Abstract

Localization-based super-resolution microscopy enables imaging of biological structures with sub-diffraction-limited accuracy, but generally requires extended acquisition time. Consequently, stage drift often limits the spatial precision. Previously, we reported a simple method to correct for this by creating an array of 1 μm3 fiducial markers, every ~8 μm, on the coverslip, using UV-nanoimprint lithography (UV-NIL). While this allowed reliable and accurate 3D drift correction, it suffered high autofluorescence background with shorter wavelength illumination, unstable adsorption to the substrate glass surface, and suboptimal biocompatibility. Here, we present an improved fiducial micro-pattern prepared by thermal nanoimprint lithography (T-NIL). The new pattern is made of a thermal plastic material with low fluorescence backgrounds across the wide excitation range, particularly in the blue-region; robust structural stability under cell culturing condition; and a high bio-compatibility in terms of cell viability and adhesion. We demonstrate drift precision to 1.5 nm for lateral (x, y) and 6.1 nm axial (z) axes every 0.2 seconds for a total of 1 min long image acquisition. As a proof of principle, we acquired 4-color wide-field fluorescence images of live mammalian cells; we also acquired super-resolution images of fixed hippocampal neurons, and super-resolution images of live glutamate receptors and postsynaptic density proteins.

© 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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References

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    [Crossref] [PubMed]
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    [Crossref] [PubMed]

2017 (2)

W. Colomb, J. Czerski, J. D. Sau, and S. K. Sarkar, “Estimation of microscope drift using fluorescent nanodiamonds as fiducial markers,” J. Microsc. 266(3), 298–306 (2017).
[Crossref] [PubMed]

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

2016 (1)

K. W. Teng, Y. Ishitsuka, P. Ren, Y. Youn, X. Deng, P. Ge, A. S. Belmont, P. R. Selvin, and P. R. Selvin, “Labeling proteins inside living cells using external fluorophores for microscopy,” eLife 5, e20378 (2016).
[Crossref] [PubMed]

2015 (1)

H. Tamai, K. Maruo, H. Ueno, K. Terao, H. Kotera, and T. Suzuki, “Development of low-fluorescence thick photoresist for high-aspect-ratio microstructure in bio-application,” Biomicrofluidics 9(2), 022405 (2015).
[Crossref] [PubMed]

2014 (1)

2013 (1)

Y. Li, Y. Ishitsuka, P. N. Hedde, and G. U. Nienhaus, “Fast and efficient molecule detection in localization-based super-resolution microscopy by parallel adaptive histogram equalization,” ACS Nano 7(6), 5207–5214 (2013).
[Crossref] [PubMed]

2012 (1)

2011 (1)

2008 (2)

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

2007 (1)

J. H. Pai, Y. Wang, G. T. Salazar, C. E. Sims, M. Bachman, G. P. Li, and N. L. Allbritton, “Photoresist with low fluorescence for bioanalytical applications,” Anal. Chem. 79(22), 8774–8780 (2007).
[Crossref] [PubMed]

2006 (3)

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging Intracellular Fluorescent Proteins at Nanometer Resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–795 (2006).
[Crossref] [PubMed]

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

2005 (1)

M. Howarth, K. Takao, Y. Hayashi, and A. Y. Ting, “Targeting quantum dots to surface proteins in living cells with biotin ligase,” Proc. Natl. Acad. Sci. U.S.A. 102(21), 7583–7588 (2005).
[Crossref] [PubMed]

2003 (2)

S. W. Hell, “Toward fluorescence nanoscopy,” Nat. Biotechnol. 21(11), 1347–1355 (2003).
[Crossref] [PubMed]

A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin, “Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5-nm Localization,” Science 300(5628), 2061–2065 (2003).
[Crossref] [PubMed]

Allbritton, N. L.

J. H. Pai, Y. Wang, G. T. Salazar, C. E. Sims, M. Bachman, G. P. Li, and N. L. Allbritton, “Photoresist with low fluorescence for bioanalytical applications,” Anal. Chem. 79(22), 8774–8780 (2007).
[Crossref] [PubMed]

Bachman, M.

J. H. Pai, Y. Wang, G. T. Salazar, C. E. Sims, M. Bachman, G. P. Li, and N. L. Allbritton, “Photoresist with low fluorescence for bioanalytical applications,” Anal. Chem. 79(22), 8774–8780 (2007).
[Crossref] [PubMed]

Baday, M.

