Advances in Multicolor Single-molecule Localization Microscopy（Invited）

Yuehan ZHAO; Xiang HAO

doi:10.3788/gzxb20225108.0851517

[1] S W HELL, J WICHMANN. Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Optics Letters, 19, 780(1994).

[2] T A KLAR, S JAKOBS, M DYBA et al. Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission. Proceedings of the National Academy of Sciences, 97, 8206-8210(2000).

[3] M G L GUSTAFSSON. Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. Journal of Microscopy, 198, 82-87(2000).

[4] M G L GUSTAFSSON. Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. Proceedings of the National Academy of Sciences of the United States of America, 102, 13081-13086(2005).

[5] E BETZIG, G H PATTERSON, R SOUGRAT et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science, 313, 1642-1645(2006).

[6] M J RUST, M BATES, Xiaowei ZHUANG. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nature Methods, 3, 793-796(2006).

[7] A SHARONOV, R M HOCHSTRASSER. Wide-field subdiffraction imaging by accumulated binding of diffusing probes. Proceedings of the National Academy of Sciences, 103, 18911-18916(2006).

[8] Lusheng GU, Yuanyuan LI, Shuwen ZHANG et al. Molecular resolution imaging by repetitive optical selective exposure. Nature Methods, 16, 1114-1118(2019).

[9] F BALZAROTTI, Y EILERS, K C GWOSCH et al. Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes. Science, 355, 606-612(2017).

[10] E BETZIG. Proposed method for molecular optical imaging. Optics Letters, 20, 237(1995).

[11] F BALZAROTTI, Y EILERS, K C GWOSCH et al. Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes. Science, 355, 606-612(2017).

[12] Ke XU, Guisheng ZHONG, Xiaowei ZHUANG. Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons. Science, 339, 452-456(2013).

[13] B FLOTTMANN, M GUNKEl, T LISAUSKAS et al. Correlative light microscopy for high-content screening. BioTechniques, Future Science, 55, 243-252(2013).

[14] J HANNE, V ZILA, M HEILEMANN et al. Super-resolved insights into human immunodeficiency virus biology. FEBS Letters, 590, 1858-1876(2016).

[15] W MURANYI, S MALKUSCH, B MÜLLER et al. Super-resolution microscopy reveals specific recruitment of HIV-1 envelope proteins to viral assembly sites dependent on the envelope C-terminal tail. PLoS Pathogens, 9, e1003198(2013).

[16] Leiting PAN, Fen HU, Xinzheng ZHANG等. Multicolor single-molecule localization super-resolution microscopy. Acta Optica Sinica, 37, 0318010(2017).

[17] R E THOMPSON, D R LARSON, W W WEBB. Precise nanometer localization analysis for individual fluorescent probes. Biophysical Journal, 82, 2775-2783(2002).

[18] M LELEK, M T GYPARAKI, G BELIU et al. Single-molecule localization microscopy. Nature Reviews Methods Primers, 1, 39(2021).

[19] R P J NIEUWENHUIZEN, K A LIDKE, M BATES et al. Measuring image resolution in optical nanoscopy. Nature Methods, 10, 557-562(2013).

[20] A LÖSCHBERGER, S VAN DE LINDE, M C DABAUVALLE et al. Super-resolution imaging visualizes the eightfold symmetry of gp210 proteins around the nuclear pore complex and resolves the central channel with nanometer resolution. Journal of Cell Science, 125, 570-575(2012).

[21] U ENDESFELDER, S MALKUSCH, B FLOTTMANN et al. Chemically induced photoswitching of fluorescent probes—a general concept for super-resolution microscopy. Molecules, 16, 3106-3118(2011).

[22] M LEHMANN, S ROCHA, B MANGEAT et al. Quantitative multicolor super-resolution microscopy reveals tetherin HIV-1 interaction. PLoS Pathogens, 7, e1002456(2011).

[23] C SPAHN, F CELLA-ZANNACCHI, U ENDESFELDER et al. Correlative super-resolution imaging of RNA polymerase distribution and dynamics, bacterial membrane and chromosomal structure in Escherichia coli. Methods and Applications in Fluorescence, 3, 014005(2015).

