Build and operation of a custom 3D, multicolor, single-molecule localization microscope

Jonas Ries, Rory M. Power, Aline Tschanz, Timo Zimmermann

Published: 2024-05-03 DOI: 10.1038/s41596-024-00989-x

Single-molecule localization microscopy

3D imaging

Multicolor SMLM

Custom microscope

Super-resolution dataset

AI 解读

Publisher Correction: A practical guide to large-scale docking

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Sections

Figures

References

Introduction
Materials
Procedure
Troubleshooting
Timing
Anticipated results
- Reporting summary
Acknowledgements

Betzig, E. et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313, 1642–1645 (2006).
Hess, S. T., Girirajan, T. P. K. & 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, 793–795 (2006).
Heilemann, M., Van De Linde, S., Mukherjee, A. & Sauer, M. Super-resolution imaging with small organic fluorophores. Angew. Chem. Int. Ed. Engl. 48, 6903–6908 (2009).
Jungmann, R. et al. Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. Nano Lett. 10, 4756–4761 (2010).
Martens, K. J. A. et al. Visualisation of dCas9 target search in vivo using an open-microscopy framework. Nat. Commun. 10, 3552 (2019).
Auer, A. et al. Nanometer-scale multiplexed super-resolution imaging with an economic 3D-DNA-PAINT microscope. ChemPhysChem 19, 3024–3034 (2018).
Ma, H., Fu, R., Xu, J. & Liu, Y. A simple and cost-effective setup for super-resolution localization microscopy. Sci. Rep. 7, 1542 (2017).
Diederich, B. et al. Nanoscopy on the chea(i)p. Preprint at bioRxiv https://doi.org/10.1101/2020.09.04.283085 (2020).
Zehrer, A. C., Martin-Villalba, A., Diederich, B. & Ewers, H. An open-source, high resolution, automated fluorescence microscope. eLife 12, RP89826 (2023).
Alsamsam, M. N., Kopūstas, A., Jurevičiūtė, M. & Tutkus, M. The miEye: bench-top super-resolution microscope with cost-effective equipment. HardwareX 12, e00368 (2022).
Coelho, S. et al. Ultraprecise single-molecule localization microscopy enables in situ distance measurements in intact cells. Sci. Adv. 6, eaay8271 (2020).
Mau, A., Friedl, K., Leterrier, C., Bourg, N. & Lévêque-Fort, S. Fast widefield scan provides tunable and uniform illumination optimizing super-resolution microscopy on large fields. Nat. Commun. 12, 3077 (2021).
Stehr, F., Stein, J., Schueder, F., Schwille, P. & Jungmann, R. Flat-top TIRF illumination boosts DNA-PAINT imaging and quantification. Nat. Commun. 10, 1268 (2019).
Khaw, I. et al. Flat-field illumination for quantitative fluorescence imaging. Opt. Express 26, 15276 (2018).
Niederauer, C., Seynen, M., Zomerdijk, J., Kamp, M. & Ganzinger, K. A. The K2: open-source simultaneous triple-color TIRF microscope for live-cell and single-molecule imaging. HardwareX 13, e00404 (2023).
Jabermoradi, A., Yang, S., Gobes, M. I., Van Duynhoven, J. P. M. & Hohlbein, J. Enabling single-molecule localization microscopy in turbid food emulsions. Philos. Trans. R. Soc. A. 380, 20200164 (2022).
Li, Y. et al. Global fitting for high-accuracy multi-channel single-molecule localization. Nat. Commun. 13, 3133 (2022).
Roy, R., Hohng, S. & Ha, T. A practical guide to single-molecule FRET. Nat. Methods 5, 507–516 (2008).
Ha, T. et al. Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. Proc. Natl Acad. Sci. USA 93, 6264–6268 (1996).
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. USA 106, 2995–2999 (2009).
Danial, J. S. H. et al. Constructing a cost-efficient, high-throughput and high-quality single-molecule localization microscope for super-resolution imaging. Nat. Protoc. 17, 2570–2619 (2022).
Carter, N., Cross, R. & Martin, D. Warwick open-source microscope. https://wosmic.org/ (2016).
Edwards, J., Whitley, K., Peneti, S., Cesbron, Y. & Holden, S. LifeHack microscope. GitHub https://github.com/HoldenLab/LifeHack (2021).
