Volume 15 Issue 6
Dec.  2022
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Chinese Optics  > 2022  >  15(6): 1243-1257.
LI Meng-fan, CHEN Jian-wei, SHI Wei, FU Shuang, LI Yun-ze, LUO Ting-dan, CHEN Jun-fan, LI Yi-ming. Advances in multi-dimensional single molecule imaging[J]. Chinese Optics, 2022, 15(6): 1243-1257. doi: 10.37188/CO.2022-0088
Citation: LI Meng-fan, CHEN Jian-wei, SHI Wei, FU Shuang, LI Yun-ze, LUO Ting-dan, CHEN Jun-fan, LI Yi-ming. Advances in multi-dimensional single molecule imaging[J]. Chinese Optics, 2022, 15(6): 1243-1257. doi: 10.37188/CO.2022-0088
shu

Advances in multi-dimensional single molecule imaging

  • Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China

Funds:  Supported by Guangdong Natural Science Foundation Joint Fund (No. 2020A1515110380); Shandong Key Research and Development Program(No. 2021CXGC010212); Shenzhen Science and Technology Innovation Commission (No. KQTD20200820113012029)
  • Received Date: 30 Apr 2022
  • Rev Recd Date: 19 May 2022
  • Accepted Date: 28 Jun 2022
    • Available Online: 20 Aug 2022
    Abstract

  • Single-molecule imaging is widely used for the reconstruction of three-dimensional subcellular structures. The point spread function is an important window to analyze the information of a single molecule. Besides 3D coordinates, it also contains abundant additional information. In this paper, we reviewed the recent progress of multi-dimensional single-molecule imaging, including spatial location, fluorescence wavelength, dipole orientation, interference phase, etc. We also briefly introduced the latest methods for molecule localization and proposed the further directions for its research.

     

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  • [1]
    GUSTAFSSON M G L. Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy[J]. Journal of Microscopy, 2000, 198(2): 82-87. doi: 10.1046/j.1365-2818.2000.00710.x
    [2]
    GUSTAFSSON M G L. Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution[J]. Proceedings of the National Academy of Sciences of the United States of America, 2005, 102(37): 13081-13086. doi: 10.1073/pnas.0406877102
    [3]
    BLOM H, WIDENGREN J. Stimulated emission depletion microscopy[J]. Chemical Reviews, 2017, 117(11): 7377-7427. doi: 10.1021/acs.chemrev.6b00653
    [4]
    HELL S W, WICHMANN J. Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy[J]. Optics Letters, 1994, 19(11): 780-782. doi: 10.1364/OL.19.000780
    [5]
    KLAR T A, JAKOBS S, DYBA M, et al. Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission[J]. Proceedings of the National Academy of Sciences of the United States of America, 2000, 97(15): 8206-8210. doi: 10.1073/pnas.97.15.8206
    [6]
    RUST M J, BATES M, ZHUANG X W. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)[J]. Nature Methods, 2006, 3(10): 793-796. doi: 10.1038/nmeth929
    [7]
    HEILEMANN M, VAN DE LINDE S, SCHÜTTPELZ M, et al. Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes[J]. Angewandte Chemie International Edition, 2008, 47(33): 6172-6176. doi: 10.1002/anie.200802376
    [8]
    ZHUANG X W. Nano-imaging with STORM[J]. Nature Photonics, 2009, 3(7): 365-367. doi: 10.1038/nphoton.2009.101
    [9]
    BETZIG E, PATTERSON G H, SOUGRAT R, et al. Imaging intracellular fluorescent proteins at nanometer resolution[J]. Science, 2006, 313(5793): 1642-1645. doi: 10.1126/science.1127344
    [10]
    SHTENGEL G, GALBRAITH J A, GALBRAITH C G, et al. Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure[J]. Proceedings of the National Academy of Sciences of the United States of America, 2009, 106(9): 3125-3130. doi: 10.1073/pnas.0813131106
    [11]
    SHROFF H, WHITE H, BETZIG E. Photoactivated localization microscopy (PALM) of adhesion complexes[J]. Current Protocols in Cell Biology, 2013, 58(1): 4.21.1-24.21.28.
