1932

Abstract

Super-resolution microscopy techniques are versatile and powerful tools for visualizing organelle structures, interactions, and protein functions in biomedical research. However, whole-cell and tissue specimens challenge the achievable resolution and depth of nanoscopy methods. We focus on three-dimensional single-molecule localization microscopy and review some of the major roadblocks and developing solutions to resolving thick volumes of cells and tissues at the nanoscale in three dimensions. These challenges include background fluorescence, system- and sample-induced aberrations, and information carried by photons, as well as drift correction, volume reconstruction, and photobleaching mitigation. We also highlight examples of innovations that have demonstrated significant breakthroughs in addressing the abovementioned challenges together with their core concepts as well as their trade-offs.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-bioeng-060418-052203
2020-06-04
2024-04-15
Loading full text...

Full text loading...

/deliver/fulltext/bioeng/22/1/annurev-bioeng-060418-052203.html?itemId=/content/journals/10.1146/annurev-bioeng-060418-052203&mimeType=html&fmt=ahah

Literature Cited

  1. 1. 
    Lichtman JW, Conchello J-A. 2005. Fluorescence microscopy. Nat. Methods 2:910–19
    [Google Scholar]
  2. 2. 
    Hell SW. 2007. Far-field optical nanoscopy. Science 316:58281153–58
    [Google Scholar]
  3. 3. 
    Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S et al. 2006. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313:57931642–45
    [Google Scholar]
  4. 4. 
    Hess ST, Girirajan TPK, Mason MD 2006. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys. J. 91:114258–72
    [Google Scholar]
  5. 5. 
    Rust MJ, Bates M, Zhuang X 2006. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods 3:793–95
    [Google Scholar]
  6. 6. 
    Heilemann M, Van De Linde S, Schüttpelz M, Kasper R, Seefeldt B et al. 2008. Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes. Angew. Chem. 47:336172–76
    [Google Scholar]
  7. 7. 
    Fölling J, Bossi M, Bock H, Medda R, Wurm CA et al. 2008. Fluorescence nanoscopy by ground-state depletion and single-molecule return. Nat. Methods 5:943–45
    [Google Scholar]
  8. 8. 
    Small A, Stahlheber S. 2014. Fluorophore localization algorithms for super-resolution microscopy. Nat. Methods 11:267–79
    [Google Scholar]
  9. 9. 
    Juette MF, Lessard MD, Mlodzianoski MJ, Nagpure BS, Bewersdorf J et al. 2008. Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples. Nat. Methods 5:527–29
    [Google Scholar]
  10. 10. 
    Huang B, Jones SA, Brandenburg B, Zhuang X 2008. Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution. Nat. Methods 5:1047–52
    [Google Scholar]
  11. 11. 
    Pavani SRP, Thompson MA, Biteen JS, Lord SJ, Liu N et al. 2009. Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function. PNAS 106:92995–99
    [Google Scholar]
  12. 12. 
    Aquino D, Schönle A, Geisler C, Middendorff CV, Wurm CA et al. 2011. Two-color nanoscopy of three-dimensional volumes by 4Pi detection of stochastically switched fluorophores. Nat. Methods 8:353–59
    [Google Scholar]
  13. 13. 
    Shtengel G, Galbraith JA, Galbraith CG, Lippincott-Schwartz J, Gillette JM et al. 2009. Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure. PNAS 106:93125–30
    [Google Scholar]
  14. 14. 
    van de Linde S, Heilemann M, Sauer M 2012. Live-cell super-resolution imaging with synthetic fluorophores. Annu. Rev. Phys. Chem. 63:519–40
    [Google Scholar]
  15. 15. 
    Lin Y, Long JJ, Huang F, Duim WC, Kirschbaum S et al. 2015. Quantifying and optimizing single-molecule switching nanoscopy at high speeds. PLOS ONE 10:5e0128135
    [Google Scholar]
  16. 16. 
    Cox S. 2015. Super-resolution imaging in live cells. Dev. Biol. 401:1175–81
    [Google Scholar]
  17. 17. 
    Hoogendoorn E, Crosby KC, Leyton-Puig D, Breedijk RMP, Jalink K et al. 2014. The fidelity of stochastic single-molecule super-resolution reconstructions critically depends upon robust background estimation. Sci. Rep. 4:3854
    [Google Scholar]
  18. 18. 