[24] S A JONES, S H SHIM, Jiang He et al. Fast, three-dimensional super-resolution imaging of live cells. Nature Methods, 8, 499-508(2011).

[25] M BATES, Bo HUANG, G T DEMPSEY et al. Multicolor super-resolution imaging with photo-switchable fluorescent probes. Science, 317, 1749-1753(2007).

[26] A DANI, Bo HUANG, J BERGAN et al. Superresolution imaging of chemical synapses in the brain. Neuron, 68, 843-856(2010).

[27] E LUBECK, Long CAI. Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nature Methods, 9, 743-748(2012).

[28] J TAM, G A CORDIER, J S BORBELY et al. Cross-talk-free multi-color STORM imaging using a single fluorophore. PLOS ONE, 9, e101772(2014).

[29] R JUNGMANN, M S AVENDAÑO, J B WOEHRSTEIN et al. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and exchange-PAINT. Nature Methods, 11, 313-318(2014).

[30] O K WADE, J B WOEHRSTEIN, P C NICKELS et al. 124-color super-resolution imaging by engineering DNA-PAINT blinking kinetics. Nano Letters, 19, 2641-2646(2019).

[31] H DESCHOUT, F C ZANACCHI, M MLODZIANOSKI et al. Precisely and accurately localizing single emitters in fluorescence microscopy. Nature Methods, 11, 253-266(2014).

[32] M BOSSI, J FÖLLING, V N BELOV et al. Multicolor far-field fluorescence nanoscopy through isolated detection of distinct molecular species. Nano Letters, 8, 2463-2468(2008).

[33] I TESTA, C A WURM, R MEDDA et al. Multicolor fluorescence nanoscopy in fixed and living cells by exciting conventional fluorophores with a single wavelength. Biophysical Journal, 99, 2686-2694(2010).

[34] A LAMPE, V HAUCKE, S J SIGRIST et al. Multi-colour direct STORM with red emitting carbocyanines. Biology of the Cell, 104, 229-237(2012).

[35] C M WINTERFLOOD, E PLATONOVA, D ALBRECHT et al. Dual-color 3D superresolution microscopy by combined spectral-demixing and biplane imaging. Biophysical journal, 109, 3-6(2015).

[36] Yongdeng ZHANG, L K SCHROEDER, M D LESSARD et al. Nanoscale subcellular architecture revealed by multicolor three-dimensional salvaged fluorescence imaging. Nature Methods, 17, 225-231(2020).

[37] A VISSA, M GIULIANI, P K KIM et al. Hyperspectral super-resolution imaging with far-red emitting fluorophores using a thin-film tunable filter. Review of Scientific Instruments, 91, 123703(2020).

[38] Yujie WANG, Weibing KUANG, Mingtao SHANG et al. Two-color super-resolution localization microscopy via joint encoding of emitter location and color. Optics Express, 29, 34797(2021).

[39] Jianwei CHEN, Benxi YAO, Zhichao YANG et al. Ratiometric 4Pi single-molecule localization with optimal resolution and color assignment. Optics Letters, 47, 325-328(2022).

[40] Yiming LI, Wei SHI, Sheng LIU et al. Global fitting for high-accuracy multi-channel single-molecule localization. Nature Communications, 13, 3133(2022).

[41] Zhengyang ZHANG, S J KENNY, M HAUSER et al. Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy. Nature Methods, 12, 935-938(2015).

[42] Biqin DONG, L ALMASSALHA, B E URBAN et al. Super-resolution spectroscopic microscopy via photon localization. Nature Communications, 7, 12290(2016).

[43] D JEONG, D KIM. Super-resolution fluorescence microscopy-based single-molecule spectroscopy. Bulletin of the Korean Chemical Society, 43, 316-327(2022).

[44] S MOON, Rui YAN, S J KENNY et al. Spectrally resolved, functional super-resolution microscopy reveals nanoscale compositional heterogeneity in live-cell membranes. Journal of the American Chemical Society, 139, 10944-10947(2017).

[45] M J MLODZIANOSKI, N M CURTHOYS, M S GUNEWARDENE et al. Super-resolution imaging of molecular emission spectra and single molecule spectral fluctuations. PLOS ONE, 11, e0147506(2016).

