Organic fluorescent probes for live-cell super-resolution imaging

Abstract

The development of super-resolution technology has made it possible to investigate the ultrastructure of intracellular organelles by fluorescence microscopy, which has greatly facilitated the development of life sciences and biomedicine. To realize super-resolution imaging of living cells, both advanced imaging systems and excellent fluorescent probes are required. Traditional fluorescent probes have good availability, but that is not the case for probes for live-cell super-resolution imaging. In this review, we first introduce the principles of various super-resolution technologies and their probe requirements, then summarize the existing designs and delivery strategies of super-resolution probes for live-cell imaging, and finally provide a brief conclusion and overview of the future.

Graphical abstract

Keywords

Super-resolution imaging / Organic fluorescent dyes / Live-cell imaging / Cell-impermeable organic probes

References

[1] Shen,K., Pender, C.L., Bar-Ziv,R., Zhang,H., Wickham, K., Willey,E., Durieux,J., Ahmad,Q., Dillin,A.: Mitochondria as cellular and organismal signaling hubs. Annu. Rev. Cell Dev. Biol. 6(1), 179–218 (2022)

[2] Wu,H., Carvalho, P., Voeltz,G.K.: Here, there, and everywhere: the importance of ER membrane contact sites. Science 361(6401), eaan5835 (2018)

[3] Abrisch,R.G., Gumbin, S.C., Wisniewski,B.T., Lackner,L.L., Voeltz, G.K.: Fission and fusion machineries converge at ER contact sites to regulate mitochondrial morphology. J. Cell Biol. 219, e201911122 (2020)

[4] Chang,X., Li,Y., Cai,C., Wu, F., He,J., Zhang,Y., Zhong,J., Tan,Y., Liu, R., Zhu,H., Zhou,H.: Mitochondrial quality control mechanisms as molecular targets in diabetic heart. Metabolism 137, 155313 (2022)

[5] Wong,Y.C., Ysselstein, D., Krainc,D.: Mitochondria-lysosome contacts regulate mitochondrial fission via RAB7 GTP hydrolysis. Nature 554(7692), 382–386 (2018)

[6] Murphy,M.P., Hartley, R.C.: Mitochondria as a therapeutic target for common pathologies. Nat. Rev. Drug Discov. 17(12), 865–886 (2018)

[7] Prokop,A.: Cytoskeletal organization of axons in vertebrates and invertebrates. J. Cell Biol. 219(7), e201912081 (2020)

[8] Sleigh,J.N., Rossor, A.M., Fellows,A.D., Tosolini,A.P., Schiavo, G.: Axonal transport and neurological disease. Nat. Rev. Neurol. 15(12), 691–703 (2019)

[9] Shanmughapriya,S., Langford, D., Natarajaseenivasan,K.: Inter and intracellular mitochondrial trafficking in health and disease. Ageing Res. Rev. 62, 101128 (2020)

[10] Sahl,S.J., Hell,S.W., Jakobs,S.: Fluorescence nanoscopy in cell biology. Nat. Rev. Mol. Cell Biol. 18(11), 685–701 (2017)

[11] Uluç,K., Kujoth, G.C., Başkaya,M.K.: Operating microscopes: past, present, and future. Neurosurg. Focus 27(3), E4 (2009)

[12] Sigal,Y.M., Zhou,R., Zhuang,X.: Visualizing and discovering cellular structures with super-resolution microscopy. Science 361(6405), 880–887 (2018)

[13] Choquet,D., Sainlos, M., Sibarita,J.B.: Advanced imaging and labelling methods to decipher brain cell organization and function. Nat. Rev. Neurosci. 22(4), 237–255 (2021)

[14] Abbe,E.: Beiträge zur Theorie des Mikroskops und der mikroskopischen Wahrnehmung. Arch. Mikrosk. Anat. 9, 413 (1873)

[15] Fernández-Suárez,M., Ting,A.Y.: Fluorescent probes for superresolution imaging in living cells. Nat. Rev. Mol. Cell Biol. 9(12), 929–943 (2008)

[16] Xu,C.S., Pang,S., Shtengel,G., Müller, A., Ritter,A.T., Hoffman,H.K., Takemura, S.Y., Lu,Z., Pasolli,H.A., Iyer,N., Chung,J., Bennett, D., Weigel,A.V., Freeman,M., van Engelenburg, S.B., Walther,T.C., Farese,R.V. Jr., Lippincott-Schwartz, J., Mellman,I., Solimena,M., Hess,H.F.: An open-access volume electron microscopy atlas of whole cells and tissues. Nature 599(7883), 147–151 (2021)