    Dong B, Almassalha LM, Stypula-Cyrus Y, Urban BE, Chandler JE et al. 2016. Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast. PNAS 113:359716–21
    [Google Scholar]
  19. 19. 
    Presley JF, Ward TH, Pfeifer AC, Siggia ED, Phair RD, Lippincott-Schwartz J 2002. Dissection of COPI and Arf1 dynamics in vivo and role in Golgi membrane transport. Nature 417:187–93
    [Google Scholar]
  20. 20. 
    Croce AC, Bottiroli G. 2014. Autofluorescence spectroscopy and imaging: a tool for biomedical research and diagnosis. Eur. J. Histochem. 58:4320–37
    [Google Scholar]
  21. 21. 
    Jungmann R, Steinhauer C, Scheible M, Kuzyk A, Tinnefeld P, Simmel FC 2010. Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. Nano Lett 10:114756–61
    [Google Scholar]
  22. 22. 
    Jungmann R, Avendaño MS, Woehrstein JB, Dai M, Shih WM, Yin P 2014. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nat. Methods 11:313–18
    [Google Scholar]
  23. 23. 
    Schoen I, Ries J, Klotzsch E, Ewers H, Vogel V 2011. Binding-activated localization microscopy of DNA. Nano Lett 11:94008–11
    [Google Scholar]
  24. 24. 
    Legant WR, Shao L, Grimm JB, Brown TA, Milkie DE et al. 2016. High-density three-dimensional localization microscopy across large volumes. Nat. Methods 13:359–65
    [Google Scholar]
  25. 25. 
    Ober RJ, Ram S, Ward ES 2004. Localization accuracy in single-molecule microscopy. Biophys. J. 86:21185–200
    [Google Scholar]
  26. 26. 
    Smith CS, Joseph N, Rieger B, Lidke KA 2010. Fast, single-molecule localization that achieves theoretically minimum uncertainty. Nat. Methods 7:373–75
    [Google Scholar]
  27. 27. 
    Zhang P, Liu S, Chaurasia A, Ma D, Mlodzianoski MJ et al. 2018. Analyzing complex single-molecule emission patterns with deep learning. Nat. Methods 15:913–16
    [Google Scholar]
  28. 28. 
    Schueder F, Lara-Gutiérrez J, Beliveau BJ, Saka SK, Sasaki HM et al. 2017. Multiplexed 3D super-resolution imaging of whole cells using spinning disk confocal microscopy and DNA-PAINT. Nat. Commun. 8:2090
    [Google Scholar]
  29. 29. 
    Wilson T. 2011. Resolution and optical sectioning in the confocal microscope. J. Microsc. 244:2113–21
    [Google Scholar]
  30. 30. 
    Lee J, Miyanaga Y, Ueda M, Hohng S 2012. Video-rate confocal microscopy for single-molecule imaging in live cells and superresolution fluorescence imaging. Biophys. J. 103:81691–97
    [Google Scholar]
  31. 31. 
    Tang J, Han KY. 2018. Extended field-of-view single-molecule imaging by highly inclined swept illumination. Optica 5:91063–69
    [Google Scholar]
  32. 32. 
    Oron D, Tal E, Silberberg Y 2005. Scanningless depth-resolved microscopy. Opt. Express 13:51468–76
    [Google Scholar]
  33. 33. 
    Zhu GH, van Howe J, Durst M, Zipfel W, Xu C 2005. Simultaneous spatial and temporal focusing of femtosecond pulses. Opt. Express 13:62153–59
    [Google Scholar]
  34. 34. 
    Vaziri A, Tang JY, Shroff H, Shank CV 2008. Multilayer three-dimensional super resolution imaging of thick biological samples. PNAS 105:5120221–26
    [Google Scholar]
  35. 35. 
    York AG, Ghitani A, Vaziri A, Davidson MW, Shroff H 2011. Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes. Nat. Methods 8:327–33
    [Google Scholar]
  36. 36. 
    Therrien OD, Aube B, Pages S, De Koninck P, Cote D 2011. Wide-field multiphoton imaging of cellular dynamics in thick tissue by temporal focusing and patterned illumination. Biomed. Opt. Express 2:3696–704
    [Google Scholar]
  37. 37. 