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

S. H. Lee, M. Baday, M. Tjioe, P. D. Simonson, R. Zhang, E. Cai, and P. R. Selvin, “Using fixed fiduciary markers for stage drift correction,” Opt. Express 20(11), 12177–12183 (2012).
[Crossref] [PubMed]

Bates, M.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–795 (2006).
[Crossref] [PubMed]

Belmont, A. S.

K. W. Teng, Y. Ishitsuka, P. Ren, Y. Youn, X. Deng, P. Ge, A. S. Belmont, P. R. Selvin, and P. R. Selvin, “Labeling proteins inside living cells using external fluorophores for microscopy,” eLife 5, e20378 (2016).
[Crossref] [PubMed]

Betzig, E.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging Intracellular Fluorescent Proteins at Nanometer Resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Bewersdorf, J.

Bonifacino, J. S.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging Intracellular Fluorescent Proteins at Nanometer Resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Cai, E.

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

S. H. Lee, M. Baday, M. Tjioe, P. D. Simonson, R. Zhang, E. Cai, and P. R. Selvin, “Using fixed fiduciary markers for stage drift correction,” Opt. Express 20(11), 12177–12183 (2012).
[Crossref] [PubMed]

Callahan, S. P.

Cheng, Y.

Colomb, W.

W. Colomb, J. Czerski, J. D. Sau, and S. K. Sarkar, “Estimation of microscope drift using fluorescent nanodiamonds as fiducial markers,” J. Microsc. 266(3), 298–306 (2017).
[Crossref] [PubMed]

Czerski, J.

W. Colomb, J. Czerski, J. D. Sau, and S. K. Sarkar, “Estimation of microscope drift using fluorescent nanodiamonds as fiducial markers,” J. Microsc. 266(3), 298–306 (2017).
[Crossref] [PubMed]

Davidson, M. W.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging Intracellular Fluorescent Proteins at Nanometer Resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

de Thomaz, A. A.

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

Delgado, J. Y.

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

Demonte, D.

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

Deng, X.

K. W. Teng, Y. Ishitsuka, P. Ren, Y. Youn, X. Deng, P. Ge, A. S. Belmont, P. R. Selvin, and P. R. Selvin, “Labeling proteins inside living cells using external fluorophores for microscopy,” eLife 5, e20378 (2016).
[Crossref] [PubMed]

Dlasková, A.

Dundas, C. M.

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

Forkey, J. N.

A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin, “Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5-nm Localization,” Science 300(5628), 2061–2065 (2003).
[Crossref] [PubMed]

Ge, P.

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

K. W. Teng, Y. Ishitsuka, P. Ren, Y. Youn, X. Deng, P. Ge, A. S. Belmont, P. R. Selvin, and P. R. Selvin, “Labeling proteins inside living cells using external fluorophores for microscopy,” eLife 5, e20378 (2016).
[Crossref] [PubMed]

Girirajan, T. P. K.

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

Goldman, Y. E.

A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin, “Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5-nm Localization,” Science 300(5628), 2061–2065 (2003).
[Crossref] [PubMed]

Green, W. N.

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

Ha, T.

A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin, “Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5-nm Localization,” Science 300(5628), 2061–2065 (2003).
[Crossref] [PubMed]

Hayashi, Y.

M. Howarth, K. Takao, Y. Hayashi, and A. Y. Ting, “Targeting quantum dots to surface proteins in living cells with biotin ligase,” Proc. Natl. Acad. Sci. U.S.A. 102(21), 7583–7588 (2005).
[Crossref] [PubMed]

Hedde, P. N.

Y. Li, Y. Ishitsuka, P. N. Hedde, and G. U. Nienhaus, “Fast and efficient molecule detection in localization-based super-resolution microscopy by parallel adaptive histogram equalization,” ACS Nano 7(6), 5207–5214 (2013).
[Crossref] [PubMed]

Heilemann, M.

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Hell, S. W.

S. W. Hell, “Toward fluorescence nanoscopy,” Nat. Biotechnol. 21(11), 1347–1355 (2003).
[Crossref] [PubMed]

Hess, H. F.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging Intracellular Fluorescent Proteins at Nanometer Resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Hess, S. T.

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

Howarth, M.