[17] Li,W., Lu,J., Xiao,K., Zhou, M., Li,Y., Zhang,X., Li,Z., Gu,L., Xu, X., Guo,Q., Xu,T., Ji,W.: Integrated multimodality microscope for accurate and efficient target-guided cryolamellae preparation. Nat. Methods 20(2), 268–275 (2023)

[18] Hell,S.W., Wichmann, J.: Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt. Lett. 19(11), 780 (1994)

[19] Klar,T.A., Jakobs, S., Dyba,M., Egner,A., Hell,S.W.: Fluo-rescence microscopy with diffraction resolution barrier broken by stimulated emission. Proc. Natl. Acad. Sci. U.S.A. 97(15), 8206–8210 (2000)

[20] Gustafsson,M.G.: Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J. Microsc. 198(2), 82–87 (2000)

[21] Gustafsson,M.G.: Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. Proc. Natl. Acad. Sci. U.S.A. 102(37), 13081–13086 (2005)

[22] Rust,M.J., Bates,M., Zhuang,X.: Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods 3(10), 793–796 (2006)

[23] Betzig,E., Patterson, G.H., Sougrat,R., Lindwasser,O.W., Olenych, S., Bonifacino,J.S., Davidson,M.W., Lippincott-Schwartz, J., Hess,H.F.: Imaging intracellular fluorescent proteins at nanometer resolution. Science 313(5793), 1642–1645 (2006)

[24] Dean,K.M., Palmer, A.E.: Advances in fluorescence labeling strategies for dynamic cellular imaging. Nat. Chem. Biol. 10(7), 512–523 (2014)

[25] Specht,E.A., Braselmann, E., Palmer,A.E.: A critical and comparative review of fluorescent tools for live-cell imaging. Annu. Rev. Physiol. 79(1), 93–117 (2017)

[26] Chen,F., Liu,W., Li,H., Deng, T., Xing,B., Liu,F.: Rhodamine fluorophores for STED super-resolution biological imaging. Analysis & Sensing 2(3), e202100066 (2022)

[27] Grimm,J.B., Lavis,L.D.: Caveat fluorophore: an insiders’ guide to small-molecule fluorescent labels. Nat. Methods 19(2), 149–158 (2022)

[28] Kikuchi,K., Adair,L.D., Lin,J., New, E.J., Kaur,A.: Photochemical mechanisms of fluorophores employed in single-molecule localization microscopy. Angew. Chem. Int. Ed. 62(1), e202204745 (2023)

[29] van de Linde,S., Aufmkolk, S., Franke,C., Holm,T., Klein,T., Löschberger,A., Proppert,S., Wolter, S., Sauer,M.: Investigating cellular structures at the nanoscale with organic fluorophores. Chem. Biol. 20(1), 8–18 (2013)

[30] Heilemann,M.: Fluorescence microscopy beyond the diffraction limit. J. Biotechnol. 149(4), 243–251 (2010)

[31] Heintzmann,R., Huser,T.: Super-resolution structured illumination microscopy. Chem. Rev. 117(23), 13890–13908 (2017)

[32] Li,D., Shao,L., Chen,B.C., Zhang, X., Zhang,M., Moses,B., Milkie, D.E., Beach,J.R., Hammer,J.A. III., Pasham, M., Kirchhausen,T., Baird,M.A., Davidson, M.W., Xu,P., Betzig,E.: Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics. Science 349(6251), aab3500 (2015)

[33] Zhao,W., Zhao,S., Li,L., Huang, X., Xing,S., Zhang,Y., Qiu,G., Han,Z., Shang, Y., Sun,D.E., Shan,C., Wu,R., Gu,L., Zhang, S., Chen,R., Xiao,J., Mo,Y., Wang,J., Ji, W., Chen,X., Ding,B., Liu,Y., Mao,H., Song, B.L., Tan,J., Liu,J., Li,H., Chen,L.: Sparse deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy. Nat. Biotechnol. 40(4), 606–617 (2022)

