3D active stabilization for single-molecule imaging

Simao Coelho, Jongho Baek, James Walsh, J. Justin Gooding, Katharina Gaus

Published: 2020-12-01 DOI: 10.1038/s41596-020-00426-9

super-resolution

active stabilization

single-molecule imaging

drift correction

real-time focus locking

AI 解读

Supplementary information

Supplementary Information

Supplementary Figs. 1–3.

Reporting Summary

Generation of mouse–human chimeric embryos

Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting

Generation of CRISPR–Cas9-mediated genetic knockout human intestinal tissue–derived enteroid lines by lentivirus transduction and single-cell cloning

A puromycin-dependent activity-based sensing probe for histochemical staining of hydrogen peroxide in cells and animal tissues

Decoding personal biotic and abiotic airborne exposome

A clinically relevant model of focal embolic cerebral ischemia by thrombus and thrombolysis in rhesus monkeys

Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds

Biomimetic tail-to-head terpene cyclizations using the resorcin[4]arene capsule catalyst

Neuroscience robotics for controlled induction and real-time assessment of hallucinations

Scanorama: integrating large and diverse single-cell transcriptomic datasets

Single-cell RNA sequencing (scRNA-seq)（单细胞RNA测序）

Data integration（数据集成）

Heterogeneity（异质性）

查看全部

Sections

Figures

References

Supplementary information

Moerner, W. E. New directions in single-molecule imaging and analysis. Proc. Natl Acad. Sci. USA 104, 12596–12602 (2007).
Coelho, S. et al. Ultraprecise single-molecule localization microscopy enables in situ distance measurements in intact cells. Sci. Adv. 6, eaay8271 (2020).
Hell, S. W. et al. The 2015 super-resolution microscopy roadmap. J. Phys. D. Appl. Phys. 48, 443001 (2015).
Betzig, E. et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313, 1642–1645 (2006).
Hess, S. T., Girirajan, T. P. & Mason, M. D. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys. J. 91, 4258–4272 (2006).
Rust, M. J., Bates, M. & Zhuang, X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods 3, 793–796 (2006).
Jungmann, R. et al. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nat. Methods 11, 313–318 (2014).
Nicovich, P. R., Owen, D. M. & Gaus, K. Turning single-molecule localization microscopy into a quantitative bioanalytical tool. Nat. Protoc. 12, 453–460 (2017).
Hell, S. W. & Wichmann, J. Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt. Lett. 19, 780–782 (1994).
Balzarotti, F. et al. Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes. Science 355, 606–612 (2017).
Gustafsson, M. G. Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. Proc. Natl Acad. Sci. USA 102, 13081–13086 (2005).
Hell, S. W. Far-field optical nanoscopy. Science 316, 1153–1158 (2007).
Pawley, J. Handbook of Biological Confocal Microscopy Vol. 236 (Springer Science & Business Media, 2006).
Schnitzbauer, J., Strauss, M. T., Schlichthaerle, T., Schueder, F. & Jungmann, R. Super-resolution microscopy with DNA-PAINT. Nat. Protoc. 12, 1198 (2017).
Deschout, H. et al. Precisely and accurately localizing single emitters in fluorescence microscopy. Nat. Methods 11, 253 (2014).
Huhle, A. et al. Camera-based three-dimensional real-time particle tracking at kHz rates and Ångström accuracy. Nat. Commun. 6, 1–8 (2015).
Fish, K. N. Total internal reflection fluorescence (TIRF) microscopy. Curr. Protoc. Cytom. 50, 12.18. 11–12.18. 13 (2009).
Kim, J. et al. Unveiling the relationship between the perovskite precursor solution and the resulting device performance. J. Am. Chem. Soc. 142, 6251–6260 (2020).
Tokunaga, M., Imamoto, N. & Sakata-Sogawa, K. Highly inclined thin illumination enables clear single-molecule imaging in cells. Nat. Methods 5, 159–161 (2008).
Huang, B., Wang, W., Bates, M. & Zhuang, X. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319, 810–813 (2008).
Pavani, S. R. P. et al. Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function. Proc. Natl Acad. Sci. 106, 2995–2999 (2009).
Shechtman, Y., Sahl, S. J., Backer, A. S. & Moerner, W. Optimal point spread function design for 3D imaging. Phys. Rev. Lett. 113, 133902 (2014).
Shtengel, G. et al. Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure. Proc. Natl Acad. Sci. 106, 3125–3130 (2009).
Shroff, H., Galbraith, C. G., Galbraith, J. A. & Betzig, E. Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics. Nat. Methods 5, 417 (2008).
Diekmann, R. et al. Chip-based wide field-of-view nanoscopy. Nat. Photonics 11, 322–328 (2017).
Huang, F. et al. Ultra-high resolution 3D imaging of whole cells. Cell 166, 1028–1040 (2016).
