1932

Abstract

Optical microscopy has become an invaluable tool for investigating complex samples. Over the years, many advances to optical microscopes have been made that have allowed us to uncover new insights into the samples studied. Dynamic changes in biological and chemical systems are of utmost importance to study. To probe these samples, multidimensional approaches have been developed to acquire a fuller understanding of the system of interest. These dimensions include the spatial information, such as the three-dimensional coordinates and orientation of the optical probes, and additional chemical and physical properties through combining microscopy with various spectroscopic techniques. In this review, we survey the field of multidimensional microscopy and provide an outlook on the field and challenges that may arise.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-physchem-090519-034100
2022-04-20
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/physchem/73/1/annurev-physchem-090519-034100.html?itemId=/content/journals/10.1146/annurev-physchem-090519-034100&mimeType=html&fmt=ahah

Literature Cited

  1. 1. 
    Bates M, Huang B, Dempsey GT, Zhuang X. 2007. Multicolor super-resolution imaging with photo-switchable fluorescent probes. Science 317:1749–53
    [Google Scholar]
  2. 2. 
    Manley S, Gillette JM, Patterson GH, Shroff H, Hess HF et al. 2008. High-density mapping of single-molecule trajectories with photoactivated localization microscopy. Nat. Methods 5:155
    [Google Scholar]
  3. 3. 
    Huang B, Bates M, Zhuang X. 2009. Super-resolution fluorescence microscopy. Annu. Rev. Biochem. 78:993–1016
    [Google Scholar]
  4. 4. 
    Axelrod D, Omann GM. 2006. Combinatorial microscopy. Nat. Rev. Mol. Cell Biol. 7:944–52
    [Google Scholar]
  5. 5. 
    Donnert G, Keller J, Wurm CA, Rizzoli SO, Westphal V et al. 2007. Two-color far-field fluorescence nanoscopy. Biophys. J. 92:L67–69
    [Google Scholar]
  6. 6. 
    Shroff H, Galbraith CG, Galbraith JA, White H, Gillette J et al. 2007. Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes. PNAS 104:20308–13
    [Google Scholar]
  7. 7. 
    Chen KH, Boettiger AN, Moffitt JR, Wang S, Zhuang X 2015. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348:aaa6090
    [Google Scholar]
  8. 8. 
    Moffitt JR, Hao J, Wang G, Chen KH, Babcock HP, Zhuang X. 2016. High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization. PNAS 113:11046–51
    [Google Scholar]
  9. 9. 
    Inavalli VVGK, Lenz MO, Butler C, Angibaud J, Compans B et al. 2019. A super-resolution platform for correlative live single-molecule imaging and STED microscopy. Nat. Methods 16:1263–68
    [Google Scholar]
  10. 10. 
    Sharonov A, Hochstrasser RM. 2006. Wide-field subdiffraction imaging by accumulated binding of diffusing probes. PNAS 103:18911–16
    [Google Scholar]
  11. 11. 
    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 10:4756–61
    [Google Scholar]
  12. 12. 
    Gómez-García PA, Garbacik ET, Otterstrom JJ, Garcia-Parajo MF, Lakadamyali M. 2018. Excitation-multiplexed multicolor superresolution imaging with fm-STORM and fm-DNA-PAINT. PNAS 115:12991–96
    [Google Scholar]
  13. 13. 
    van Wee R, Filius M, Joo C 2021. Completing the canvas: advances and challenges for DNA-PAINT super-resolution imaging. Trends Biochem. Sci. 46:918–30
    [Google Scholar]
  14. 14. 
    Lelek M, Gyparaki MT, Beliu G, Schueder F, Griffié J et al. 2021. Single-molecule localization microscopy. Nat. Rev. Methods Primers 1:39
    [Google Scholar]
  15. 15. 
    Hohng S, Joo C, Ha T. 2004. Single-molecule three-color FRET. Biophys. J. 87:1328–37
    [Google Scholar]
  16. 16. 
    Lee J, Lee S, Ragunathan K, Joo C, Ha T, Hohng S 2010. Single-molecule four-color FRET. Angew. Chem. Int. Ed. 49:9922–25
    [Google Scholar]
  17. 17. 
    Jeffet J, Ionescu A, Michaeli Y, Torchinsky D, Perlson E et al. 2021. Multimodal single-molecule microscopy with continuously controlled spectral resolution. Biophys. Rep. 1:100013
    [Google Scholar]
  18. 18. 
    Keller AM, DeVore MS, Stich DG, Vu DM, Causgrove T, Werner JH 2018. Multicolor three-dimensional tracking for single-molecule fluorescence resonance energy transfer measurements. Anal. Chem. 90:6109–15
    [Google Scholar]
  19. 19. 
    Hohng S, Lee S, Lee J, Jo MH 2014. Maximizing information content of single-molecule FRET experiments: multi-color FRET and FRET combined with force or torque. Chem. Soc. Rev. 43:1007–13
    [Google Scholar]
  20. 20. 
    Bartels K, Lasitza-Male T, Hofmann H, Löw C. 2021. Single-molecule FRET of membrane transport proteins. ChemBioChem 22:2657–71
    [Google Scholar]
  21. 21. 
    Heintzmann R, Huser T. 2017. Super-resolution structured illumination microscopy. Chem. Rev. 117:13890–908
    [Google Scholar]
  22. 22. 
    Wu Y, Shroff H. 2018. Faster, sharper, and deeper: structured illumination microscopy for biological imaging. Nat. Methods 15:1011–19
    [Google Scholar]
  23. 23. 
    Wan Y, McDole K, Keller PJ 2019. Light-sheet microscopy and its potential for understanding developmental processes. Annu. Rev. Cell Dev. Biol. 35:655–81
    [Google Scholar]
  24. 24. 
    Girkin JM, Carvalho MT. 2018. The light-sheet microscopy revolution. J. Opt. 20:053002
    [Google Scholar]
  25. 25. 
    Aaron J, Wait E, DeSantis M, Chew T-L 2019. Practical considerations in particle and object tracking and analysis. Curr. Protoc. Cell Biol. 83:e88
    [Google Scholar]
  26. 26. 
    von Diezmann A, Shechtman Y, Moerner WE. 2017. Three-dimensional localization of single molecules for super-resolution imaging and single-particle tracking. Chem. Rev. 117:7244–75
    [Google Scholar]
  27. 27. 