[34] Lukinavičius,G., Reymond, L., D’Este,E., Masharina,A., Göttfert, F., Ta,H., Güther,A., Fournier, M., Rizzo,S., Waldmann,H., Blaukopf, C., Sommer,C., Gerlich,D.W., Arndt,H.D., Hell,S.W., Johnsson, K.: Fluorogenic probes for live-cell imaging of the cytoskeleton. Nat. Methods 11(7), 731–733 (2014)

[35] Lukinavičius,G., Blaukopf, C., Pershagen,E., Schena,A., Reymond, L., Derivery,E., Gonzalez-Gaitan,M., D’Este, E., Hell,S.W., Gerlich,D.W., Johnsson, K.: SiR–Hoechst is a far-red DNA stain for live-cell nanoscopy. Nat. Commun. 6(1), 8497 (2015)

[36] Fan,F., Nie,S., Yang,D., Luo, M., Shi,H., Zhang,Y.H.: Labeling lysosomes and tracking lysosome-dependent apoptosis with a cell-permeable activity-based probe. Bioconjug. Chem. 23(6), 1309–1317 (2012)

[37] Zielonka,J., Joseph, J., Sikora,A., Hardy,M., Ouari,O., Vasquez-Vivar,J., Cheng,G., Lopez,M., Kalyanaraman,B.: Mitochondria-targeted triphenylphosphonium-based compounds: syntheses, mechanisms of action, and therapeutic and diagnostic applications. Chem. Rev. 117(15), 10043–10120 (2017)

[38] Aryal,S.P., Xia,M., Adindu,E., Davis, C., Ortinski,P.I., Richards,C.I.: ER-GCaMP6f: an endoplasmic reticulum-targeted genetic probe to measure calcium activity in astrocytic processes. Anal. Chem. 94(4), 2099–2108 (2022)

[39] Lukinavičius,G., Mitronova, G.Y., Schnorrenberg,S., Butkevich,A.N., Barthel, H., Belov,V.N., Hell,S.W.: Fluorescent dyes and probes for super-resolution microscopy of microtubules and tracheoles in living cells and tissues. Chem. Sci. (Camb.) 9(13), 3324–3334 (2018)

[40] Gerasimaitė,R., Seikowski, J., Schimpfhauser,J., Kostiuk,G., Gilat,T., D’Este,E., Schnorrenberg,S., Lukinavičius, G.: Efflux pump insensitive rhodamine-jasplakinolide conjugates for G-and F-actin imaging in living cells. Org. Biomol. Chem. 18(15), 2929–2937 (2020)

[41] Takagi,T., Ueno,T., Ikawa,K., Asanuma, D., Nomura,Y., Uno,S.N., Komatsu, T., Kamiya,M., Hanaoka,K., Okimura, C., Iwadate,Y., Hirose,K., Nagano, T., Sugimura,K., Urano,Y.: Discovery of an F-actin-binding small molecule serving as a fluorescent probe and a scaffold for functional probes. Sci. Adv. 19(47), eabg8585 (2021)

[42] Keppler,A., Gendreizig, S., Gronemeyer,T., Pick,H., Vogel,H., Johnsson,K.: A general method for the covalent labeling of fusion proteins with small molecules in vivo. Nat. Biotechnol. 21(1), 86–89 (2003)

[43] Gautier,A., Juillerat, A., Heinis,C., Corrêa,I.R. Jr., Kindermann, M., Beaufils,F., Johnsson,K.: An engineered protein tag for multiprotein labeling in living cells. Chem. Biol. 15(2), 128–136 (2008)

[44] Holtmannspötter,M., Wienbeuker,E., Dellmann, T., Watrinet,I., Garcia-Sáez,A.J., Johnsson,K., Kurre,R., Piehler,J.: Reversible live-cell labeling with retro-engineered HaloTags enables long-term high- and super-resolution imaging. Angew. Chem. Int. Ed. 62(18), e202219050 (2023)

[45] Wilhelm,J., Kühn, S., Tarnawski,M., Gotthard,G., Tünnermann, J., Tänzer,T., Karpenko,J., Mertes, N., Xue,L., Uhrig,U., Reinstein, J., Hiblot,J., Johnsson,K.: Kinetic and structural characterization of the self-labeling protein tags HaloTag7, SNAP-tag, and CLIP-tag. Biochemistry 60(33), 2560–2575 (2021)