    Choi H, Yew EYS, Hallacoglu B, Fantini S, Sheppard CJR, So PTC 2013. Improvement of axial resolution and contrast in temporally focused widefield two-photon microscopy with structured light illumination. Biomed. Opt. Express 4:7995–1005
    [Google Scholar]
  38. 38. 
    Isobe K, Takeda T, Mochizuki K, Song QY, Suda A et al. 2013. Enhancement of lateral resolution and optical sectioning capability of two-photon fluorescence microscopy by combining temporal-focusing with structured illumination. Biomed. Opt. Express 4:112396–410
    [Google Scholar]
  39. 39. 
    Hernandez O, Papagiakoumou E, Tanese D, Fidelin K, Wyart C, Emiliani V 2016. Three-dimensional spatiotemporal focusing of holographic patterns. Nat. Commun. 7:11928
    [Google Scholar]
  40. 40. 
    Tajahuerce E, Durán V, Clemente P, Irles E, Soldevila F et al. 2014. Image transmission through dynamic scattering media by single-pixel photodetection. Opt. Express 22:1416945–55
    [Google Scholar]
  41. 41. 
    Durán V, Soldevila F, Irles E, Clemente P, Tajahuerce E et al. 2015. Compressive imaging in scattering media. Opt. Express 23:1114424–33
    [Google Scholar]
  42. 42. 
    Pégard NC, Mardinly AR, Oldenburg IA, Sridharan S, Waller L, Adesnik H 2017. Three-dimensional scanless holographic optogenetics with temporal focusing (3D-SHOT). Nat. Commun. 8:11228
    [Google Scholar]
  43. 43. 
    Huisken J, Swoger J, Del Bene F, Wittbrodt J, Stelzer EHK 2004. Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science 305:56861007–9
    [Google Scholar]
  44. 44. 
    Wu Y, Ghitani A, Christensen R, Santella A, Du Z et al. 2011. Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans. . PNAS 108:4317708–13
    [Google Scholar]
  45. 45. 
    Kumar A, Wu Y, Christensen R, Chandris P, Gandler W et al. 2014. Dual-view plane illumination microscopy for rapid and spatially isotropic imaging. Nat. Protoc. 9:112555–73
    [Google Scholar]
  46. 46. 
    Cella Zanacchi F, Lavagnino Z, Perrone Donnorso M, Del Bue A, Furia L et al. 2011. Live-cell 3D super-resolution imaging in thick biological samples. Nat. Methods 8:1047–50
    [Google Scholar]
  47. 47. 
    Chen B, Legant WR, Wang K, Shao L, Milkie DE et al. 2014. Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science 346:62081257998
    [Google Scholar]
  48. 48. 
    Power RM, Huisken J. 2017. A guide to light-sheet fluorescence microscopy for multiscale imaging. Nat. Methods 14:360–73
    [Google Scholar]
  49. 49. 
    Huisken J, Stainier DYR. 2007. Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM). Opt. Lett. 32:172608–10
    [Google Scholar]
  50. 50. 
    Manton JD, Rees EJ. 2016. triSPIM: light sheet microscopy with isotropic super-resolution. Opt. Lett. 41:184170–73
    [Google Scholar]
  51. 51. 
    Theer P, Dragneva D, Knop M 2016. πSPIM: high NA high resolution isotropic light-sheet imaging in cell culture dishes. Sci. Rep. 6:32880
    [Google Scholar]
  52. 52. 
    Yang B, Chen X, Wang Y, Feng S, Pessino V et al. 2019. Epi-illumination SPIM for volumetric imaging with high spatial-temporal resolution. Nat. Methods 16:501–4
    [Google Scholar]
  53. 53. 
    Kim J, Wojcik M, Wang Y, Moon S, Zin EA et al. 2019. Oblique-plane single-molecule localization microscopy for tissues and small intact animals. Nat. Methods 16:853–57
    [Google Scholar]
  54. 54. 
    Gebhardt JCM, Suter DM, Roy R, Zhao ZW, Chapman AR et al. 2013. Single-molecule imaging of transcription factor binding to DNA in live mammalian cells. Nat. Methods 10:421–26
    [Google Scholar]
  55. 55. 
    Gustavsson AK, Petrov PN, Lee MY, Shechtman Y, Moerner WE 2018. 3D single-molecule super-resolution microscopy with a tilted light sheet. Nat. Commun. 9:1123
    [Google Scholar]
  56. 56. 