    Shen H, Tauzin LJ, Baiyasi R, Wang W, Moringo N et al. 2017. Single particle tracking: from theory to biophysical applications. Chem. Rev. 117:7331–76
    [Google Scholar]
  28. 28. 
    Zhong Y, Wang G. 2020. Three-dimensional single particle tracking and its applications in confined environments. Annu. Rev. Anal. Chem. 13:381–403
    [Google Scholar]
  29. 29. 
    Speidel M, Jonáš A, Florin E-L. 2003. Three-dimensional tracking of fluorescent nanoparticles with subnanometer precision by use of off-focus imaging. Opt. Lett. 28:69–71
    [Google Scholar]
  30. 30. 
    Germann JA, Davis LM. 2014. Three-dimensional tracking of a single fluorescent nanoparticle using four-focus excitation in a confocal microscope. Opt. Express 22:5641–50
    [Google Scholar]
  31. 31. 
    Welsher K, Yang H. 2014. Multi-resolution 3D visualization of the early stages of cellular uptake of peptide-coated nanoparticles. Nat. Nanotechnol. 9:198–203
    [Google Scholar]
  32. 32. 
    Guerra LF, Muir TW, Yang H. 2019. Single-particle dynamic light scattering: shapes of individual nanoparticles. Nano Lett 19:5530–36
    [Google Scholar]
  33. 33. 
    Prabhat P, Ram S, Ward ES, Ober RJ 2004. Simultaneous imaging of different focal planes in fluorescence microscopy for the study of cellular dynamics in three dimensions. IEEE Trans. NanoBiosci. 3:237–42
    [Google Scholar]
  34. 34. 
    Ram S, Prabhat P, Ward ES, Ober RJ 2009. Improved single particle localization accuracy with dual objective multifocal plane microscopy. Opt. Express 17:6881–98
    [Google Scholar]
  35. 35. 
    Juette MF, Bewersdorf J. 2010. Three-dimensional tracking of single fluorescent particles with submillisecond temporal resolution. Nano Lett 10:4657–63
    [Google Scholar]
  36. 36. 
    Jiang C, Kaul N, Campbell J, Meyhofer E. 2017. A novel dual-color bifocal imaging system for single-molecule studies. Rev. Sci. Instrum. 88:053705
    [Google Scholar]
  37. 37. 
    Toprak E, Balci H, Blehm BH, Selvin PR. 2007. Three-dimensional particle tracking via bifocal imaging. Nano Lett 7:2043–45
    [Google Scholar]
  38. 38. 
    Wang X, Yi H, Gdor I, Hereld M, Scherer NF. 2019. Nanoscale resolution 3D snapshot particle tracking by multifocal microscopy. Nano Lett 19:6781–87
    [Google Scholar]
  39. 39. 
    Abrahamsson S, Chen J, Hajj B, Stallinga S, Katsov AY et al. 2013. Fast multicolor 3D imaging using aberration-corrected multifocus microscopy. Nat. Methods 10:60–63
    [Google Scholar]
  40. 40. 
    Louis B, Camacho R, Bresolí-Obach R, Abakumov S, Vandaele J et al. 2020. Fast-tracking of single emitters in large volumes with nanometer precision. Opt. Express 28:28656–71
    [Google Scholar]
  41. 41. 
    Huang B, Wang W, Bates M, Zhuang X. 2008. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319:810–13
    [Google Scholar]
  42. 42. 
    Kao HP, Verkman A. 1994. Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position. Biophys. J. 67:1291–300
    [Google Scholar]
  43. 43. 
    Holtzer L, Meckel T, Schmidt T. 2007. Nanometric three-dimensional tracking of individual quantum dots in cells. Appl. Phys. Lett. 90:053902
    [Google Scholar]
  44. 44. 
    Zhao L, Zhong Y, Wei Y, Ortiz N, Chen F, Wang G 2016. Microscopic movement of slow-diffusing nanoparticles in cylindrical nanopores studied with three-dimensional tracking. Anal. Chem. 88:5122–30
    [Google Scholar]
  45. 45. 
    Backlund MP, Lew MD, Backer AS, Sahl SJ, Grover G et al. 2012. Simultaneous, accurate measurement of the 3D position and orientation of single molecules. PNAS 109:19087–92
    [Google Scholar]
  46. 46. 
    Thompson MA, Lew MD, Badieirostami M, Moerner WE. 2010. Localizing and tracking single nanoscale emitters in three dimensions with high spatiotemporal resolution using a double-helix point spread function. Nano Lett 10:211–18
    [Google Scholar]
  47. 47. 
    Shechtman Y, Weiss LE, Backer AS, Sahl SJ, Moerner WE. 2015. Precise three-dimensional scan-free multiple-particle tracking over large axial ranges with tetrapod point spread functions. Nano Lett 15:4194–99
    [Google Scholar]
  48. 48. 
    Yajima J, Mizutani K, Nishizaka T. 2008. A torque component present in mitotic kinesin Eg5 revealed by three-dimensional tracking. Nat. Struct. Mol. Biol. 15:1119–21
    [Google Scholar]
  49. 49. 
    Sun Y, McKenna JD, Murray JM, Ostap EM, Goldman YE. 2009. Parallax: high accuracy three-dimensional single molecule tracking using split images. Nano Lett 9:2676–82
    [Google Scholar]
  50. 50. 
    Chen K, Gu Y, Sun W, Bin D, Wang G et al. 2017. Characteristic rotational behaviors of rod-shaped cargo revealed by automated five-dimensional single particle tracking. Nat. Commun. 8:887
    [Google Scholar]
  51. 51. 
    Wang G, Sun W, Luo Y, Fang N. 2010. Resolving rotational motions of nano-objects in engineered environments and live cells with gold nanorods and differential interference contrast microscopy. J. Am. Chem. Soc. 132:16417–22
    [Google Scholar]
  52. 52. 