[46] Mo,J., Chen,J., Shi,Y., Sun, J., Wu,Y., Liu,T., Zhang,J., Zheng,Y., Li, Y., Chen,Z.: Third-generation covalent TMP-Tag for fast labeling and multiplexed imaging of cellular proteins. Angew. Chem. Int. Ed. 61(36), e202207905 (2022)

[47] Uno,S.N., Kamiya, M., Yoshihara,T., Sugawara,K., Okabe,K., Tarhan,M.C., Fujita, H., Funatsu,T., Okada,Y., Tobita, S., Urano,Y.: A spontaneously blinking fluorophore based on intra-molecular spirocyclization for live-cell super-resolution imaging. Nat. Chem. 6(8), 681–689 (2014)

[48] Macdonald,P.J., Gayda,S., Haack,R.A., Ruan, Q., Himmelsbach,R.J., Tetin,S.Y.: Rhodamine-derived fluorescent dye with inherent blinking behavior for super-resolution imaging. Anal. Chem. 90(15), 9165–9173 (2018)

[49] Tang,J., Robichaux, M.A., Wu,K.L., Pei,J., Nguyen, N.T., Zhou,Y., Wensel,T.G., Xiao,H.: Single-atom fluorescence switch: a general approach toward visible-light-activated dyes for biological imaging. J. Am. Chem. Soc. 141(37), 14699–14706 (2019)

[50] Grimm,J.B., English, B.P., Chen,J., Slaughter,J.P., Zhang,Z., Revyakin,A., Patel, R., Macklin,J.J., Normanno,D., Singer, R.H., Lionnet,T., Lavis,L.D.: A general method to improve fluorophores for live-cell and single-molecule microscopy. Nat. Methods 12(3), 244–250 (2015)

[51] Grimm,J.B., Muthusamy, A.K., Liang,Y., Brown,T.A., Lemon,W.C., Patel,R., Lu, R., Macklin,J.J., Keller,P.J., Ji,N., Lavis,L.D.: A general method to fine-tune fluorophores for live-cell and in vivo imaging. Nat. Methods 14(10), 987–994 (2017)

[52] Grimm,J.B., Tkachuk, A.N., Xie,L., Choi,H., Mohar,B., Falco,N., Schaefer, K., Patel,R., Zheng,Q., Liu,Z., Lippincott-Schwartz,J., Brown,T.A., Lavis,L.D.: A general method to optimize and functionalize red-shifted rhodamine dyes. Nat. Methods 17(8), 815–821 (2020)

[53] Zheng,Q., Ayala,A.X., Chung,I., Weigel, A.V., Ranjan,A., Falco,N., Grimm,J.B., Tkachuk,A.N., Wu,C., Lippincott-Schwartz, J., Singer,R.H., Lavis,L.D.: Rational design of fluorogenic and spontaneously blinking labels for super-resolution imaging. ACS Cent. Sci. 5(9), 1602–1613 (2019)

[54] Chi,W., Qi,Q., Lee,R., Xu, Z., Liu,X.: A unified push–pull model for understanding the ring-opening mechanism of rhodamine dyes. J. Phys. Chem. C 124(6), 3793–3801 (2020)

[55] Chi,Q., Qiao,Q., Wang,C., Zheng, J., Zhou,W., Xu,N., Wu,X., Jiang,X., Tan, D., Xu,Z., Liu,X.: Descriptor ΔGC-O enables the quantitative design of spontaneously blinking rhodamines for live-cell super-resolution imaging. Angew. Chem. 132(45), 20390–20398 (2020)

[56] Tyson,K., Hu,K., Zheng,S., Kidd, P., Dadina,N., Chu,L., Toomre, D., Bewersdorf,J., Schepartz,A.: Extremely bright, near-IR emitting spontaneously blinking fluorophores enable ratiometric multicolor nanoscopy in live cells. ACS Cent. Sci. 7(8), 1419–1426 (2021)

[57] Wang,L., Wang,S., Tang,J., Espinoza, V.B., Loredo,A., Tian,Z., Weisman, R.B., Xiao,H.: Oxime as a general photocage for the design of visible light photo-activatable fluorophores. Chem. Sci. (Camb.) 12(47), 15572–15580 (2021)

[58] Zheng,Y., Ye,Z., Zhang,X., Xiao, Y.: Recruiting rate determines the blinking propensity of rhodamine fluorophores for super-resolution imaging. J. Am. Chem. Soc. 145(9), 5125–5133 (2023)