    Hu YS, Zhu Q, Elkins K, Tse K, Li Yet al 2013. Light-sheet Bayesian microscopy enables deep-cell super-resolution imaging of heterochromatin in live human embryonic stem cells. Opt. Nanoscopy 2:7
    [Google Scholar]
  57. 57. 
    Tokunaga M, Imamoto N, Sakata-Sogawa K 2008. Highly inclined thin illumination enables clear single-molecule imaging in cells. Nat. Methods 5:159–61
    [Google Scholar]
  58. 58. 
    Galland R, Grenci G, Aravind A, Viasnoff V, Studer V, Sibarita JB 2015. 3D high- and super-resolution imaging using single-objective SPIM. Nat. Methods 12:641–44
    [Google Scholar]
  59. 59. 
    Meddens MBM, Liu S, Finnegan PS, Edwards TL, James CD, Lidke KA 2016. Single objective light-sheet microscopy for high-speed whole-cell 3D super-resolution. Biomed. Opt. Express 7:62219–36
    [Google Scholar]
  60. 60. 
    Durnin J. 1987. Exact solutions for nondiffracting beams. I. The scalar theory. J. Opt. Soc. Am. A. 4:4651–54
    [Google Scholar]
  61. 61. 
    Bouchal Z. 2003. Nondiffracting optical beams: physical properties, experiments, and applications. Czechoslov. J. Phys. 53:7537–78
    [Google Scholar]
  62. 62. 
    Piestun R, Schechner YY, Shamir J 2000. Propagation-invariant wave fields with finite energy. J. Opt. Soc. Am. A. 17:2294–303
    [Google Scholar]
  63. 63. 
    Fahrbach FO, Simon P, Rohrbach A 2010. Microscopy with self-reconstructing beams. Nat. Photonics 4:11780–85
    [Google Scholar]
  64. 64. 
    Fahrbach FO, Gurchenkov V, Alessandri K, Nassoy P, Rohrbach A 2013. Self-reconstructing sectioned Bessel beams offer submicron optical sectioning for large fields of view in light-sheet microscopy. Opt. Express 21:911425–40
    [Google Scholar]
  65. 65. 
    Chen Y, Liu JTC. 2015. Characterizing the beam steering and distortion of Gaussian and Bessel beams focused in tissues with microscopic heterogeneities. Biomed. Opt. Express 6:41318–30
    [Google Scholar]
  66. 66. 
    Gohn-Kreuz C, Rohrbach A. 2016. Light-sheet generation in inhomogeneous media using self-reconstructing beams and the STED-principle. Opt. Express. 24:65855–65
    [Google Scholar]
  67. 67. 
    Planchon TA, Gao L, Milkie DE, Davidson MW, Galbraith JA et al. 2011. Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination. Nat. Methods 8:417–23
    [Google Scholar]
  68. 68. 
    Gao L, Shao L, Higgins CD, Poulton JS, Peifer M et al. 2012. Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens. Cell 151:61370–85
    [Google Scholar]
  69. 69. 
    Yang Z, Prokopas M, Nylk J, Coll-Lladó C, Gunn-Moore FJ et al. 2014. A compact Airy beam light sheet microscope with a tilted cylindrical lens. Biomed. Opt. Express 5:103434–42
    [Google Scholar]
  70. 70. 
    Vettenburg T, Dalgarno HIC, Nylk J, Coll-Lladó C, Ferrier DEK et al. 2014. Light-sheet microscopy using an Airy beam. Nat. Methods 11:541–44
    [Google Scholar]
  71. 71. 
    Booth M, Andrade D, Burke D, Patton B, Zurauskas M 2015. Aberrations and adaptive optics in super-resolution microscopy. Microscopy 64:4251–61
    [Google Scholar]
  72. 72. 
    Klein MV, Furtak TE. 1986. Optics New York: Wiley. , 2nd ed..
  73. 73. 
    Gibson SF, Lanni F. 1992. Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy. J. Opt. Soc. Am. A. 9:1154–66
    [Google Scholar]
  74. 74. 
    Li T, Ota S, Kim J, Wong ZJ, Wang Y et al. 2014. Axial plane optical microscopy. Sci. Rep. 4:7253
    [Google Scholar]
  75. 75. 
    Pluta M. 1988. Advanced Light Microscopy Warsaw: PWN
  76. 76. 