    Gu Y, Sun W, Wang G, Fang N 2011. Single particle orientation and rotation tracking discloses distinctive rotational dynamics of drug delivery vectors on live cell membranes. J. Am. Chem. Soc. 133:5720–23
    [Google Scholar]
  53. 53. 
    Stender AS, Marchuk K, Liu C, Sander S, Meyer MW et al. 2013. Single cell optical imaging and spectroscopy. Chem. Rev 113:2469–527
    [Google Scholar]
  54. 54. 
    Gu Y, Ha JW, Augspurger AE, Chen K, Zhu S, Fang N 2013. Single Particle Orientation and Rotational Tracking (SPORT) in biophysical studies. Nanoscale 5:10753–64
    [Google Scholar]
  55. 55. 
    Waga S, Stillman B. 1998. The DNA replication fork in eukaryotic cells. Annu. Rev. Biochem. 67:721–51
    [Google Scholar]
  56. 56. 
    Fass D, Bogden CE, Berger JM. 1999. Quaternary changes in topoisomerase II may direct orthogonal movement of two DNA strands. Nat. Struct. Biol. 6:322–6
    [Google Scholar]
  57. 57. 
    Yasuda R, Noji H, Yoshida M, Kinosita K, Itoh H 2001. Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase. Nature 410:898–904
    [Google Scholar]
  58. 58. 
    Cingolani G, Duncan TM. 2011. Structure of the ATP synthase catalytic complex (F1) from Escherichia coli in an autoinhibited conformation. Nat. Struct. Mol. Biol. 18:701–7
    [Google Scholar]
  59. 59. 
    Forkey JN, Quinlan ME, Alexander Shaw M, Corrie JET, Goldman YE 2003. Three-dimensional structural dynamics of myosin V by single-molecule fluorescence polarization. Nature 422:399–404
    [Google Scholar]
  60. 60. 
    Kural C, Kim H, Syed S, Goshima G, Gelfand VI, Selvin PR. 2005. Kinesin and dynein move a peroxisome in vivo: a tug-of-war or coordinated movement?. Science 308:1469–72
    [Google Scholar]
  61. 61. 
    Guo P, Noji H, Yengo CM, Zhao Z, Grainge I. 2016. Biological nanomotors with a revolution, linear, or rotation motion mechanism. Microbiol. Mol. Biol. Rev. 80:161–86
    [Google Scholar]
  62. 62. 
    Enoki S, Iino R, Niitani Y, Minagawa Y, Tomishige M, Noji H 2015. High-speed angle-resolved imaging of a single gold nanorod with microsecond temporal resolution and one-degree angle precision. Anal. Chem. 87:2079–86
    [Google Scholar]
  63. 63. 
    Shroder DY, Lippert LG, Goldman YE. 2016. Single molecule optical measurements of orientation and rotations of biological macromolecules. Methods Appl. Fluoresc. 4:042004
    [Google Scholar]
  64. 64. 
    Toprak E, Enderlein J, Syed S, McKinney SA, Petschek RG et al. 2006. Defocused orientation and position imaging (DOPI) of myosin V. PNAS 103:6495–99
    [Google Scholar]
  65. 65. 
    Zhang O, Lu J, Ding T, Lew MD 2019. Erratum: “Imaging the three-dimensional orientation and rotational mobility of fluorescent emitters using the Tri-spot point spread function” [Appl. Phys. Lett. 113, 031103 2018]. Appl. Phys. Lett. 115:069901
    [Google Scholar]
  66. 66. 
    Zhang O, Lew MD. 2019. Fundamental limits on measuring the rotational constraint of single molecules using fluorescence microscopy. Phys. Rev. Lett. 122:198301
    [Google Scholar]
  67. 67. 
    Ha T, Enderle T, Chemla DS, Selvin PR, Weiss S. 1996. Single molecule dynamics studied by polarization modulation. Phys. Rev. Lett. 77:3979–82
    [Google Scholar]
  68. 68. 
    Fourkas JT. 2001. Rapid determination of the three-dimensional orientation of single molecules. Opt. Lett. 26:211–13
    [Google Scholar]
  69. 69. 
    Böhmer M, Enderlein J. 2003. Orientation imaging of single molecules by wide-field epifluorescence microscopy. J. Opt. Soc. Am. B 20:554–59
    [Google Scholar]
  70. 70. 
    Lieb MA, Zavislan JM, Novotny L. 2004. Single-molecule orientations determined by direct emission pattern imaging. J. Opt. Soc. Am. B 21:1210–15
    [Google Scholar]
  71. 71. 
    Sikorski Z, Davis LM. 2008. Engineering the collected field for single-molecule orientation determination. Opt. Express 16:3660–73
    [Google Scholar]
  72. 72. 
    Backer AS, Moerner WE. 2015. Determining the rotational mobility of a single molecule from a single image: a numerical study. Opt. Express 23:4255–76
    [Google Scholar]
  73. 73. 
    Backer AS, Lee MY, Moerner WE. 2016. Enhanced DNA imaging using super-resolution microscopy and simultaneous single-molecule orientation measurements. Optica 3:659–66
    [Google Scholar]
  74. 74. 
    Li Q, Chen X-J, Xu Y, Lan S, Liu H-Y et al. 2010. Photoluminescence properties of the CdSe quantum dots accompanied with rotation of the defocused wide-field fluorescence images. J. Phys. Chem. C 114:13427–32
    [Google Scholar]
  75. 75. 
    Kukura P, Ewers H, Müller C, Renn A, Helenius A, Sandoghdar V. 2009. High-speed nanoscopic tracking of the position and orientation of a single virus. Nat. Methods 6:923–27
    [Google Scholar]
  76. 76. 
    Ohmachi M, Komori Y, Iwane AH, Fujii F, Jin T, Yanagida T 2012. Fluorescence microscopy for simultaneous observation of 3D orientation and movement and its application to quantum rod-tagged myosin V. PNAS 109:5294–98
    [Google Scholar]
  77. 77. 
    Forkey JN, Quinlan ME, Goldman YE 2001. Protein structural dynamics by single-molecule fluorescence polarization. Biology at the Single-Molecule Level SH Leuba, J Zlatanova 1–35 Amsterdam: Pergamon
    [Google Scholar]
  78. 78. 