[59] Zheng,Y., Ye,Z., Xiao,Y.: Subtle structural translation magically modulates the super-resolution imaging of self-blinking rhodamines. Anal. Chem. 95(8), 4172–4179 (2023)

[60] Bond,C., Santiago-Ruiz, A.N., Tang,Q., Lakadamyali,M.: Technological advances in super-resolution microscopy to study cellular processes. Mol. Cell 82(2), 315–332 (2022)

[61] Vicidomini,G., Moneron, G., Han,K.Y., Westphal,V., Ta,H., Reuss,M., Engelhardt, J., Eggeling,C., Hell,S.W.: Sharper low-power STED nanoscopy by time gating. Nat. Methods 8(7), 571–573 (2011)

[62] Willig,K.I., Harke,B., Medda,R., Hell, S.W.: STED microscopy with continuous wave beams. Nat. Methods 4(11), 915–918 (2007)

[63] Wurm,C.A., Kolmakov, K., Göttfert,F., Ta,H., Bossi,M., Schill,H., Schill, H., Berning,S., Jakobs,S., Donnert, G., Belov,V.N., Hell,S.W.: Novel red fluorophores with superior performance in STED microscopy. Opt. Nanoscopy 1(1), 1 (2012)

[64] Bückers,J., Wildanger, D., Vicidomini,G., Kastrup,L., Hell,S.W.: Simultaneous multi-lifetime multi-color STED imaging for colocalization analyses. Opt. Express 19(4), 3130 (2011)

[65] Hua,Y., Sinha,R., Thiel,C.S., Schmidt, R., Hüve,J., Martens,H., Hell,S.W., Egner,A., Klingauf, J.: A readily retrievable pool of synaptic vesicles. Nat. Neurosci. 14(7), 833–839 (2011)

[66] Lukinavičius,G., Umezawa, K., Olivier,N., Honigmann,A., Yang,G., Plass,T., Mueller, V., Reymond,L., Corrêa,I.R. Jr., Luo, Z.G., Schultz,C., Lemke,E.A., Heppenstall, P., Eggeling,C., Manley,S., Johnsson, K.: A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins. Nat. Chem. 5(2), 132–139 (2013)

[67] Bottanelli,F., Kromann, E.B., Allgeyer,E.S., Erdmann,R.S., Wood Baguley, S., Sirinakis,G., Schepartz,A., Baddeley, D., Toomre,D.K., Rothman,J.E., Bewersdorf, J.: Two-colour live-cell nanoscale imaging of intracellular targets. Nat. Commun. 7(1), 10778 (2016)

[68] Butkevich,A.N., Mitronova, G.Y., Sidenstein,S.C., Klocke,J.L., Kamin,D., Meineke,D.N., D’Este,E., Kraemer, P.T., Danzl,J.G., Belov,V.N., Hell,S.W.: Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells. Angew. Chem. Int. Ed. 55(10), 3290–3294 (2016)

[69] Lukinavičius,G., Reymond, L., Umezawa,K., Sallin,O., D’Este, E., Göttfert,F., Ta,H., Hell,S.W., Urano,Y., Johnsson, K.: Fluorogenic probes for multicolor imaging in living cells. J. Am. Chem. Soc. 138(30), 9365–9368 (2016)

[70] Wang,L., Tran,M., D’Este,E., Roberti,J., Koch,B., Xue,L., Johnsson, K.: A general strategy to develop cell permeable and fluorogenic probes for multicolour nanoscopy. Nat. Chem. 12(2), 165–172 (2020)

[71] Kompa,J., Bruins, J., Glogger,M., Wilhelm,J., Frei,M.S., Tarnawski,M., D’Este,E., Heilemann, M., Hiblot,J., Johnsson,K.: Exchangeable HaloTag ligands for super-resolution fluorescence microscopy. J. Am. Chem. Soc. 145(5), 3075–3083 (2023)

[72] Bucevičius,J., Kostiuk, G., Gerasimaitė,R., Gilat,T., Lukinavičius, G.: Enhancing the biocompatibility of rhodamine fluorescent probes by a neighbouring group effect. Chem. Sci. (Camb.) 11(28), 7313–7323 (2020)