    Arimoto R, Murray JM. 2004. A common aberration with water-immersion objective lenses. J. Microsc. 216:49–51
    [Google Scholar]
  77. 77. 
    Cutler PJ, Malik MD, Liu S, Byars JM, Lidke DS, Lidke KA 2013. Multi-color quantum dot tracking using a high-speed hyperspectral line-scanning microscope. PLOS ONE 8:5e64320
    [Google Scholar]
  78. 78. 
    Abrahamsson S, Chen J, Hajj B, Stallinga S, Katsov AY et al. 2013. Fast multicolor 3D imaging using aberration-corrected multifocus microscopy. Nat. Methods 10:160–63
    [Google Scholar]
  79. 79. 
    Siemons M, Hulleman CN, Thorsen RO, Smith CS, Stallinga S 2018. High precision wavefront control in point spread function engineering for single emitter localization. Opt. Express 26:78397–416
    [Google Scholar]
  80. 80. 
    Mlodzianoski MJ, Cheng-Hathaway PJ, Bemiller SM, McCray TJ, Liu S et al. 2018. Active PSF shaping and adaptive optics enable volumetric localization microscopy through brain sections. Nat. Methods 15:583–86
    [Google Scholar]
  81. 81. 
    Liu S, Kromann EB, Krueger WD, Bewersdorf J, Lidke KA 2013. Three dimensional single molecule localization using a phase retrieved pupil function. Opt. Express 21:2429462–87
    [Google Scholar]
  82. 82. 
    Booth MJ, Neil MAA, Wilson T 1998. Aberration correction for confocal imaging in refractive-index-mismatched media. J. Microsc. 192:290–98
    [Google Scholar]
  83. 83. 
    McGorty R, Schnitzbauer J, Zhang W, Huang B 2014. Correction of depth-dependent aberrations in 3D single-molecule localization and super-resolution microscopy. Opt. Lett. 39:2275–78
    [Google Scholar]
  84. 84. 
    Wyant JC, Creath K. 1992. Basic wavefront aberration theory for optical metrology. Applied Optics and Optical Engineering 11: RR Shannon, JC Wyant 2–53 New York: Academic
    [Google Scholar]
  85. 85. 
    Ji N. 2017. Adaptive optical fluorescence microscopy. Nat. Methods 14:4374–80
    [Google Scholar]
  86. 86. 
    Pavani SRP, Piestun R. 2008. High-efficiency rotating point spread functions. Opt. Express 16:53484–89
    [Google Scholar]
  87. 87. 
    Jia S, Vaughan JC, Zhuang X 2014. Isotropic three-dimensional super-resolution imaging with a self-bending point spread function. Nat. Photonics 8:4302–6
    [Google Scholar]
  88. 88. 
    Shechtman Y, Sahl SJ, Backer AS, Moerner WE 2014. Optimal point spread function design for 3D imaging. Phys. Rev. Lett. 113:133902
    [Google Scholar]
  89. 89. 
    Shechtman Y, Weiss LE, Backer AS, Moerner WE 2015. Precise three-dimensional scan-free multiple-particle tracking over large axial ranges with tetrapod point spread functions. Nano Lett 15:64194–99
    [Google Scholar]
  90. 90. 
    Baddeley D, Cannell MB, Soeller C 2011. Three-dimensional sub-100 nm super-resolution imaging of biological samples using a phase ramp in the objective pupil. Nano Res 4:6589–98
    [Google Scholar]
  91. 91. 
    Xu K, Babcock HP, Zhuang X 2012. Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton. Nat. Methods 9:2185–88
    [Google Scholar]
  92. 92. 
    Huang F, Sirinakis G, Allgeyer ES, Schroeder LK, Duim WC et al. 2016. Ultra-high resolution 3D imaging of whole cells. Cell 166:41028–40
    [Google Scholar]
  93. 93. 
    Liu S, Huang F. 2019. Enhanced 4Pi single-molecule localization microscopy with coherent pupil based localization and light sheet illumination. bioRxiv 586404. https://doi.org/10.1101/586404
    [Crossref]
  94. 94. 
    Bon P, Linarès-Loyez J, Feyeux M, Alessandri K, Lounis B et al. 2018. Self-interference 3D super-resolution microscopy for deep tissue investigations. Nat. Methods 15:449–54
    [Google Scholar]
  95. 95. 