    Peterman EJG, Sosa H, Moerner WE. 2004. Single-molecule fluorescence spectroscopy and microscopy of biomolecular motors. Annu. Rev. Phys. Chem 55:79–96
    [Google Scholar]
  79. 79. 
    Rosenberg SA, Quinlan ME, Forkey JN, Goldman YE. 2005. Rotational motions of macro-molecules by single-molecule fluorescence microscopy. Acc. Chem. Res. 38:583–93
    [Google Scholar]
  80. 80. 
    Jain PK, Huang X, El-Sayed IH, El-Sayed MA. 2008. Noble metals on the nanoscale: optical and photothermal properties and some applications in imaging, sensing, biology, and medicine. Acc. Chem. Res 41:1578–86
    [Google Scholar]
  81. 81. 
    Olson J, Dominguez-Medina S, Hoggard A, Wang L-Y, Chang W-S, Link S. 2015. Optical characterization of single plasmonic nanoparticles. Chem. Soc. Rev. 44:40–57
    [Google Scholar]
  82. 82. 
    Xiao L, Yeung ES 2014. Optical imaging of individual plasmonic nanoparticles in biological samples. Annu. Rev. Anal. Chem. 7:89–111
    [Google Scholar]
  83. 83. 
    Peng Y, Xiong B, Peng L, Li H, He Y, Yeung ES. 2015. Recent advances in optical imaging with anisotropic plasmonic nanoparticles. Anal. Chem. 87:200–15
    [Google Scholar]
  84. 84. 
    Ha JW. 2016. Recent advances in single particle rotational tracking of plasmonic anisotropic gold nanoparticles under far-field optical microscopy. Appl. Spectrosc. Rev. 51:552–69
    [Google Scholar]
  85. 85. 
    Ma Y, Wang X, Liu H, Wei L, Xiao L 2019. Recent advances in optical microscopic methods for single-particle tracking in biological samples. Anal. Bioanal. Chem. 411:4445–63
    [Google Scholar]
  86. 86. 
    Wu Y, Ali MRK, Chen K, Fang N, El-Sayed MA 2019. Gold nanoparticles in biological optical imaging. NanoToday 24:120–40
    [Google Scholar]
  87. 87. 
    Wang G, Stender AS, Sun W, Fang N 2010. Optical imaging of non-fluorescent nanoparticle probes in live cells. Analyst 135:215–21
    [Google Scholar]
  88. 88. 
    Rong G, Wang H, Reinhard BM 2010. Insights from a nanoparticle minuet: two-dimensional membrane profiling through silver plasmon ruler tracking. Nano Lett 10:230–38
    [Google Scholar]
  89. 89. 
    Ha JW, Chen K, Fang N 2013. Differential interference contrast microscopy imaging of micrometer-long plasmonic nanowires. Chem. Commun. 49:11038–40
    [Google Scholar]
  90. 90. 
    Culver KSB, Liu T, Hryn AJ, Fang N, Odom TW. 2018. In situ identification of nanoparticle structural information using optical microscopy. J. Phys. Chem. Lett. 9:2886–92
    [Google Scholar]
  91. 91. 
    Jeon HB, Tsalu PV, Ha JW. 2019. Shape effect on the refractive index sensitivity at localized surface plasmon resonance inflection points of single gold nanocubes with vertices. Sci. Rep. 9:13635
    [Google Scholar]
  92. 92. 
    Lee SY, Tsalu PV, Kim GW, Seo MJ, Hong JW, Ha JW 2019. Tuning chemical interface damping: interfacial electronic effects of adsorbate molecules and sharp tips of single gold bipyramids. Nano Lett 19:2568–74
    [Google Scholar]
  93. 93. 
    Kaplan L, Ierokomos A, Chowdary P, Bryant Z, Cui B 2018. Rotation of endosomes demonstrates coordination of molecular motors during axonal transport. Sci. Adv. 4:e1602170
    [Google Scholar]
  94. 94. 
    Kim GW, Ha JW. 2018. Direct visualization of wavelength-dependent single dipoles generated on single gold nanourchins with sharp branches. Nanoscale Res. Lett. 13:256
    [Google Scholar]
  95. 95. 
    Lee J, Ha JW 2018. Elucidating the contribution of dipole resonance mode to polarization-dependent optical properties in single triangular gold nanoplates. Chem. Phys. Lett. 713:121–24
    [Google Scholar]
  96. 96. 
    Lee SY, Han Y, Hong JW, Ha JW 2017. Single gold bipyramids with sharp tips as sensitive single particle orientation sensors in biological studies. Nanoscale 9:12060–67
    [Google Scholar]
  97. 97. 
    Lee J, Ha JW 2019. Single-particle correlation study: polarization-dependent differential interference contrast imaging of two-dimensional gold nanoplates. Anal. Sci. 35:1237–41
    [Google Scholar]
  98. 98. 
    Lee J, Ha JW 2017. Defocused dark-field orientation imaging of single gold microrods on synthetic membranes. Phys. Chem. Chem. Phys. 19:24453–57
    [Google Scholar]
  99. 99. 
    Stender AS, Wei X, Augspurger AE, Fang N. 2013. Plasmonic behavior of single gold dumbbells and simple dumbbell geometries. J. Phys. Chem. C 117:16195–202
    [Google Scholar]
  100. 100. 
    Sönnichsen C, Alivisatos AP. 2005. Gold nanorods as novel nonbleaching plasmon-based orientation sensors for polarized single-particle microscopy. Nano Lett 5:301–4
    [Google Scholar]
  101. 101. 
    Chang W-S, Ha JW, Slaughter LS, Link S. 2010. Plasmonic nanorod absorbers as orientation sensors. PNAS 107:2781–86
    [Google Scholar]
  102. 102. 
    Stender AS, Wang G, Sun W, Fang N 2010. Influence of gold nanorod geometry on optical response. ACS Nano 4:7667–75
    [Google Scholar]
  103. 103. 
    Chen H, Shao L, Li Q, Wang J 2013. Gold nanorods and their plasmonic properties. Chem. Soc. Rev. 42:2679–724
    [Google Scholar]
  104. 104. 