M. Howarth, K. Takao, Y. Hayashi, and A. Y. Ting, “Targeting quantum dots to surface proteins in living cells with biotin ligase,” Proc. Natl. Acad. Sci. U.S.A. 102(21), 7583–7588 (2005).
[Crossref] [PubMed]

Hu, Z.

Huang, B.

Huang, Z. L.

Ishitsuka, Y.

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

K. W. Teng, Y. Ishitsuka, P. Ren, Y. Youn, X. Deng, P. Ge, A. S. Belmont, P. R. Selvin, and P. R. Selvin, “Labeling proteins inside living cells using external fluorophores for microscopy,” eLife 5, e20378 (2016).
[Crossref] [PubMed]

Y. Li, Y. Ishitsuka, P. N. Hedde, and G. U. Nienhaus, “Fast and efficient molecule detection in localization-based super-resolution microscopy by parallel adaptive histogram equalization,” ACS Nano 7(6), 5207–5214 (2013).
[Crossref] [PubMed]

Jeyifous, O.

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

Ježek, P.

Jin, C.

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

Kasper, R.

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Kotera, H.

H. Tamai, K. Maruo, H. Ueno, K. Terao, H. Kotera, and T. Suzuki, “Development of low-fluorescence thick photoresist for high-aspect-ratio microstructure in bio-application,” Biomicrofluidics 9(2), 022405 (2015).
[Crossref] [PubMed]

Lee, S. H.

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

S. H. Lee, M. Baday, M. Tjioe, P. D. Simonson, R. Zhang, E. Cai, and P. R. Selvin, “Using fixed fiduciary markers for stage drift correction,” Opt. Express 20(11), 12177–12183 (2012).
[Crossref] [PubMed]

Li, G. P.

J. H. Pai, Y. Wang, G. T. Salazar, C. E. Sims, M. Bachman, G. P. Li, and N. L. Allbritton, “Photoresist with low fluorescence for bioanalytical applications,” Anal. Chem. 79(22), 8774–8780 (2007).
[Crossref] [PubMed]

Li, X.

Li, Y.

Y. Li, Y. Ishitsuka, P. N. Hedde, and G. U. Nienhaus, “Fast and efficient molecule detection in localization-based super-resolution microscopy by parallel adaptive histogram equalization,” ACS Nano 7(6), 5207–5214 (2013).
[Crossref] [PubMed]

Lindwasser, O. W.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging Intracellular Fluorescent Proteins at Nanometer Resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Lippincott-Schwartz, J.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging Intracellular Fluorescent Proteins at Nanometer Resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Maruo, K.

H. Tamai, K. Maruo, H. Ueno, K. Terao, H. Kotera, and T. Suzuki, “Development of low-fluorescence thick photoresist for high-aspect-ratio microstructure in bio-application,” Biomicrofluidics 9(2), 022405 (2015).
[Crossref] [PubMed]

Mason, M. D.

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

McKinney, S. A.

A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin, “Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5-nm Localization,” Science 300(5628), 2061–2065 (2003).
[Crossref] [PubMed]

Mlodzianoski, M. J.

Mukherjee, A.

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Nall, D.

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

Nienhaus, G. U.

Y. Li, Y. Ishitsuka, P. N. Hedde, and G. U. Nienhaus, “Fast and efficient molecule detection in localization-based super-resolution microscopy by parallel adaptive histogram equalization,” ACS Nano 7(6), 5207–5214 (2013).
[Crossref] [PubMed]

Olenych, S.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging Intracellular Fluorescent Proteins at Nanometer Resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Pai, J. H.

J. H. Pai, Y. Wang, G. T. Salazar, C. E. Sims, M. Bachman, G. P. Li, and N. L. Allbritton, “Photoresist with low fluorescence for bioanalytical applications,” Anal. Chem. 79(22), 8774–8780 (2007).
[Crossref] [PubMed]

Park, S.

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

Patterson, G. H.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging Intracellular Fluorescent Proteins at Nanometer Resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Ren, P.

K. W. Teng, Y. Ishitsuka, P. Ren, Y. Youn, X. Deng, P. Ge, A. S. Belmont, P. R. Selvin, and P. R. Selvin, “Labeling proteins inside living cells using external fluorophores for microscopy,” eLife 5, e20378 (2016).
[Crossref] [PubMed]

Rust, M. J.

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–795 (2006).
[Crossref] [PubMed]

Salazar, G. T.