    Hajj B, Wisniewski J, El Beheiry M, Chen J, Revyakin A et al. 2014. Whole-cell, multicolor superresolution imaging using volumetric multifocus microscopy. PNAS 111:4917480–85
    [Google Scholar]
  96. 96. 
    Hajj B, El Beheiry M, Dahan M 2016. PSF engineering in multifocus microscopy for increased depth volumetric imaging. Biomed. Opt. Express 7:3726–31
    [Google Scholar]
  97. 97. 
    Oudjedi L, Fiche J, Abrahamsson S, Mazenq L, Lecestre A et al. 2016. Astigmatic multifocus microscopy enables deep 3D super-resolved imaging. Biomed. Opt. Express 7:62163–73
    [Google Scholar]
  98. 98. 
    Hanser BM, Gustafsson MGL, Agard DA, Sedat JW 2003. Phase retrieval for high-numerical-aperture optical systems. Opt. Lett. 28:10801–3
    [Google Scholar]
  99. 99. 
    Hanser BM, Gustafsson MGL, Agard DA, Sedat JW 2004. Phase-retrieved pupil functions in wide-field fluorescence microscopy. J. Microsc. 216:132–48
    [Google Scholar]
  100. 100. 
    Quirin S, Pavani SRP, Piestun R 2012. Optimal 3D single-molecule localization for superresolution microscopy with aberrations and engineered point spread functions. PNAS 109:3675–79
    [Google Scholar]
  101. 101. 
    Petrov PN, Shechtman Y, Moerner WE 2017. Measurement-based estimation of global pupil functions in 3D localization microscopy. Opt. Express 25:77945–59
    [Google Scholar]
  102. 102. 
    Sakamoto JA, Barrett HH. 2012. Maximum-likelihood estimation of parameterized wavefronts from multifocal data. Opt. Express 20:1415928–44
    [Google Scholar]
  103. 103. 
    Babcock HP, Zhuang X. 2017. Analyzing single molecule localization microscopy data using cubic splines. Sci. Rep. 7:552
    [Google Scholar]
  104. 104. 
    Li Y, Mund M, Hoess P, Deschamps J, Matti U et al. 2018. Real-time 3D single-molecule localization using experimental point spread functions. Nat. Methods 15:5367–69
    [Google Scholar]
  105. 105. 
    Saleh BEA, Lu K. 1990. Theory and design of the liquid crystal TV as an optical spatial phase modulator. Opt. Eng. 29:3240
    [Google Scholar]
  106. 106. 
    Platt BC, Shack R. 2001. History and principles of Shack–Hartmann wavefront sensing. J. Refract. Surg. 17:5S573–77
    [Google Scholar]
  107. 107. 
    Burke D, Patton B, Huang F, Bewersdorf J, Booth MJ 2015. Adaptive optics correction of specimen-induced aberrations in single-molecule switching microscopy. Optica 2:2177–85
    [Google Scholar]
  108. 108. 
    Tehrani KF, Xu J, Zhang Y, Shen P, Kner P 2015. Adaptive optics stochastic optical reconstruction microscopy (AO-STORM) using a genetic algorithm. Opt. Express 23:1013677–92
    [Google Scholar]
  109. 109. 
    Tehrani KF, Zhang Y, Shen P, Kner P 2017. Adaptive optics stochastic optical reconstruction microscopy (AO-STORM) by particle swarm optimization. Biomed. Opt. Express 8:115087–97
    [Google Scholar]
  110. 110. 
    Rao CR. 2001. Linear Statistical Inference and Its Applications New York: Wiley. , 2nd ed..
  111. 111. 
    Backlund MP, Shechtman Y, Walsworth RL 2018. Fundamental precision bounds for three-dimensional optical localization microscopy with Poisson statistics. Phys. Rev. Lett. 121:023904
    [Google Scholar]
  112. 112. 
    Shechtman Y, Weiss LE, Backer AS, Lee MY, Moerner WE 2016. Multicolour localization microscopy by point-spread-function engineering. Nat. Photonics 10:9590–94
    [Google Scholar]
  113. 113. 
    Balzarotti F, Eilers Y, Gwosch KC, Gynnå AH, Westphal V et al. 2017. Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes. Science 355:6325606–12
    [Google Scholar]
  114. 114. 