[46] Tao HUANG, C PHELPS, Jing WANG et al. Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging. Biophysical Journal, 114, 301-310(2018).

[47] Yang ZHANG, K H SONG, Biqin DONG et al. Multicolor super-resolution imaging using spectroscopic single-molecule localization microscopy with optimal spectral dispersion. Applied Optics, 58, 2248-2255(2019).

[48] Zhen CAI, Yang ZHANG, Zheyuan ZHANG et al. Super-resolution imaging of flat-mounted whole mouse cornea. Experimental Eye Research, 205, 108499(2021).

[49] K H SONG, Yang ZHANG, Gaoxiang WANG et al. Three-dimensional biplane spectroscopic single-molecule localization microscopy. Optica, 6, 709(2019).

[50] G KIM, J CHUNG, H PARK et al. Single-molecule sensing by grating-based spectrally resolved super-resolution microscopy. Bulletin of the Korean Chemical Society, 42, 270-278(2021).

[51] K H SONG, B BRENNER, W H YEO et al. Monolithic dual-wedge prism-based spectroscopic single-molecule localization microscopy. Nanophotonics, 11, 1527-1535(2022).

[52] D I DANYLCHUK, S MOON, Ke XU et al. Switchable solvatochromic probes for live‐cell super‐resolution imaging of plasma membrane organization. Angewandte Chemie International Edition, 58, 14920-14924(2019).

[53] J CHUNG, U JEONG, D JEONG et al. Development of a new approach for low-laser-power super-resolution fluorescence imaging. Analytical Chemistry, American Chemical Society, 94, 618-627(2022).

[54] K H SONG, Yang ZHANG, B BRENNER et al. Symmetrically dispersed spectroscopic single-molecule localization microscopy. Light: Science & Applications, 9, 92(2020).

[55] C SMITH, M HUISMAN, M SIEMONS et al. Simultaneous measurement of emission color and 3D position of single molecules. Optics Express, 24, 4996-5013(2016).

[56] Y SHECHTMAN, L E WEISS, A S BACKER et al. Multicolour localization microscopy by point-spread-function engineering. Nature Photonics, 10, 590-594(2016).

[57] Y SHECHTMAN, A K GUSTAVSSON, P N PETROV et al. Observation of live chromatin dynamics in cells via 3D localization microscopy using Tetrapod point spread functions. Biomedical Optics Express, 8, 5735-5748(2017).

[58] M SIEMONS, C N HULLEMAN, R O THORSEN et al. High precision wavefront control in point spread function engineering for single emitter localization. Optics Express, 26, 8397-8416(2018).

[59] Xin LIU, Cuifang KUANG, Xu LIU等. Research progress of computational microsco pyima gingbased on point spread function engineer. Laser & Optoelectronics Progress, 58, 1811008(2021).

[60] T KIM, S MOON, Ke XU. Information-rich localization microscopy through machine learning. Nature Communications, 10, 1996(2019).

[61] E HERSHKO, L E WEISS, T MICHAELI et al. Multicolor localization microscopy and point-spread-function engineering by deep learning. Optics Express, 27, 6158-6183(2019).

[62] E NEHME, D FREEDMAN, R GORDON et al. DeepSTORM3D: dense 3D localization microscopy and PSF design by deep learning. Nature Methods, 17, 734-740(2020).

[63] E NEHME, B FERDMAN, L E WEISS et al. Learning optimal wavefront shaping for multi-channel imaging. IEEE Transactions on Pattern Analysis and Machine Intelligence, 43, 2179-2192(2021).

[64] N OPATOVSKI, Y SHALEV EZRA, L E WEISS et al. Multiplexed PSF engineering for three-dimensional multicolor particle tracking. Nano Letters, 21, 5888-5895(2021).

[65] A E S BARENTINE, Yu LIN, Miao LIU et al. 3D multicolor nanoscopy at 10,000 cells a day. bioRxiv, 606954(2019).

[66] D SAGE, T A PHAM, H BABCOCK et al. Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software. Nature Methods, 16, 387-395(2019).

[67] T DERTINGER, R COLYER, G IYER et al. Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI). Proceedings of the National Academy of Sciences, 106, 22287-22292(2009).