    Ha JW, Sun W, Wang G, Fang N 2011. Differential interference contrast polarization anisotropy for tracking rotational dynamics of gold nanorods. Chem. Commun. 47:7743–45
    [Google Scholar]
  105. 105. 
    Gu Y, Di X, Sun W, Wang G, Fang N 2012. Three-dimensional super-localization and tracking of single gold nanoparticles in cells. Anal. Chem. 84:4111–17
    [Google Scholar]
  106. 106. 
    Gu Y, Sun W, Wang G, Jeftinija K, Jeftinija S, Fang N 2012. Rotational dynamics of cargos at pauses during axonal transport. Nat. Commun. 3:1030
    [Google Scholar]
  107. 107. 
    Ha JW, Sun W, Stender AS, Fang N. 2012. Dual-wavelength detection of rotational diffusion of single anisotropic nanocarriers on live cell membranes. J. Phys. Chem. C 116:2766–71
    [Google Scholar]
  108. 108. 
    Sun W, Gu Y, Wang G, Fang N 2012. Dual-modality single particle orientation and rotational tracking of intracellular transport of nanocargos. Anal. Chem. 84:1134–38
    [Google Scholar]
  109. 109. 
    Gu Y, Sun W, Wang G, Zimmermann MT, Jernigan RL, Fang N 2013. Revealing rotational modes of functionalized gold nanorods on live cell membranes. Small 9:785
    [Google Scholar]
  110. 110. 
    Gu Y, Wang G, Fang N. 2013. Simultaneous single-particle superlocalization and rotational tracking. ACS Nano 7:1658–65
    [Google Scholar]
  111. 111. 
    Wei L, Xu J, Ye Z, Zhu X, Zhong M et al. 2016. Orientational imaging of a single gold nanorod at the liquid/solid interface with polarized evanescent field illumination. Anal. Chem. 88:1995–99
    [Google Scholar]
  112. 112. 
    Xu D, He Y, Yeung ES. 2014. Direct observation of the orientation dynamics of single protein-coated nanoparticles at liquid/solid interfaces. Angew. Chem. Int. Ed. 53:6951–55
    [Google Scholar]
  113. 113. 
    Xiao L, Qiao Y, He Y, Yeung ES. 2011. Imaging translational and rotational diffusion of single anisotropic nanoparticles with planar illumination microscopy. J. Am. Chem. Soc. 133:10638–45
    [Google Scholar]
  114. 114. 
    Xiao L, Qiao Y, He Y, Yeung ES. 2010. Three dimensional orientational imaging of nanoparticles with darkfield microscopy. Anal. Chem. 82:5268–74
    [Google Scholar]
  115. 115. 
    Chowdary PD, Kaplan L, Che DL, Cui B 2018. Dynamic clustering of dyneins on axonal endosomes: evidence from high-speed darkfield imaging. Biophys. J. 115:230–41
    [Google Scholar]
  116. 116. 
    Xu D, He Y, Yeung ES. 2014. Direct imaging of transmembrane dynamics of single nanoparticles with darkfield microscopy: improved orientation tracking at cell sidewall. Anal. Chem. 86:3397–404
    [Google Scholar]
  117. 117. 
    Xiao L, Wei L, Liu C, He Y, Yeung ES. 2012. Unsynchronized translational and rotational diffusion of nanocargo on a living cell membrane. Angew. Chem. Int. Ed. 51:4181–84
    [Google Scholar]
  118. 118. 
    Ha JW, Marchuk K, Fang N 2012. Focused orientation and position imaging (FOPI) of single anisotropic plasmonic nanoparticles by total internal reflection scattering microscopy. Nano Lett 12:4282–88
    [Google Scholar]
  119. 119. 
    Marchuk K, Ha JW, Fang N. 2013. Three-dimensional high-resolution rotational tracking with superlocalization reveals conformations of surface-bound anisotropic nanoparticles. Nano Lett 13:1245–50
    [Google Scholar]
  120. 120. 
    Marchuk K, Fang N. 2013. Three-dimensional orientation determination of stationary anisotropic nanoparticles with sub-degree precision under total internal reflection scattering microscopy. Nano Lett 13:5414–19
    [Google Scholar]
  121. 121. 
    Tcherniak A, Dominguez-Medina S, Chang W-S, Swanglap P, Slaughter LS et al. 2011. One-photon plasmon luminescence and its application to correlation spectroscopy as a probe for rotational and translational dynamics of gold nanorods. J. Phys. Chem. C 115:15938–49
    [Google Scholar]
  122. 122. 
    Zhang B, Lan T, Huang X, Dong C, Ren J 2013. Sensitive single particle method for characterizing rapid rotational and translational diffusion and aspect ratio of anisotropic nanoparticles and its application in immunoassays. Anal. Chem. 85:9433–38
    [Google Scholar]
  123. 123. 
    Sun W, Wang G, Fang N, Yeung ES. 2009. Wavelength-dependent differential interference contrast microscopy: selectively imaging nanoparticle probes in live cells. Anal. Chem. 81:9203–8
    [Google Scholar]
  124. 124. 
    Luo Y, Sun W, Gu Y, Wang G, Fang N 2010. Wavelength-dependent differential interference contrast microscopy: multiplexing detection using nonfluorescent nanoparticles. Anal. Chem. 82:6675–79
    [Google Scholar]
  125. 125. 
    Stender AS, Augspurger AE, Wang G, Fang N 2012. Influence of polarization setting on gold nanorod signal at nonplasmonic wavelengths under differential interference contrast microscopy. Anal. Chem. 84:5210–15
    [Google Scholar]
  126. 126. 
    Chen K, Lin C-C, Vela J, Fang N. 2015. Multishell Au/Ag/SiO2 nanorods with tunable optical properties as single particle orientation and rotational tracking probes. Anal. Chem. 87:4096–99
    [Google Scholar]
  127. 127. 
    Pan Q, Zhao H, Lin X, He Y 2019. Spatiotemporal heterogeneity of reactions in solution observed with high-speed single-nanorod rotational sensing. Angew. Chem. Int. Ed. 58:8389–93
    [Google Scholar]
  128. 128. 
    Kim GW, Lee SY, Ha JW 2017. Three-dimensional defocused orientation sensing of single bimetallic core–shell gold nanorods as multifunctional optical probes. Analyst 142:899–903
    [Google Scholar]
  129. 129. 