    Cnossen J, Hinsdale T, Thorsen R, Schueder F, Jungmann R et al. 2019. Localization microscopy at doubled precision with patterned illumination. bioRxiv 554337. https://doi.org/10.1101/554337
    [Crossref]
  115. 115. 
    Gwosch KC, Pape JK, Balzarotti F, Hoess P, Ellenberg J et al. 2019. MINFLUX nanoscopy delivers multicolor nanometer 3D-resolution in (living) cells. bioRxiv 734251. https://doi.org/10.1101/734251
    [Crossref]
  116. 116. 
    Bates M, Huang B, Dempsey GT, Zhuang XW 2007. Multicolor super-resolution imaging with photo-switchable fluorescent probes. Science 317:58451749–53
    [Google Scholar]
  117. 117. 
    Rust MJ, Bates M, Zhuang XW 2006. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods 3:10793–95
    [Google Scholar]
  118. 118. 
    Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S et al. 2006. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313:57931642–45
    [Google Scholar]
  119. 119. 
    Grover G, Mohrman W, Piestun R 2015. Real-time adaptive drift correction for super-resolution localization microscopy. Opt. Express 23:1823887–98
    [Google Scholar]
  120. 120. 
    Gustavsson AK, Petrov PN, Lee MY, Shechtman Y, Moerner WE 2018. 3D single-molecule super-resolution microscopy with a tilted light sheet. Nat. Commun. 9:1123
    [Google Scholar]
  121. 121. 
    Carter AR, King GM, Ulrich TA, Halsey W, Alchenberger D, Perkins TT 2007. Stabilization of an optical microscope to 0.1 nm in three dimensions. Appl. Opt. 46:3421–27
    [Google Scholar]
  122. 122. 
    Lee SH, Baday M, Tjioe M, Simonson PD, Zhang R et al. 2012. Using fixed fiduciary markers for stage drift correction. Opt. Express 20:1112177–83
    [Google Scholar]
  123. 123. 
    Youn Y, Ishitsuka Y, Jin C, Selvin PR 2018. Thermal nanoimprint lithography for drift correction in super-resolution fluorescence microscopy. Opt. Express 26:21670–80
    [Google Scholar]
  124. 124. 
    Tang Y, Wang X, Zhang X, Li J, Dai L 2014. Sub-nanometer drift correction for super-resolution imaging. Opt. Lett. 39:195685–88
    [Google Scholar]
  125. 125. 
    Ma HQ, Xu JQ, Jin JY, Huang Y, Liu Y 2017. A simple marker-assisted 3D nanometer drift correction method for superresolution microscopy. Biophys. J. 112:102196–208
    [Google Scholar]
  126. 126. 
    Abrahamsson S, Chen JJ, Hajj B, Stallinga S, Katsov AY et al. 2013. Fast multicolor 3D imaging using aberration-corrected multifocus microscopy. Nat. Methods 10:160–63
    [Google Scholar]
  127. 127. 
    McGorty R, Kamiyama D, Huang B 2013. Active microscope stabilization in three dimensions using image correlation. Opt. Nanoscopy 2:3
    [Google Scholar]
  128. 128. 
    Park S, Kang W, Kwon YD, Shim J, Kim S et al. 2018. Superresolution fluorescence microscopy for 3D reconstruction of thick samples. Mol. Brain 11:17
    [Google Scholar]
  129. 129. 
    Mlodzianoski MJ, Schreiner JM, Callahan SP, Smolková K, Dlasková A et al. 2011. Sample drift correction in 3D fluorescence photoactivation localization microscopy. Opt. Express 19:1615009–19
    [Google Scholar]
  130. 130. 
    Wang Y, Schnitzbauer J, Hu Z, Li X, Cheng Y et al. 2014. Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm. Opt. Express 22:1315982–91
    [Google Scholar]
  131. 131. 
    Li X, Mooney P, Zheng S, Booth CR, Braunfeld MB et al. 2013. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods 10:6584–90
    [Google Scholar]
  132. 132. 
    Fernández-Suárez M, Ting AY. 2008. Fluorescent probes for super-resolution imaging in living cells. Nat. Rev. Mol. Cell Biol. 9:12929–43
    [Google Scholar]
  133. 133. 
    Ha T, Tinnefeld P. 2012. Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging. Annu. Rev. Phys. Chem. 63:595–617
    [Google Scholar]
  134. 134. 