    [12]
    LIU Y J, LU Y Q, YANG X S, et al. Amplified stimulated emission in upconversion nanoparticles for super-resolution nanoscopy[J]. Nature, 2017, 543(7644): 229-233. doi: 10.1038/nature21366
    [13]
    ZHAN Q Q, LIU H CH, WANG B J, et al. Achieving high-efficiency emission depletion nanoscopy by employing cross relaxation in upconversion nanoparticles[J]. Nature Communications, 2017, 8(1): 1058. doi: 10.1038/s41467-017-01141-y
    [14]
    LIANG L L, FENG Z W, ZHANG Q M, et al. Continuous-wave near-infrared stimulated-emission depletion microscopy using downshifting lanthanide nanoparticles[J]. Nature Nanotechnology, 2021, 16(9): 975-980. doi: 10.1038/s41565-021-00927-y
    [15]
    SCHNITZBAUER J, STRAUSS M T, SCHLICHTHAERLE T, et al. Super-resolution microscopy with DNA-PAINT[J]. Nature Protocols, 2017, 12(6): 1198-1228. doi: 10.1038/nprot.2017.024
    [16]
    SCHUEDER F, LARA-GUTIéRREZ J, BELIVEAU B J, et al. Multiplexed 3D super-resolution imaging of whole cells using spinning disk confocal microscopy and DNA-PAINT[J]. Nature Communications, 2017, 8(1): 2090. doi: 10.1038/s41467-017-02028-8
    [17]
    JIA H, YANG J K, LI X J. Minimum variance unbiased subpixel centroid estimation of point image limited by photon shot noise[J]. Journal of the Optical Society of America A, 2010, 27(9): 2038-2045. doi: 10.1364/JOSAA.27.002038
    [18]
    STALLINGA S, RIEGER B. Accuracy of the gaussian point spread function model in 2D localization microscopy[J]. Optics Express, 2010, 18(24): 24461-24476. doi: 10.1364/OE.18.024461
    [19]
    SMALL A, STAHLHEBER S. Fluorophore localization algorithms for super-resolution microscopy[J]. Nature Methods, 2014, 11(3): 267-279. doi: 10.1038/nmeth.2844
    [20]
    PATTERSON G, DAVIDSON M, MANLEY S, et al. Superresolution imaging using single-molecule localization[J]. Annual Review of Physical Chemistry, 2010, 61: 345-367. doi: 10.1146/annurev.physchem.012809.103444
    [21]
    HERBERT S, SOARES H, ZIMMER C, et al. Single-molecule localization super-resolution microscopy: deeper and faster[J]. Microscopy and Microanalysis, 2012, 18(6): 1419-1429. doi: 10.1017/S1431927612013347
    [22]
    HUANG B, WANG W Q, BATES M, et al. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy[J]. Science, 2008, 319(5864): 810-813. doi: 10.1126/science.1153529
    [23]
    HOLTZER L, MECKEL T, SCHMIDT T. Nanometric three-dimensional tracking of individual quantum dots in cells[J]. Applied Physics Letters, 2007, 90(5): 053902. doi: 10.1063/1.2437066
    [24]
    FU SH, LI M F, ZHOU L L, et al. Deformable mirror based optimal PSF engineering for 3D super-resolution imaging[J]. Optics Letters, 2022, 47(12): 3031-3034. doi: 10.1364/OL.460949
    [25]
    PIESTUN R, SCHECHNER Y Y, SHAMIR J. Propagation-invariant wave fields with finite energy[J]. Journal of the Optical Society of America A, 2000, 17(2): 294-303. doi: 10.1364/JOSAA.17.000294
    [26]
    GREENGARD A, SCHECHNER Y Y, PIESTUN R. Depth from diffracted rotation[J]. Optics Letters, 2006, 31(2): 181-183. doi: 10.1364/OL.31.000181
    [27]
    PAVANI S R P, PIESTUN R. High-efficiency rotating point spread functions[J]. Optics Express, 2008, 16(5): 3484-3489. doi: 10.1364/OE.16.003484
    [28]
    PAVANI S R P, THOMPSON M A, BITEEN J S, et al. Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function[J]. Proceedings of the National Academy of Sciences of the United States of America, 2009, 106(9): 2995-2999. doi: 10.1073/pnas.0900245106