J. H. Pai, Y. Wang, G. T. Salazar, C. E. Sims, M. Bachman, G. P. Li, and N. L. Allbritton, “Photoresist with low fluorescence for bioanalytical applications,” Anal. Chem. 79(22), 8774–8780 (2007).
[Crossref] [PubMed]

Santorová, J.

Sarkar, S. K.

W. Colomb, J. Czerski, J. D. Sau, and S. K. Sarkar, “Estimation of microscope drift using fluorescent nanodiamonds as fiducial markers,” J. Microsc. 266(3), 298–306 (2017).
[Crossref] [PubMed]

Sau, J. D.

W. Colomb, J. Czerski, J. D. Sau, and S. K. Sarkar, “Estimation of microscope drift using fluorescent nanodiamonds as fiducial markers,” J. Microsc. 266(3), 298–306 (2017).
[Crossref] [PubMed]

Sauer, M.

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Schnitzbauer, J.

Schreiner, J. M.

Schüttpelz, M.

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Seefeldt, B.

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Selvin, P. R.

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

K. W. Teng, Y. Ishitsuka, P. Ren, Y. Youn, X. Deng, P. Ge, A. S. Belmont, P. R. Selvin, and P. R. Selvin, “Labeling proteins inside living cells using external fluorophores for microscopy,” eLife 5, e20378 (2016).
[Crossref] [PubMed]

K. W. Teng, Y. Ishitsuka, P. Ren, Y. Youn, X. Deng, P. Ge, A. S. Belmont, P. R. Selvin, and P. R. Selvin, “Labeling proteins inside living cells using external fluorophores for microscopy,” eLife 5, e20378 (2016).
[Crossref] [PubMed]

S. H. Lee, M. Baday, M. Tjioe, P. D. Simonson, R. Zhang, E. Cai, and P. R. Selvin, “Using fixed fiduciary markers for stage drift correction,” Opt. Express 20(11), 12177–12183 (2012).
[Crossref] [PubMed]

A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin, “Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5-nm Localization,” Science 300(5628), 2061–2065 (2003).
[Crossref] [PubMed]

Simonson, P. D.

Sims, C. E.

J. H. Pai, Y. Wang, G. T. Salazar, C. E. Sims, M. Bachman, G. P. Li, and N. L. Allbritton, “Photoresist with low fluorescence for bioanalytical applications,” Anal. Chem. 79(22), 8774–8780 (2007).
[Crossref] [PubMed]

Smolková, K.

Sougrat, R.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging Intracellular Fluorescent Proteins at Nanometer Resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Suzuki, T.

H. Tamai, K. Maruo, H. Ueno, K. Terao, H. Kotera, and T. Suzuki, “Development of low-fluorescence thick photoresist for high-aspect-ratio microstructure in bio-application,” Biomicrofluidics 9(2), 022405 (2015).
[Crossref] [PubMed]

Takao, K.

M. Howarth, K. Takao, Y. Hayashi, and A. Y. Ting, “Targeting quantum dots to surface proteins in living cells with biotin ligase,” Proc. Natl. Acad. Sci. U.S.A. 102(21), 7583–7588 (2005).
[Crossref] [PubMed]

Tamai, H.

H. Tamai, K. Maruo, H. Ueno, K. Terao, H. Kotera, and T. Suzuki, “Development of low-fluorescence thick photoresist for high-aspect-ratio microstructure in bio-application,” Biomicrofluidics 9(2), 022405 (2015).
[Crossref] [PubMed]

Teng, K. W.

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

K. W. Teng, Y. Ishitsuka, P. Ren, Y. Youn, X. Deng, P. Ge, A. S. Belmont, P. R. Selvin, and P. R. Selvin, “Labeling proteins inside living cells using external fluorophores for microscopy,” eLife 5, e20378 (2016).
[Crossref] [PubMed]

Terao, K.

H. Tamai, K. Maruo, H. Ueno, K. Terao, H. Kotera, and T. Suzuki, “Development of low-fluorescence thick photoresist for high-aspect-ratio microstructure in bio-application,” Biomicrofluidics 9(2), 022405 (2015).
[Crossref] [PubMed]

Ting, A. Y.

M. Howarth, K. Takao, Y. Hayashi, and A. Y. Ting, “Targeting quantum dots to surface proteins in living cells with biotin ligase,” Proc. Natl. Acad. Sci. U.S.A. 102(21), 7583–7588 (2005).
[Crossref] [PubMed]

Tinnefeld, P.