Deschamps, J., Rowald, A. & Ries, J. Efficient homogeneous illumination and optical sectioning for quantitative single-molecule localization microscopy. Opt. Express 24, 28080 (2016).
Li, Y. et al. Real-time 3D single-molecule localization using experimental point spread functions. Nat. Methods 15, 367–369 (2018).
Deschamps, J. & Ries, J. EMU: reconfigurable graphical user interfaces for Micro-Manager. BMC Bioinforma. 21, 456 (2020).
Diekmann, R. et al. Optimizing imaging speed and excitation intensity for single-molecule localization microscopy. Nat. Methods 17, 909–912 (2020).
Ries, J. SMAP: a modular super-resolution microscopy analysis platform for SMLM data. Nat. Methods 17, 870–872 (2020).
Dasgupta, A. et al. Direct supercritical angle localization microscopy for nanometer 3D superresolution. Nat. Commun. 12, 1180 (2021).
Diekmann, R. et al. Photon-free (s)CMOS camera characterization for artifact reduction in high- and super-resolution microscopy. Nat. Commun. 13, 3362 (2022).
Ries, J., Kaplan, C., Platonova, E., Eghlidi, H. & Ewers, H. A simple, versatile method for GFP-based super-resolution microscopy via nanobodies. Nat. Methods 9, 582–584 (2012).
Mund, M. et al. Systematic nanoscale analysis of endocytosis links efficient vesicle formation to patterned actin nucleation. Cell 174, 884–896.e17 (2018).
Mund, M. et al. Clathrin coats partially preassemble and subsequently bend during endocytosis. J. Cell Biol. 222, e202206038 (2023).
Cieslinski, K. et al. Nanoscale structural organization and stoichiometry of the budding yeast kinetochore. J. Cell Biol. 222, e202209094 (2023).
Edelstein, A., Amodaj, N., Hoover, K., Vale, R. & Stuurman, N. Computer control of microscopes using manager. Curr. Protoc. Mol. Biol. https://doi.org/10.1002/0471142727.mb1420s92 (2010).
Deschamps, J., Kieser, C., Hoess, P., Deguchi, T. & Ries, J. MicroFPGA: an affordable FPGA platform for microscope control. HardwareX 13, e00407 (2023).
Schermelleh, L. et al. Super-resolution microscopy demystified. Nat. Cell Biol. 21, 72–84 (2019).
Vangindertael, J. et al. An introduction to optical super-resolution microscopy for the adventurous biologist. Methods Appl. Fluoresc. 6, 22003 (2018).
Jacquemet, G., Carisey, A. F., Hamidi, H., Henriques, R. & Leterrier, C. The cell biologist’s guide to super-resolution microscopy. J. Cell Sci. 133, jcs240713 (2020).
Bond, C., Santiago-Ruiz, A. N., Tang, Q. & Lakadamyali, M. Technological advances in super-resolution microscopy to study cellular processes. Mol. Cell 82, 315–332 (2022).
Hell, S. W. & Wichmann, J. Breaking the diffraction resolution limit by stimulated emission. Opt. Lett. 19, 780–782 (1994).
Gustafsson, M. G. Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J. Microsc. 198, 82–87 (2000).
Müller, C. B. & Enderlein, J. Image scanning microscopy. Phys. Rev. Lett. 104, 1–4 (2010).
Strauss, M. T. Picasso-server: a community-based, open-source processing framework for super-resolution data. Commun. Biol. 5, 1–3 (2022).
Ovesný, M., Křížek, P., Borkovec, J., Švindrych, Z. & Hagen, G. M. ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging. Bioinformatics 30, 2389–2390 (2014).
Sage, D. et al. Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software. Nat. Methods 16, 387–395 (2019).
Von Appen, A. et al. In situ structural analysis of the human nuclear pore complex. Nature 526, 140–143 (2015).
Thevathasan, J. V. et al. Nuclear pores as versatile reference standards for quantitative superresolution microscopy. Nat. Methods 16, 1045–1053 (2019).
Smith, C. S., Joseph, N., Rieger, B. & Lidke, K. A. Fast, single-molecule localization that achieves theoretically minimum uncertainty. Nat. Methods 7, 373–375 (2010).
Wu, Y.-L. et al. Maximum-likelihood model fitting for quantitative analysis of SMLM data. Nat. Methods 20, 139–148 (2023).

Build and operation of a custom 3D, multicolor, single-molecule localization microscope

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