    [29]
    BADDELEY D, CANNELL M B, SOELLER C. Three-dimensional sub-100 nm super-resolution imaging of biological samples using a phase ramp in the objective pupil[J]. Nano Research, 2011, 4(6): 589-598. doi: 10.1007/s12274-011-0115-z
    [30]
    LEW M D, LEE S F, BADIEIROSTAMI M, et al. Corkscrew point spread function for far-field three-dimensional nanoscale localization of pointlike objects[J]. Optics Letters, 2011, 36(2): 202-204. doi: 10.1364/OL.36.000202
    [31]
    SIVILOGLOU G A, BROKY J, DOGARIU A, et al. Observation of accelerating airy beams[J]. Physical Review Letters, 2007, 99(21): 213901. doi: 10.1103/PhysRevLett.99.213901
    [32]
    SIVILOGLOU G A, CHRISTODOULIDES D N. Accelerating finite energy airy beams[J]. Optics Letters, 2007, 32(8): 979-981. doi: 10.1364/OL.32.000979
    [33]
    JIA SH, VAUGHAN J C, ZHUANG X W. Isotropic three-dimensional super-resolution imaging with a self-bending point spread function[J]. Nature Photonics, 2014, 8(4): 302-306. doi: 10.1038/nphoton.2014.13
    [34]
    LIU SH, KROMANN E B, KRUEGER W D, et al. Three dimensional single molecule localization using a phase retrieved pupil function[J]. Optics Express, 2013, 21(24): 29462-29487. doi: 10.1364/OE.21.029462
    [35]
    ZELGER P, KASER K, ROSSBOTH B, et al. Three-dimensional localization microscopy using deep learning[J]. Optics Express, 2018, 26(25): 33166-33179. doi: 10.1364/OE.26.033166
    [36]
    SHECHTMAN Y, SAHL S J, BACKER A S, et al. Optimal point spread function design for 3D imaging[J]. Physical Review Letters, 2014, 113(13): 133902. doi: 10.1103/PhysRevLett.113.133902
    [37]
    SHECHTMAN Y, WEISS L E, BACKER A S, et al. Precise three-dimensional scan-free multiple-particle tracking over large axial ranges with tetrapod point spread functions[J]. Nano Letters, 2015, 15(6): 4194-4199. doi: 10.1021/acs.nanolett.5b01396
    [38]
    GORDON-SOFFER R, WEISS L E, ESHEL R, et al. Microscopic scan-free surface profiling over extended axial ranges by point-spread-function engineering[J]. Science Advances, 2020, 6(44): eabc0332. doi: 10.1126/sciadv.abc0332
    [39]
    ZHOU Y ZH, CARLES G. Precise 3D particle localization over large axial ranges using secondary astigmatism[J]. Optics Letters, 2020, 45(8): 2466-2469. doi: 10.1364/OL.388695
    [40]
    WEISS L E, SHALEV EZRA Y, GOLDBERG S, et al. Three-dimensional localization microscopy in live flowing cells[J]. Nature Nanotechnology, 2020, 15(6): 500-506. doi: 10.1038/s41565-020-0662-0
    [41]
    JIN D Y, XI P, WANG B M, et al. Nanoparticles for super-resolution microscopy and single-molecule tracking[J]. Nature Methods, 2018, 15(6): 415-423. doi: 10.1038/s41592-018-0012-4
    [42]
    NEHME E, WEISS L E, MICHAELI T, et al. Deep-STORM: super-resolution single-molecule microscopy by deep learning[J]. Optica, 2018, 5(4): 458-464. doi: 10.1364/OPTICA.5.000458
    [43]
    NEHME E, FREEDMAN D, GORDON R, et al. DeepSTORM3D: dense 3D localization microscopy and PSF design by deep learning[J]. Nature Methods, 2020, 17(7): 734-740. doi: 10.1038/s41592-020-0853-5
    [44]
    BALZAROTTI F, EILERS Y, GWOSCH K C, et al. Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes[J]. Science, 2017, 355(6325): 606-612. doi: 10.1126/science.aak9913
    [45]