    Dempsey GT, Vaughan JC, Chen KH, Bates M, Zhuang X 2011. Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging. Nat. Methods 8:121027–36
    [Google Scholar]
  135. 135. 
    Dave R, Terry DS, Munro JB, Blanchard SC 2009. Mitigating unwanted photophysical processes for improved single-molecule fluorescence imaging. Biophys. J. 96:62371–81
    [Google Scholar]
  136. 136. 
    Altman RB, Terry DS, Zhou Z, Zheng Q, Geggier P et al. 2012. Cyanine fluorophore derivatives with enhanced photostability. Nat. Methods 9:168–71
    [Google Scholar]
  137. 137. 
    Basu S, Needham LM, Lando D, Taylor EJR, Wohlfahrt KJ et al. 2018. FRET-enhanced photostability allows improved single-molecule tracking of proteins and protein complexes in live mammalian cells. Nat. Commun. 9:12520
    [Google Scholar]
  138. 138. 
    Halabi EA, Pinotsi D, Rivera-Fuentes P 2019. Photoregulated fluxional fluorophores for live-cell super-resolution microscopy with no apparent photobleaching. Nat. Commun. 10:11232
    [Google Scholar]
  139. 139. 
    Chen F, Tillberg PW, Boyden ES 2015. Expansion microscopy. Science 347:6221534–48
    [Google Scholar]
  140. 140. 
    Chozinski TJ, Halpern AR, Okawa H, Kim HJ, Tremel GJ et al. 2016. Expansion microscopy with conventional antibodies and fluorescent proteins. Nat. Methods 13:6485–88
    [Google Scholar]
  141. 141. 
    Shi X, Li Q, Dai Z, Tran A, Feng S et al. 2019. Label-retention expansion microscopy. bioRxiv 687954. https://doi.org/10.1101/687954
    [Crossref]
  142. 142. 
    Agasti SS, Wang Y, Schueder F, Sukumar A, Jungmann R, Yin P 2017. DNA-barcoded labeling probes for highly multiplexed Exchange-PAINT imaging. Chem. Sci. 8:3080–91
    [Google Scholar]
  143. 143. 
    Ku T, Swaney J, Park JY, Albanese A, Murray E et al. 2016. Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues. Nat. Biotechnol. 34:9973–81
    [Google Scholar]
  144. 144. 
    Dean KM, Roudot P, Welf ES, Danuser G, Fiolka R 2015. Deconvolution-free subcellular imaging with axially swept light sheet microscopy. Biophys. J. 108:122807–15
    [Google Scholar]
  145. 145. 
    Gao L. 2015. Extend the field of view of selective plan illumination microscopy by tiling the excitation light sheet. Opt. Express 23:56102–11
    [Google Scholar]
  146. 146. 
    Fu Q, Martin BL, Matus DQ, Gao L 2016. Imaging multicellular specimens with real-time optimized tiling light-sheet selective plane illumination microscopy. Nat. Commun. 7:11088
    [Google Scholar]
  147. 147. 
    Bouchard MB, Voleti V, Mendes CS, Lacefield C, Grueber WB et al. 2015. Swept confocally-aligned planar excitation (SCAPE) microscopy for high-speed volumetric imaging of behaving organisms. Nat. Photonics 9:2113–19
    [Google Scholar]
  148. 148. 
    Dunsby C. 2008. Optically sectioned imaging by oblique plane microscopy. Opt. Express 16:2520306–16
    [Google Scholar]
  149. 149. 
    Keller PJ, Schmidt AD, Wittbrodt J, Stelzer EHK 2008. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 322:59041065–69
    [Google Scholar]
  150. 150. 
    Fadero TC, Gerbich TM, Rana K, Suzuki A, DiSalvo M et al. 2018. LITE microscopy: tilted light-sheet excitation of model organisms offers high resolution and low photobleaching. J. Cell Biol. 217:51869–82
    [Google Scholar]
  151. 151. 
    Meddens MBM, Liu S, Finnegan PS, Edwards TL, James CD, Lidke KA 2016. Single objective light-sheet microscopy for high-speed whole-cell 3D super-resolution. Biomed. Opt. Express 7:62219–36
    [Google Scholar]
/content/journals/10.1146/annurev-bioeng-060418-052203
Loading
/content/journals/10.1146/annurev-bioeng-060418-052203
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error