    Kim GW, Ha JW. 2017. Platinum-coated core-shell gold nanorods as multifunctional orientation sensors in differential interference contrast microscopy. Anal. Sci. 33:1021–25
    [Google Scholar]
  130. 130. 
    Xiong B, Zhou R, Hao J, Jia Y, He Y, Yeung ES. 2013. Highly sensitive sulphide mapping in live cells by kinetic spectral analysis of single Au-Ag core-shell nanoparticles. Nat. Commun. 4:1708
    [Google Scholar]
  131. 131. 
    Zhao F, Chen K, Dong B, Yang K, Gu Y, Fang N 2017. Localization accuracy of gold nanoparticles in single particle orientation and rotational tracking. Opt. Express 25:9860–71
    [Google Scholar]
  132. 132. 
    Cheng X, Chen K, Dong B, Filbrun SL, Wang G, Fang N 2021. Resolving cargo-motor-track interactions with bifocal parallax single-particle tracking. Biophys. J. 120:1378–86
    [Google Scholar]
  133. 133. 
    Cheng X, Chen K, Dong B, Yang M, Filbrun S et al. 2021. Dynamin-dependent vesicle twist at the final stage of clathrin-mediated endocytosis. Nat. Cell Biol 23:85969
    [Google Scholar]
  134. 134. 
    Lattuada M, Hatton TA. 2011. Synthesis, properties and applications of Janus nanoparticles. Nano Today 6:286–308
    [Google Scholar]
  135. 135. 
    Walther A, Müller AHE. 2013. Janus particles: synthesis, self-assembly, physical properties, and applications. Chem. Rev 113:5194–261
    [Google Scholar]
  136. 136. 
    Anker JN, Behrend C, Kopelman R. 2003. Aspherical magnetically modulated optical nanoprobes (MagMOONs). J. Appl. Phys. 93:6698–700
    [Google Scholar]
  137. 137. 
    Anker JN, Kopelman R. 2003. Magnetically modulated optical nanoprobes. Appl. Phys. Lett. 82:1102–4
    [Google Scholar]
  138. 138. 
    Anthony SM, Hong L, Kim M, Granick S 2006. Single-particle colloid tracking in four dimensions. Langmuir 22:9812–15
    [Google Scholar]
  139. 139. 
    Anthony SM, Yu Y. 2015. Tracking single particle rotation: probing dynamics in four dimensions. Anal. Methods 7:7020–28
    [Google Scholar]
  140. 140. 
    Nguyen KT, Anker JN. 2014. Detecting de-gelation through tissue using magnetically modulated optical nanoprobes (MagMOONs). Sens. Actuators B Chem. 205:313–21
    [Google Scholar]
  141. 141. 
    Sanchez L, Patton P, Anthony SM, Yi Y, Yu Y 2015. Tracking single-particle rotation during macrophage uptake. Soft Matter 11:5346–52
    [Google Scholar]
  142. 142. 
    Gao Y, Yu Y, Sanchez L, Yu Y. 2017. Seeing the unseen: imaging rotation in cells with designer anisotropic particles. Micron 101:123–31
    [Google Scholar]
  143. 143. 
    Gao Y, Anthony SM, Yi Y, Li W, Yu Y, Yu Y 2018. Single-Janus rod tracking reveals the “rock-and-roll” of endosomes in living cells. Langmuir 34:1151–58
    [Google Scholar]
  144. 144. 
    Gao Y, Anthony SM, Yu Y, Yi Y, Yu Y 2018. Cargos rotate at microtubule intersections during intracellular trafficking. Biophys. J. 114:2900–9
    [Google Scholar]
  145. 145. 
    Lee K, Zhang L, Yi Y, Wang X, Yu Y 2018. Rupture of lipid membranes induced by amphiphilic Janus nanoparticles. ACS Nano 12:3646–57
    [Google Scholar]
  146. 146. 
    Yu Y, Gao Y, Yu Y. 2018.. “ Waltz” of cell membrane-coated nanoparticles on lipid bilayers: tracking single particle rotation in ligand–receptor binding. ACS Nano 12:11871–80
    [Google Scholar]
  147. 147. 
    Lee K, Yu Y 2019. Lipid bilayer disruption induced by amphiphilic Janus nanoparticles: the non-monotonic effect of charged lipids. Soft Matter 15:2373–80
    [Google Scholar]
  148. 148. 
    Li W, Wojcik M, Xu K. 2019. Optical microscopy unveils rapid, reversible electrochemical oxidation and reduction of graphene. Nano Lett 19:983–89
    [Google Scholar]
  149. 149. 
    Chen X, Shen Z, He Y, Guan T, He Q et al. 2019. Dual-wavelength digital holographic phase and fluorescence microscopy combining with Raman spectroscopy for micro-quartz pieces-based dual-channel encoded suspension array. Opt. Express 27:1894–910
    [Google Scholar]
  150. 150. 
    Choi Y-W, Mistry H, Cuenya BR. 2017. New insights into working nanostructured electrocatalysts through operando spectroscopy and microscopy. Curr. Opin. Electrochem. 1:95–103
    [Google Scholar]
  151. 151. 
    Gong Z, Pan Y-L, Videen G, Wang C 2018. Optical trapping-Raman spectroscopy (OT-RS) with embedded microscopy imaging for concurrent characterization and monitoring of physical and chemical properties of single particles. Anal. Chim. Acta 1020:86–94
    [Google Scholar]
  152. 152. 
    Yang Y-C, Chang W-T, Huang S-K, Liau I. 2014. Characterization of the pharmaceutical effect of drugs on atherosclerotic lesions in vivo using integrated fluorescence imaging and Raman spectral measurements. Anal. Chem. 86:3863–68
    [Google Scholar]
  153. 153. 
    Kong K, Rowlands CJ, Varma S, Perkins W, Leach IH et al. 2013. Diagnosis of tumors during tissue-conserving surgery with integrated autofluorescence and Raman scattering microscopy. PNAS 110:15189–94
    [Google Scholar]
  154. 154. 