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Tjioe, M.

Ueno, H.

H. Tamai, K. Maruo, H. Ueno, K. Terao, H. Kotera, and T. Suzuki, “Development of low-fluorescence thick photoresist for high-aspect-ratio microstructure in bio-application,” Biomicrofluidics 9(2), 022405 (2015).
[Crossref] [PubMed]

van de Linde, S.

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Wang, W.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

Wang, Y.

Y. Wang, J. Schnitzbauer, Z. Hu, X. Li, Y. Cheng, Z. L. Huang, and B. Huang, “Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm,” Opt. Express 22(13), 15982–15991 (2014).
[Crossref] [PubMed]

J. H. Pai, Y. Wang, G. T. Salazar, C. E. Sims, M. Bachman, G. P. Li, and N. L. Allbritton, “Photoresist with low fluorescence for bioanalytical applications,” Anal. Chem. 79(22), 8774–8780 (2007).
[Crossref] [PubMed]

Yildiz, A.

A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin, “Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5-nm Localization,” Science 300(5628), 2061–2065 (2003).
[Crossref] [PubMed]

Youn, Y.

K. W. Teng, Y. Ishitsuka, P. Ren, Y. Youn, X. Deng, P. Ge, A. S. Belmont, P. R. Selvin, and P. R. Selvin, “Labeling proteins inside living cells using external fluorophores for microscopy,” eLife 5, e20378 (2016).
[Crossref] [PubMed]

Zhang, R.

Zhuang, X.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–795 (2006).
[Crossref] [PubMed]

ACS Nano (1)

Y. Li, Y. Ishitsuka, P. N. Hedde, and G. U. Nienhaus, “Fast and efficient molecule detection in localization-based super-resolution microscopy by parallel adaptive histogram equalization,” ACS Nano 7(6), 5207–5214 (2013).
[Crossref] [PubMed]

Anal. Chem. (1)

J. H. Pai, Y. Wang, G. T. Salazar, C. E. Sims, M. Bachman, G. P. Li, and N. L. Allbritton, “Photoresist with low fluorescence for bioanalytical applications,” Anal. Chem. 79(22), 8774–8780 (2007).
[Crossref] [PubMed]

Angew. Chem. Int. Ed. Engl. (1)

M. Heilemann, S. van de Linde, M. Schüttpelz, R. Kasper, B. Seefeldt, A. Mukherjee, P. Tinnefeld, and M. Sauer, “Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes,” Angew. Chem. Int. Ed. Engl. 47(33), 6172–6176 (2008).
[Crossref] [PubMed]

Biomicrofluidics (1)

H. Tamai, K. Maruo, H. Ueno, K. Terao, H. Kotera, and T. Suzuki, “Development of low-fluorescence thick photoresist for high-aspect-ratio microstructure in bio-application,” Biomicrofluidics 9(2), 022405 (2015).
[Crossref] [PubMed]

Biophys. J. (1)

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref] [PubMed]

eLife (2)

S. H. Lee, C. Jin, E. Cai, P. Ge, Y. Ishitsuka, K. W. Teng, A. A. de Thomaz, D. Nall, M. Baday, O. Jeyifous, D. Demonte, C. M. Dundas, S. Park, J. Y. Delgado, W. N. Green, and P. R. Selvin, “Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with different-sized fluorescent probes,” eLife 6, e27744 (2017).
[PubMed]

K. W. Teng, Y. Ishitsuka, P. Ren, Y. Youn, X. Deng, P. Ge, A. S. Belmont, P. R. Selvin, and P. R. Selvin, “Labeling proteins inside living cells using external fluorophores for microscopy,” eLife 5, e20378 (2016).
[Crossref] [PubMed]

J. Microsc. (1)

W. Colomb, J. Czerski, J. D. Sau, and S. K. Sarkar, “Estimation of microscope drift using fluorescent nanodiamonds as fiducial markers,” J. Microsc. 266(3), 298–306 (2017).
[Crossref] [PubMed]

Nat. Biotechnol. (1)

S. W. Hell, “Toward fluorescence nanoscopy,” Nat. Biotechnol. 21(11), 1347–1355 (2003).
[Crossref] [PubMed]

Nat. Methods (1)

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–795 (2006).
[Crossref] [PubMed]