[73] Lincoln,R., Bossi,M.L., Remmel,M., D’Este, E., Butkevich,A.N., Hell,S.W.: A general design of caging-group-free photoactivatable fluorophores for live-cell nanoscopy. Nat. Chem. 14(9), 1013–1020 (2022)

[74] Yang,Z., Kang,D.H., Lee,H., Shin, J., Yan,W., Rathore,B., Kim,H.R., Kim,S.J., Singh, H., Liu,L., Qu,J., Kang,C., Kim,J.S.: A fluorescent probe for stimulated emission depletion super-resolution imaging of vicinal-dithiol-proteins on mitochondrial membrane. Bioconjug, Chem. 29(4), 1446–1453 (2018)

[75] Wang,C., Taki,M., Sato,Y., Tamura, Y., Yaginuma,H., Okada,Y., Yamaguchi, S.: A photostable fluorescent marker for the super-resolution live imaging of the dynamic structure of the mitochondrial cristae. Proc. Natl. Acad. Sci. U.S.A. 116(32), 15817–15822 (2019)

[76] Zhu,F., Yang,Z., Wang,F., Li, D., Cao,H., Tian,Y., Tian,X.: 4-Dimensional observation ER-mitochondria interaction in living cells under nanoscopy by a stable pyridium salt as biosensor. Sens. Actuators B Chem. 305, 127492 (2020)

[77] Yang,X., Yang,Z., Wu,Z., He, Y., Shan,C., Chai,P., Ma,C., Tian,M., Teng, J., Jin,D., Yan,W., Das,P., Qu,J., Xi, P.: Mitochondrial dynamics quantitatively revealed by STED nanoscopy with an enhanced squaraine variant probe. Nat. Commun. 11(1), 3699 (2020)

[78] Wen,S., Li,S., Wang,L., Chen, X., Sun,Z., Liang,Y., Jin,X., Xing,Y., Jiu, Y., Tang,Y., Li,H.: High-fidelity structured illumination microscopy by point-spread-function engineering. Light Sci. Appl. 10(1), 70 (2021)

[79] Wen,G., Li,S., Liang,Y., Wang, L., Zhang,J., Chen,X., Jin,X., Chen,C., Tang, Y., Li,H.: Spectrum-optimized direct image reconstruction of super-resolution structured illumination microscopy. PhotoniX 4(1), 19 (2023)

[80] Huang,X., Fan,J., Li,L., Liu, H., Wu,R., Wu,Y., Wei,L., Mao,H., Lal, A., Xi,P., Tang,L., Zhang,Y., Liu,Y., Tan, S., Chen,L.: Fast, long-term, super-resolution imaging with Hessian structured illumination microscopy. Nat. Biotechnol. 36(5), 451–459 (2018)

[81] Guo,Y., Li,D., Zhang,S., Yang, Y., Liu,J., Wang,X., Liu,C., Milkie,D.E., Moore, R.P., Tulu,U.S., Kiehart,D.P., Hu,J., Lippincott-Schwartz,J., Betzig,E., Li,D.: Visualizing intracellular organelle and cytoskeletal interactions at nanoscale resolution on millisecond timescales. Cell 175(5), 1430-1442.e17 (2018)

[82] Panchuk-Voloshina,N., Haugland, R.P., Bishop-Stewart,J., Bhalgat,M.K., Millard, P.J., Mao,F., Leung,W.Y., Haugland, R.P.: Alexa dyes, a series of new fluorescent dyes that yield exceptionally bright, photostable conjugates. J. Histochem. Cytochem. 47(9), 1179–1188 (1999)

[83] Jimenez,A., Friedl, K., Leterrier,C.: About samples, giving examples: optimized single molecule localization microscopy. Methods 174, 100–114 (2020)

[84] Oleksiievets,N., Mathew, C., Thiele,J.C., Gallea,J.I., Nevskyi, O., Gregor,I., Weber,A., Tsukanov, R., Enderlein,J.: Single-molecule fluorescence lifetime imaging using wide-field and confocallaser scanning microscopy: a comparative analysis. Nano Lett. 22(15), 6454–6461 (2022)

[85] Wegel,E., Göhler, A., Lagerholm,B.C., Wainman,A., Uphoff, S., Kaufmann,R., Dobbie,I.M.: Imaging cellular structures in super-resolution with SIM, STED and localisation microscopy: a practical comparison. Sci. Rep. 6(1), 27290 (2016)