    Jhan J-W, Chang W-T, Chen H-C, Lee Y-T, Wu M-F et al. 2008. Integrated multiple multi-photon imaging and Raman spectroscopy for characterizing structure-constituent correlation of tissues. Opt. Express 16:16431–41
    [Google Scholar]
  155. 155. 
    Nallala J, Piot O, Diebold M-D, Gobinet C, Bouché O et al. 2014. Infrared and Raman imaging for characterizing complex biological materials: a comparative morpho-spectroscopic study of colon tissue. Appl. Spectrosc. 68:57–68
    [Google Scholar]
  156. 156. 
    Depciuch J, Kaznowska E, Zawlik I, Wojnarowska R, Cholewa M et al. 2016. Application of Raman spectroscopy and infrared spectroscopy in the identification of breast cancer. Appl. Spectrosc. 70:251–63
    [Google Scholar]
  157. 157. 
    Perez-Guaita D, Kochan K, Martin M, Andrew DW, Heraud P et al. 2017. Multimodal vibrational imaging of cells. Vib. Spectrosc. 91:46–58
    [Google Scholar]
  158. 158. 
    Kochan K, Peng H, Wood BR, Haritos VS. 2018. Single cell assessment of yeast metabolic engineering for enhanced lipid production using Raman and AFM-IR imaging. Biotechnol. Biofuels 11:106
    [Google Scholar]
  159. 159. 
    Dazzi A, Prater CB, Hu Q, Chase DB, Rabolt JF, Marcott C. 2012. AFM–IR: combining atomic force microscopy and infrared spectroscopy for nanoscale chemical characterization. Appl. Spectrosc. 66:1365–84
    [Google Scholar]
  160. 160. 
    Zhang D, Li C, Zhang C, Slipchenko MN, Eakins G, Cheng J-X. 2016. Depth-resolved mid-infrared photothermal imaging of living cells and organisms with submicrometer spatial resolution. Sci. Adv. 2:e1600521
    [Google Scholar]
  161. 161. 
    Li C, Zhang D, Slipchenko MN, Cheng J-X. 2017. Mid-infrared photothermal imaging of active pharmaceutical ingredients at submicrometer spatial resolution. Anal. Chem. 89:4863–67
    [Google Scholar]
  162. 162. 
    Bai Y, Zhang D, Li C, Liu C, Cheng J-X. 2017. Bond-selective imaging of cells by mid-infrared photothermal microscopy in high wavenumber region. J. Phys. Chem. B 121:10249–55
    [Google Scholar]
  163. 163. 
    Li Z, Aleshire K, Kuno M, Hartland GV. 2017. Super-resolution far-field infrared imaging by photothermal heterodyne imaging. J. Phys. Chem. B 121:8838–46
    [Google Scholar]
  164. 164. 
    Li X, Zhang D, Bai Y, Wang W, Liang J, Cheng J-X 2019. Fingerprinting a living cell by Raman integrated mid-infrared photothermal microscopy. Anal. Chem. 91:10750–56
    [Google Scholar]
  165. 165. 
    Bossi M, Fölling J, Belov VN, Boyarskiy VP, Medda R et al. 2008. Multicolor far-field fluorescence nanoscopy through isolated detection of distinct molecular species. Nano Lett 8:2463–68
    [Google Scholar]
  166. 166. 
    Testa I, Wurm CA, Medda R, Rothermel E, von Middendorf C et al. 2010. Multicolor fluorescence nanoscopy in fixed and living cells by exciting conventional fluorophores with a single wavelength. Biophys. J. 99:2686–94
    [Google Scholar]
  167. 167. 
    Gunewardene MS, Subach FV, Gould TJ, Penoncello GP, Gudheti MV et al. 2011. Superresolution imaging of multiple fluorescent proteins with highly overlapping emission spectra in living cells. Biophys. J. 101:1522–28
    [Google Scholar]
  168. 168. 
    Zhang Z, Kenny SJ, Hauser M, Li W, Xu K 2015. Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy. Nat. Methods 12:935–38
    [Google Scholar]
  169. 169. 
    Mlodzianoski MJ, Curthoys NM, Gunewardene MS, Carter S, Hess ST 2016. Super-resolution imaging of molecular emission spectra and single molecule spectral fluctuations. PLOS ONE 11:e0147506-e
    [Google Scholar]
  170. 170. 
    Comtet J, Glushkov E, Navikas V, Feng J, Babenko V et al. 2019. Wide-field spectral super-resolution mapping of optically active defects in hexagonal boron nitride. Nano Lett 19:2516–23
    [Google Scholar]
  171. 171. 
    Moon S, Yan R, Kenny SJ, Shyu Y, Xiang L et al. 2017. Spectrally resolved, functional super-resolution microscopy reveals nanoscale compositional heterogeneity in live-cell membranes. J. Am. Chem. Soc. 139:10944–47
    [Google Scholar]
  172. 172. 
    Dong B, Almassalha L, Urban BE, Nguyen T-Q, Khuon S et al. 2016. Super-resolution spectroscopic microscopy via photon localization. Nat. Commun. 7:12290
    [Google Scholar]
  173. 173. 
    Bongiovanni MN, Godet J, Horrocks MH, Tosatto L, Carr AR et al. 2016. Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping. Nat. Commun. 7:13544
    [Google Scholar]
  174. 174. 
    Kim D, Zhang Z, Xu K. 2017. Spectrally resolved super-resolution microscopy unveils multipath reaction pathways of single spiropyran molecules. J. Am. Chem. Soc. 139:9447–50
    [Google Scholar]
  175. 175. 
    Zhao F, Filbrun SL, Huang T, Dong B, Fang N 2021. Multiscale evolution of bulk heterojunction solar cell active layers under thermal stress. Anal. Chem. 93:1232–36
    [Google Scholar]
  176. 176. 
    Berera R, van Grondelle R, Kennis JTM. 2009. Ultrafast transient absorption spectroscopy: principles and application to photosynthetic systems. Photosynth. Res. 101:105–18
    [Google Scholar]
  177. 177. 
    Jones AC, Kearns NM, Ho J-J, Flach JT, Zanni MT. 2020. Impact of non-equilibrium molecular packings on singlet fission in microcrystals observed using 2D white-light microscopy. Nat. Chem. 12:40–47
    [Google Scholar]
  178. 178. 