    GWOSCH K C, PAPE J K, BALZAROTTI F, et al. MINFLUX nanoscopy delivers 3D multicolor nanometer resolution in cells[J]. Nature Methods, 2020, 17(2): 217-224. doi: 10.1038/s41592-019-0688-0
    [46]
    TESTA I, WURM C A, MEDDA R, et al. Multicolor fluorescence nanoscopy in fixed and living cells by exciting conventional fluorophores with a single wavelength[J]. Biophysical Journal, 2010, 99(8): 2686-2694. doi: 10.1016/j.bpj.2010.08.012
    [47]
    BROEKEN J, RIEGER B, STALLINGA S. Simultaneous measurement of position and color of single fluorescent emitters using diffractive optics[J]. Optics Letters, 2014, 39(11): 3352-3355. doi: 10.1364/OL.39.003352
    [48]
    SMITH C, HUISMAN M, SIEMONS M, et al. Simultaneous measurement of emission color and 3D position of single molecules[J]. Optics Express, 2016, 24(5): 4996-5013. doi: 10.1364/OE.24.004996
    [49]
    ZHANG ZH Y, KENNY S J, HAUSER M, et al. Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy[J]. Nature Methods, 2015, 12(10): 935-938. doi: 10.1038/nmeth.3528
    [50]
    SHECHTMAN Y, WEISS L E, BACKER A S, et al. Multicolour localization microscopy by point-spread-function engineering[J]. Nature Photonics, 2016, 10(9): 590-594. doi: 10.1038/nphoton.2016.137
    [51]
    HERSHKO E, WEISS L E, MICHAELI T, et al. Multicolor localization microscopy and point-spread-function engineering by deep learning[J]. Optics Express, 2019, 27(5): 6158-6183. doi: 10.1364/OE.27.006158
    [52]
    KIM T, MOON S, XU K. Information-rich localization microscopy through machine learning[J]. Nature Communications, 2019, 10(1): 1996. doi: 10.1038/s41467-019-10036-z
    [53]
    LEW M D, BACKLUND M P, MOERNER W E. Rotational mobility of single molecules affects localization accuracy in super-resolution fluorescence microscopy[J]. Nano Letters, 2013, 13(9): 3967-3972. doi: 10.1021/nl304359p
    [54]
    ENGELHARDT J, KELLER J, HOYER P, et al. Molecular orientation affects localization accuracy in superresolution far-field fluorescence microscopy[J]. Nano Letters, 2011, 11(1): 209-213. doi: 10.1021/nl103472b
    [55]
    ZHANGHAO K, CHEN L, YANG X S, et al. Super-resolution dipole orientation mapping via polarization demodulation[J]. Light:Science &Applications, 2016, 5(10): e16166.
    [56]
    ZHANGHAO K, GAO J T, JIN D Y, et al. Super-resolution fluorescence polarization microscopy[J]. Journal of Innovative Optical Health Sciences, 2018, 11(1): 1730002. doi: 10.1142/S1793545817300026
    [57]
    ZHANGHAO K, CHEN X Y, LIU W H, et al. Super-resolution imaging of fluorescent dipoles via polarized structured illumination microscopy[J]. Nature Communications, 2019, 10(1): 4694. doi: 10.1038/s41467-019-12681-w
    [58]
    BACKLUND M P, LEW M D, BACKER A S, et al. Simultaneous, accurate measurement of the 3D position and orientation of single molecules[J]. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(47): 19087-19092. doi: 10.1073/pnas.1216687109
    [59]
    WILLIG K I, RIZZOLI S O, WESTPHAL V, et al. STED microscopy reveals that synaptotagmin remains clustered after synaptic vesicle exocytosis[J]. Nature, 2006, 440(7086): 935-939. doi: 10.1038/nature04592
    [60]
    HULLEMAN C N, THORSEN R Ø, KIM E, et al. Simultaneous orientation and 3D localization microscopy with a Vortex point spread function[J]. Nature Communications, 2021, 12(1): 5934. doi: 10.1038/s41467-021-26228-5
    [61]