[86] Wäldchen,F., Schlegel, J., Götz,R., Luciano,M., Schnermann, M., Doose,S., Sauer,M.: Whole-cell imaging of plasma membrane receptors by 3D lattice light-sheet dSTORM. Nat. Commun. 11(1), 887 (2020)

[87] Zelger,P., Bodner, L., Offterdinger,M., Velas,L., Schütz, G.J., Jesacher,A.: Three-dimensional single molecule localization close to the coverslip: a comparison of methods exploiting super-critical angle fluorescence. Biomed. Opt. Express 12(2), 802 (2021)

[88] Jones,A., Shim,S.H., He,J., Zhuang, X.: Fast, three-dimensional super-resolution imaging of live cells. Nat. Methods 8(6), 499–505 (2011)

[89] Ma,Y., Gong,C., Ma,Y., Fan, F., Luo,M., Yang,F., Zhang,Y.H.: Direct cytosolic delivery of cargoes in vivo by a chimera consisting of D- and L-arginine residues. J. Control. Release 162(2), 286–294 (2012)

[90] Pan,D., Hu,Z., Qiu,F., Huang, Z.L., Ma,Y., Wang,Y., Qin,L., Zhang,Z., Zeng, S., Zhang,Y.H.: A general strategy for developing cell-permeable photo-modulatable organic fluorescent probes for live-cell super-resolution imaging. Nat. Commun. 5(1), 55573 (2014)

[91] Hennig,S., van de Linde, S., Lummer,M., Simonis,M., Huser,T., Sauer,M.: Instant live-cell super-resolution imaging of cellular structures by nanoinjection of fluorescent probes. Nano Lett. 15(2), 1374–1381 (2015)

[92] Liu,J., Fraire, J.C., De Smedt,S.C., Xiong,R., Braeckmans, K.: Intracellular labeling with extrinsic probes: delivery strategies and applications. Small 16(22), e2000146 (2020)

[93] Han,Y., Li,M., Qiu,F., Zhang, M., Zhang,Y.H.: Cell-permeable organic fluorescent probes for live-cell long-term super-resolution imaging reveal lysosome-mitochondrion interactions. Nat. Commun. 8(1), 1307 (2017)

[94] Zhang,M., Li,M., Zhang,W., Han, Y., Zhang,Y.H.: Simple and efficient delivery of cell-impermeable organic fluorescent probes into live cells for live-cell superresolution imaging. Light Sci. Appl 8(1), 73 (2019)

[95] Zhao,Y., Zhang,M., Zhang,W., Zhou, Y., Chen,L., Liu,Q., Wang,P., Chen,R., Duan, X., Chen,F., Deng,H., Wei,Y., Fei,P., Zhang, Y.H.: Isotropic super-resolution light-sheet microscopy of dynamic intracellular structures at subsecond timescales. Nat. Methods 19(3), 359–369 (2022)

[96] Kim,D., Stoldt, S., Weber,M., Jakobs,S., Belov,V.N., Hell,S.W.: A bright surprise: live-cell labeling with negatively charged fluorescent probes based on disulfonated rhodamines and HaloTag. Chem. Methods 3(9), 202200076 (2023)

[97] Qiao,D., Li,D., Liu,Y., Zhang, S., Liu,K., Liu,C., Guo,Y., Jiang,T., Fang, C., Li,N., Zeng,Y., He,K., Zhu,X., Lippincott-Schwartz, J., Dai,Q., Li,D.: Rationalized deep learning super-resolution microscopy for sustained live imaging of rapid subcellular processes. Nat. Biotechnol. 41(3), 367–377 (2023)

[98] Hao,X., Allgeyer, E.S., Lee,D.R., Antonello,J., Watters, K., Gerdes,J.A., Schroeder,L.K., Bottanelli, F., Zhao,J., Kidd,P., Lessard, M.D., Rothman,J.E., Cooley,L., Biederer, T., Booth,M.J., Bewersdorf,J.: Three-dimensional adaptive optical nanoscopy for thick specimen imaging at sub-50-nm resolution. Nat. Methods 18(6), 688–693 (2021)

[99] Bodén,F., Pennacchietti, F., Coceano,G., Damenti,M., Ratz,M., Testa,I.: Volumetric live cell imaging with three-dimensional parallelized RESOLFT microscopy. Nat. Biotechnol. 39(5), 609–618 (2021)

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