    Jones AC, Kearns NM, Bohlmann Kunz M, Flach JT, Zanni MT 2019. Multidimensional spectroscopy on the microscale: development of a multimodal imaging system incorporating 2D white-light spectroscopy, broadband transient absorption, and atomic force microscopy. J. Phys. Chem. A 123:10824–36
    [Google Scholar]
  179. 179. 
    Wang X, Huang S-C, Huang T-X, Su H-S, Zhong J-H et al. 2017. Tip-enhanced Raman spectroscopy for surfaces and interfaces. Chem. Soc. Rev. 46:4020–41
    [Google Scholar]
  180. 180. 
    Huang T-X, Cong X, Wu S-S, Lin K-Q, Yao X et al. 2019. Probing the edge-related properties of atomically thin MoS2 at nanoscale. Nat. Commun. 10:5544
    [Google Scholar]
  181. 181. 
    Zeng Z-C, Huang S-C, Wu D-Y, Meng L-Y, Li M-H et al. 2015. Electrochemical tip-enhanced Raman spectroscopy. J. Am. Chem. Soc. 137:11928–31
    [Google Scholar]
  182. 182. 
    Park K-D, Khatib O, Kravtsov V, Clark G, Xu X, Raschke MB 2016. Hybrid tip-enhanced nanospectroscopy and nanoimaging of monolayer WSe2 with local strain control. Nano Lett 16:2621–27
    [Google Scholar]
  183. 183. 
    Tang C, Jia S, Chen W, Lou J, Voronine DV 2017. Nano-optical imaging of monolayer MoSe2 using tip-enhanced photoluminescence. arXiv:1704.02396v2 [physics.optics]
  184. 184. 
    Huth F, Govyadinov A, Amarie S, Nuansing W, Keilmann F, Hillenbrand R 2012. Nano-FTIR absorption spectroscopy of molecular fingerprints at 20 nm spatial resolution. Nano Lett 12:3973–78
    [Google Scholar]
  185. 185. 
    Fei Z, Rodin AS, Andreev GO, Bao W, McLeod AS et al. 2012. Gate-tuning of graphene plasmons revealed by infrared nano-imaging. Nature 487:82–85
    [Google Scholar]
  186. 186. 
    van Schrojenstein Lantman EM, Deckert-Gaudig T, Mank AJG, Deckert V, Weckhuysen BM 2012. Catalytic processes monitored at the nanoscale with tip-enhanced Raman spectroscopy. Nat. Nanotechnol. 7:583–86
    [Google Scholar]
  187. 187. 
    Zhang R, Zhang Y, Dong ZC, Jiang S, Zhang C et al. 2013. Chemical mapping of a single molecule by plasmon-enhanced Raman scattering. Nature 498:82–86
    [Google Scholar]
  188. 188. 
    Hoffman DP, Shtengel G, Xu CS, Campbell KR, Freeman M et al. 2020. Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells. Science 367:eaaz5357
    [Google Scholar]
  189. 189. 
    Matusovsky OS, Mansson A, Persson M, Cheng Y-S, Rassier DE. 2019. High-speed AFM reveals subsecond dynamics of cardiac thin filaments upon Ca2+ activation and heavy meromyosin binding. PNAS 116:16384–93
    [Google Scholar]
  190. 190. 
    Petti MK, Lomont JP, Maj M, Zanni MT 2018. Two-dimensional spectroscopy is being used to address core scientific questions in biology and materials science. J. Phys. Chem. B 122:1771–80
    [Google Scholar]
  191. 191. 
    Lomont JP, Ostrander JS, Ho J-J, Petti MK, Zanni MT. 2017. Not all β-sheets are the same: amyloid infrared spectra, transition dipole strengths, and couplings investigated by 2D IR spectroscopy. J. Phys. Chem. B 121:8935–45
    [Google Scholar]
  192. 192. 
    Dunkelberger EB, Grechko M, Zanni MT. 2015. Transition dipoles from 1D and 2D infrared spectroscopy help reveal the secondary structures of proteins: application to amyloids. J. Phys. Chem. B 119:14065–75
    [Google Scholar]
  193. 193. 
    Kearns NM, Mehlenbacher RD, Jones AC, Zanni MT. Broadband 2D electronic spectrometer using white light and pulse shaping: noise and signal evaluation at 1 and 100 kHz. Opt. Express 25:7869–83
    [Google Scholar]
  194. 194. 
    Hamm P. 2014. 2D-Raman-THz spectroscopy: a sensitive test of polarizable water models. J. Chem. Phys. 141:184201
    [Google Scholar]
  195. 195. 
    Shalit A, Ahmed S, Savolainen J, Hamm P 2017. Terahertz echoes reveal the inhomogeneity of aqueous salt solutions. Nat. Chem. 9:273–78
    [Google Scholar]
  196. 196. 
    Courtney TL, Fox ZW, Slenkamp KM, Lynch MS, Khalil M 2015. Two-dimensional Fourier transform infrared-visible and infrared-Raman spectroscopies. Ultrafast Phenomena XIX K Yamanouchi, S Cundiff, R de Vivie-Riedle, M Kuwata-Gonokami, L DiMauro 503–5 Springer Proc. Phys. , Vol. 162 Cham, Switz: Springer Int.
    [Google Scholar]
  197. 197. 
    Newby JM, Schaefer AM, Lee PT, Forest MG, Lai SK 2018. Convolutional neural networks automate detection for tracking of submicron-scale particles in 2D and 3D. PNAS 115:9026–31
    [Google Scholar]
  198. 198. 
    Zhong Y, Li C, Zhou H, Wang G. 2018. Developing noise-resistant three-dimensional single particle tracking using deep neural networks. Anal. Chem. 90:10748–57
    [Google Scholar]
  199. 199. 
    Christiansen EM, Yang SJ, Ando DM, Javaherian A, Skibinski G et al. 2018. In silico labeling: predicting fluorescent labels in unlabeled images. Cell 173:792–803.e19
    [Google Scholar]
/content/journals/10.1146/annurev-physchem-090519-034100
Loading
/content/journals/10.1146/annurev-physchem-090519-034100
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