    HELL S, STELZER E H K. Properties of a 4Pi confocal fluorescence microscope[J]. Journal of the Optical Society of America A, 1992, 9(12): 2159-2166. doi: 10.1364/JOSAA.9.002159
    [62]
    HAO X, LI Y M, FU SH, et al. Review of 4Pi fluorescence nanoscopy[J]. Engineering, 2022, 11: 146-153. doi: 10.1016/j.eng.2020.07.028
    [63]
    AQUINO D, SCHÖNLE A, GEISLER C, et al. Two-color nanoscopy of three-dimensional volumes by 4Pi detection of stochastically switched fluorophores[J]. Nature Methods, 2011, 8(4): 353-359. doi: 10.1038/nmeth.1583
    [64]
    HUANG F, SIRINAKIS G, ALLGEYER E S, et al. Ultra-high resolution 3D imaging of whole cells[J]. Cell, 2016, 166(4): 1028-1040. doi: 10.1016/j.cell.2016.06.016
    [65]
    LI Y M, BUGLAKOVA E, ZHANG Y D, et al. Accurate 4Pi single-molecule localization using an experimental PSF model[J]. Optics Letters, 2020, 45(13): 3765-3768. doi: 10.1364/OL.397754
    [66]
    CHEN J W, YAO B X, YANG ZH CH, et al. Ratiometric 4Pi single-molecule localization with optimal resolution and color assignment[J]. Optics Letters, 2022, 47(2): 325-328. doi: 10.1364/OL.446987
    [67]
    ZHANG Y D, SCHROEDER L K, LESSARD M D, et al. Nanoscale subcellular architecture revealed by multicolor three-dimensional salvaged fluorescence imaging[J]. Nature Methods, 2020, 17(2): 225-231. doi: 10.1038/s41592-019-0676-4
    [68]
    STETSON P B. DAOPHOT: A computer program for crowded-field stellar photometry[J]. Publications of the Astronomical Society of the Pacific, 1987, 99(613): 191.
    [69]
    LEUTENEGGER M, RAO R, LEITGEB R A, et al. Fast focus field calculations[J]. Optics Express, 2006, 14(23): 11277-11291. doi: 10.1364/OE.14.011277
    [70]
    HANSER B M, GUSTAFSSON M G L, AGARD D A, et al. Phase retrieval for high-numerical-aperture optical systems[J]. Optics Letters, 2003, 28(10): 801-803. doi: 10.1364/OL.28.000801
    [71]
    BABCOCK H P, ZHUANG X W. Analyzing single molecule localization microscopy data using cubic splines[J]. Scientific Reports, 2017, 7(1): 552. doi: 10.1038/s41598-017-00622-w
    [72]
    LI Y M, MUND M, HOESS P, et al. Real-time 3D single-molecule localization using experimental point spread functions[J]. Nature Methods, 2018, 15(5): 367-369. doi: 10.1038/nmeth.4661
    [73]
    SPEISER A, MÜLLER L R, HOESS P, et al. Deep learning enables fast and dense single-molecule localization with high accuracy[J]. Nature Methods, 2021, 18(9): 1082-1090. doi: 10.1038/s41592-021-01236-x
    [74]
    THIELE J C, HELMERICH D A, OLEKSIIEVETS N, et al. Confocal fluorescence-lifetime single-molecule localization microscopy[J]. ACS Nano, 2020, 14(10): 14190-14200. doi: 10.1021/acsnano.0c07322
    [75]
    LIN Y, SHARIFI F, ANDERSSON S B. Three-dimensional localization refinement and motion model parameter estimation for confined single particle tracking under low-light conditions[J]. Biomedical Optics Express, 2021, 12(9): 5793-5811. doi: 10.1364/BOE.432187
    [76]
    LI Y M, WU Y L, HOESS P, et al. Depth-dependent PSF calibration and aberration correction for 3D single-molecule localization[J]. Biomedical Optics Express, 2019, 10(6): 2708-2718. doi: 10.1364/BOE.10.002708
    [77]
    LI Y M, SHI W, LIU SH, et al. Global fitting for high-accuracy multi-channel single-molecule localization[J]. Nature Communications, 2022, 13(1): 3133. doi: 10.1038/s41467-022-30719-4
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