Opt. Express (3)

Proc. Natl. Acad. Sci. U.S.A. (1)

M. Howarth, K. Takao, Y. Hayashi, and A. Y. Ting, “Targeting quantum dots to surface proteins in living cells with biotin ligase,” Proc. Natl. Acad. Sci. U.S.A. 102(21), 7583–7588 (2005).
[Crossref] [PubMed]

Science (3)

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin, “Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5-nm Localization,” Science 300(5628), 2061–2065 (2003).
[Crossref] [PubMed]

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging Intracellular Fluorescent Proteins at Nanometer Resolution,” Science 313(5793), 1642–1645 (2006).
[Crossref] [PubMed]

Supplementary Material (2)

NameDescription
» Visualization 1       3-dimensional visualization of the PALM image of actin-mEos3.2 of fixed neurons.
» Visualization 2       3-dimensional visualization of the super-resolution image of Homer1c-mGeos (green) and streptavidin-Atto647N labeled AMPAR (red) of live neurons.

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Figures (8)

Fig. 1
Fig. 1 Fabrication of the T-NIL fiduciary marker patterns. (a) Schematic for the process of the fabrication of the T-NIL fiduciary marker patterned coverslips. (b) Scanning electron microscopy image of patterned coverslips (Au coating). Inset is the magnified side view (45°) of single dot. The measured height after angle correction is 1.2 μm. (c) Fabrication of PDMS stamp for T-NIL. Microscope slides (Fisherfinest Premium Plain Glass Microscope Slides, Fisher Scientific) were placed on the silicon master around the pattern as spacers (left) and additional slides was placed on top of the poured PDMS mixture to make the stamps flat and have the same thickness.
Fig. 2
Fig. 2 The representative x, y and z positions from 4 fiduciary markers and the averages over the course of 1000 frames (top). The deviation from the average are plotted as histograms. The precision is defined as the standard deviation of the Gaussian fit (bottom).
Fig. 3
Fig. 3 z-axis calibration curve. The width (s) of the 2D Gaussian fit is linearly proportional to the z-position of the sample at 2 – 7 μm range. The bright field images of a marker show the progression of change in s as a function of the z-position.
Fig. 4
Fig. 4 Quantification of the auto-fluorescence of micro-pattern prepared using different resists under illumination with (a) 405 nm, (b) 488 nm, (c) 561 nm, or (d) 640 nm laser. The intensity of each illumination laser was fixed at 1 mW. The intensity value (y axis of the plots) is normalized with the value obtained from the glass (non-coated) surface. The shown error is standard deviation.
Fig. 5
Fig. 5 Bio-compatibility and adhesion to glass surface of T-NIL materials. (a) Bright field images of cultured cells and fluorescent protein expressions of the cells. (b, left) Under culture media, UV-curable resist (NOA81) locally detaches from the glass surface and forms large bubbles, indicated by the dotted white line (b, right), while T-NIL pattern (mr-I T85) remains stable for weeks.
Fig. 6
Fig. 6 Live cell fluorescence images. (a) Fluorescent images of Hela cells on T-NIL fiduciary marker (left) and on glass surface (right). Cells were labeled by Hoecsht and SiR-actin, and expressed GFP-mitochondria and mScarlett-tubulin. (b) Measured Signal-to-Noise Ratio (SNR) of fluorescent beads on T-NIL and glass surface in 4 channels. The error bars indicate the standard deviation.
Fig. 7
Fig. 7 Super-resolution images of fixed neurons. Neurons. (a) PALM image of actin-mEos3.2 of fixed neurons before and after correction. The insets show the 3D visualization of the spines inside of the white rectangles (see Visualization 1). (b) The position of the fiduciary marker used for the image in 3D. The drift along z axis is relatively smaller (100 nm) than that of lateral dimension (~500 nm, x and y). (c) The linear profile of the selected area shows the width of the spine before and after the drift correction as FWHM of the Gaussian fit.
Fig. 8
Fig. 8 Super-resolution images of live neurons. Neurons. Overlay of the fluorescent image of Homer1c-mGeos (green) and streptavidin-Atto647N labeled AMPAR (red) of live neurons (left). 3-dimensional visualization of the super-resolution image of the neuron using VMD (right, see Visualization 2). Inset shows the visualization of a representative synapse of the neuron using VMD. The synapse is shown with rotation by 90° along two perpendicular axes.

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