Gao, L., Shao, L., Chen, B.-C. & Betzig, E. 3D live fluorescence imaging of cellular dynamics using Bessel beam plane illumination microscopy. Nat. Protoc. 9, 1083–1101 (2014).
Baek, J. et al. Imaging galectin-3 dependent endocytosis with lattice light-sheet microscopy. SPIE Proceedings Vol. 10340 (eds. Sampson, D. D. et al.) (SPIE, 2017).
Aoki, K. & Matsuda, M. Visualization of small GTPase activity with fluorescence resonance energy transfer-based biosensors. Nat. Protoc. 4, 1623 (2009).
Poland, S. P. et al. A high speed multifocal multiphoton fluorescence lifetime imaging microscope for live-cell FRET imaging. Biomed. Opt. Express 6, 277–296 (2015).
Poland, S. P. et al. Time-resolved multifocal multiphoton microscope for high speed FRET imaging in vivo. Opt. Lett. 39, 6013–6016 (2014).
Suhling, K. et al. Fluorescence lifetime imaging (FLIM): Basic concepts and some recent developments. Med. Photonics 27, 3–40 (2015).
Suhling, K. et al. in Handbook of Photonics for Biomedical Engineering 353–405 (Springer, 2017).
Suhling, K. et al. in Advanced Time-Correlated Single Photon Counting Applications 119–188 (Springer, 2015).
Burke, D., Patton, B., Huang, F., Bewersdorf, J. & Booth, M. J. Adaptive optics correction of specimen-induced aberrations in single-molecule switching microscopy. Optica 2, 177–185 (2015).
Coelho, S. et al. Multifocal multiphoton microscopy with adaptive optical correction. SPIE Proceedings Vol. 8588 (SPIE, 2013).
Coelho, S., Poland, S. P., Devauges, V. & Ameer-Beg, S. M. Adaptive optics for a time-resolved Förster resonance energy transfer (FRET) and fluorescence lifetime imaging microscopy (FLIM) in vivo. Opt. Lett. 45, 2732–2735 (2020).
Eggeling, C. et al. Direct observation of the nanoscale dynamics of membrane lipids in a living cell. Nature 457, 1159–1162 (2009).
Boutros, M., Heigwer, F. & Laufer, C. Microscopy-based high-content screening. Cell 163, 1314–1325 (2015).
Gustavsson, A.-K., Petrov, P. N., Lee, M. Y., Shechtman, Y. & Moerner, W. 3D single-molecule super-resolution microscopy with a tilted light sheet. Nat. Commun. 9, 1–8 (2018).
Giessibl, F. J. Advances in atomic force microscopy. Rev. Mod. Phys. 75, 949 (2003).
Schmidt, P. D., Reichert, B. H., Lajoie, J. G. & Sivasankar, S. Method for high frequency tracking and sub-nm sample stabilization in single molecule fluorescence microscopy. Sci. Rep. 8, 13912 (2018).
Balinovic, A., Albrecht, D. & Endesfelder, U. Spectrally red-shifted fluorescent fiducial markers for optimal drift correction in localization microscopy. J. Phys. D. Appl. Phys. 52, 204002 (2019).
Henriques, R. et al. QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ. Nat. Methods 7, 339–340 (2010).
Wang, Y. et al. Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm. Opt. Express 22, 15982–15991 (2014).
Pertsinidis, A., Zhang, Y. & Chu, S. Subnanometre single-molecule localization, registration and distance measurements. Nature 466, 647–651 (2010).
McGorty, R., Kamiyama, D. & Huang, B. Active microscope stabilization in three dimensions using image correlation. Opt. Nanoscopy 2, 3 (2013).
Grover, G., Mohrman, W. & Piestun, R. Real-time adaptive drift correction for super-resolution localization microscopy. Opt. Express 23, 23887–23898 (2015).
Ma, H., Xu, J., Jin, J., Huang, Y. & Liu, Y. A simple marker-assisted 3D nanometer drift correction method for superresolution microscopy. Biophys. J. 112, 2196–2208 (2017).
Gosse, C. & Croquette, V. Magnetic tweezers: micromanipulation and force measurement at the molecular level. Biophys. J. 82, 3314–3329 (2002).
van Loenhout, M. T. J., Kerssemakers, J. W. J., De Vlaminck, I. & Dekker, C. Non-bias-limited tracking of spherical particles, enabling nanometer resolution at low magnification. Biophys. J. 102, 2362–2371 (2012).
Chivers, C. E., Koner, A. L., Lowe, E. D. & Howarth, M. How the biotin–streptavidin interaction was made even stronger: investigation via crystallography and a chimaeric tetramer. Biochem. J. 435, 55–63 (2011).
Haber, C. & Wirtz, D. Magnetic tweezers for DNA micromanipulation. Rev. Sci. Instrum. 71, 4561–4570 (2000).
Bormuth, V. et al. Optical trapping of coated microspheres. Opt. Express 16, 13831–13844 (2008).
Huang, B., Jones, S. A., Brandenburg, B. & Zhuang, X. Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution. Nat. Methods 5, 1047–1052 (2008).
van de Linde, S. Single-molecule localization microscopy analysis with ImageJ. J. Phys. D. Appl. Phys. 52, 203002 (2019).

3D active stabilization for single-molecule imaging

Supplementary information

Supplementary Information

Reporting Summary

推荐阅读