 2022;19(190):20220088. https://doi.org/10.1098/rsif.2022.0088.
Lew MD, et al. Three-dimensional superresolution colocalization of intracellular protein superstructures and the cell surface in live Caulobacter crescentus. Proc Natl Acad Sci USA. 2011;108(46):E1102–10. https://doi.org/10.1073/pnas.1114444108.
Shepherd JW, Lecinski S, Wragg J, Shashkova S, MacDonald C, Leake MC. Molecular crowding in single eukaryotic cells: using cell environment biosensing and single-molecule optical microscopy to probe dependence on extracellular ionic strength, local glucose conditions, and sensor copy number. bioRxiv. 2021;193:54–61. https://doi.org/10.1101/2020.08.14.251363.
Babazadeh R, Adiels CB, Smedh M, Petelenz-Kurdziel E, Goksör M, Hohmann S. Osmostress-induced cell volume loss delays yeast Hog1 signaling by limiting diffusion processes and by Hog1-specific effects. PLoS One. 2013;8(11):e80901. https://doi.org/10.1371/journal.pone.0080901.
Wollman AJM, Shashkova S, Hedlund EG, Friemann R, Hohmann S, Leake MC. Transcription factor clusters regulate genes in eukaryotic cells. Elife. 2017;6:1–36. https://doi.org/10.7554/eLife.27451.
Jin X, et al. Membraneless organelles formed by liquid-liquid phase separation increase bacterial fitness. Sci Adv. 2021;7(43):eabh2929. https://doi.org/10.1126/sciadv.abh2929.
Horrocks MH, et al. Single-molecule imaging of individual amyloid protein aggregates in human biofluids. ACS Chem Neurosci. 2016;7(3):399–406. https://doi.org/10.1021/acschemneuro.5b00324.
Cella Zanacchi F, Manzo C, Alvarez AS, Derr ND, Garcia-Parajo MF, Lakadamyali M. A DNA origami platform for quantifying protein copy number in super-resolution. Nat Methods. 2017;14(8):789–92. https://doi.org/10.1038/nmeth.4342.
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This work was supported by the Leverhulme Trust (RPG-2019-156) and EPSRC (EP/T002166/1).
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Shepherd, J.W., Leake, M.C. (2022). Localization Microscopy: A Review of the Progress in Methods and Applications. In: Nechyporuk-Zloy, V. (eds) Principles of Light Microscopy: From Basic to Advanced . Springer, Cham. https://doi.org/10.1007/978-3-031-04477-9_13
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