Abstract

Optical flat-fielding systems, such as field-mapping or integration-based beam shapers, are used to transform nonuniform illumination into uniform illumination. Thus, flat-fielding paves the way for imaging that is independent of position within a field of view and enables more quantitative analysis. Here, we characterize and compare three systems for homogenizing both widefield and multifocal illumination. Our analysis includes two refractive field-mapping beam shapers: PiShaper and TopShape, as well as one integration-based: Köhler integrator. The comparison is based on figures of merit including ISO-standard values, such as the plateau uniformity and edge steepness, transmission efficiency, stability of the beams along propagation and multifocal intensity, pitch, and point width. By characterizing and comparing existing beam shapers, we facilitate the choice of the appropriate flat-fielding solution and increase their accessibility for different applications.

© 2020 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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2019 (2)

F. Stehr, J. Stein, F. Schueder, P. Schwille, and R. Jungmann, “Flat-top TIRF illumination boosts DNA-PAINT imaging and quantification,” Nat. Commun. 10(1), 1268 (2019).
[Crossref]

A. Archetti, E. Glushkov, C. Sieben, A. Stroganov, A. Radenovic, and S. Manley, “Waveguide-PAINT offers an open platform for large field-of-view super-resolution imaging,” Nat. Commun. 10(1), 1267 (2019).
[Crossref]

2018 (5)

S.-Y. Chen, F. Bestvater, W. Schaufler, R. Heintzmann, and C. Cremer, “Patterned illumination single molecule localization microscopy (piSMLM): user defined blinking regions of interest,” Opt. Express 26(23), 30009–30020 (2018).
[Crossref]

M. Hausmann, E. Wagner, J.-H. Lee, G. Schrock, W. Schaufler, M. Krufczik, F. Papenfuß, M. Port, F. Bestvater, and H. Scherthan, “Super-resolution localization microscopy of radiation-induced histone H2AX-phosphorylation in relation to H3K9-trimethylation in HeLa cells,” Nanoscale 10(9), 4320–4331 (2018).
[Crossref]

D. J. Heath, T. H. Rana, R. A. Bapty, J. A. Grant-Jacob, Y. Xie, R. W. Eason, and B. Mills, “Ultrafast multi-layer subtractive patterning,” Opt. Express 26(9), 11928–11933 (2018).
[Crossref]

I. Khaw, B. Croop, J. Tang, A. Möhl, U. Fuchs, and K. Y. Han, “Flat-field illumination for quantitative fluorescence imaging,” Opt. Express 26(12), 15276–15288 (2018).
[Crossref]

C. J. Rowlands, F. Ströhl, P. P. V. Ramirez, K. M. Scherer, and C. F. Kaminski, “Flat-field super-resolution localization microscopy with a low-cost refractive beam-shaping element,” Sci. Rep. 8(1), 5630 (2018).
[Crossref]

2017 (1)

2016 (2)

K. M. Douglass, C. Sieben, A. Archetti, A. Lambert, and S. Manley, “Super-resolution imaging of multiple cells by optimized flat-field epi-illumination,” Nat. Photonics 10(11), 705–708 (2016).
[Crossref]

J. Deschamps, A. Rowald, and J. Ries, “Efficient homogeneous illumination and optical sectioning for quantitative single-molecule localization microscopy,” Opt. Express 24(24), 28080–28090 (2016).
[Crossref]

2015 (1)

K. Smith, Y. Li, F. Piccinini, G. Csucs, C. Balazs, A. Bevilacqua, and P. Horvath, “CIDRE: an illumination-correction method for optical microscopy,” Nat. Methods 12(5), 404–406 (2015).
[Crossref]

2014 (1)

J. S. Verdaasdonk, J. Lawrimore, and K. Bloom, “Determining absolute protein numbers by quantitative fluorescence microscopy,” Methods Cell Biol. 123, 347–365 (2014).
[Crossref]

2013 (2)

B. Mills, J. A. Grant-Jacob, M. Feinaeugle, and R. W. Eason, “Single-pulse multiphoton polymerization of complex structures using a digital multimirror device,” Opt. Express 21(12), 14853–14858 (2013).
[Crossref]

A. G. York, P. Chandris, D. D. Nogare, J. Head, P. Wawrzusin, R. S. Fischer, A. Chitnis, and H. Shroff, “Instant super-resolution imaging in live cells and embryos via analog image processing,” Nat. Methods 10(11), 1122–1126 (2013).
[Crossref]

2012 (1)

A. G. York, S. H. Parekh, D. D. Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
[Crossref]

2011 (4)

A. Schweinsberg, J. Kuper, and R. W. Boyd, “Loss of spatial coherence and limiting of focal plane intensity by small-scale laser-beam filamentation,” Phys. Rev. A 84(5), 053837 (2011).
[Crossref]

J. J. Toriz-Garcia, G. L. Williams, R. McWilliam, N. L. Seed, A. Purvis, F. B. Soulard, J. J. Cowling, and P. A. Ivey, “Vertical tracks on the sidewall of a silicon die using 3D holographic photolithography,” J. Micromech. Microeng. 21(8), 085034 (2011).
[Crossref]

R. C. Y. Auyeung, H. Kim, N. A. Charipar, A. J. Birnbaum, S. A. Mathews, and A. Piqué, “Laser forward transfer based on a spatial light modulator,” Appl. Phys. A 102(1), 21–26 (2011).
[Crossref]

G. Račiukaitis, E. Stankevičius, P. Gečys, M. Gedvilas, C. Bischoff, E. Jäger, U. Umhoffer, and F. Völklein, “Laser processing by using diffractive optical laser beam shaping,” J. Laser Micro/Nanoeng. 6(1), 37–43 (2011).
[Crossref]

2010 (2)

2008 (1)

2006 (3)

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

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]

S. T. Hess, T. P. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[Crossref]

2005 (1)

C. Eggeling, A. Volkmer, and C. A. M. Seidel, “Molecular photobleaching kinetics of Rhodamine 6G by one- and two-photon induced confocal fluorescence microscopy,” ChemPhysChem 6(5), 791–804 (2005).
[Crossref]

2003 (1)

1996 (1)

R. Völkel, H. P. Herzig, P. Nussbaum, and R. Dändliker, “Microlens array imaging system for photolithography,” Opt. Eng. 35(11), 3323–3330 (1996).
[Crossref]

1965 (1)

AdlOptica,

AdlOptica, “PiShaper 6_6 Manual,” 2019.

Andor,

Andor, “Enhanced illumination and imaging upgrade for CSU spinning disks,” [Online]. Available: https://biochimie.umontreal.ca/wp-content/uploads/sites/37/2016/02/Borealis_Specifications.pdf. [Accessed 1 June 2020].

Antolini, R.

Archetti, A.

A. Archetti, E. Glushkov, C. Sieben, A. Stroganov, A. Radenovic, and S. Manley, “Waveguide-PAINT offers an open platform for large field-of-view super-resolution imaging,” Nat. Commun. 10(1), 1267 (2019).
[Crossref]

K. M. Douglass, C. Sieben, A. Archetti, A. Lambert, and S. Manley, “Super-resolution imaging of multiple cells by optimized flat-field epi-illumination,” Nat. Photonics 10(11), 705–708 (2016).
[Crossref]

asphericon,

asphericon, “ https://www.asphericon.com/shop/en/beamtuning/a-topshape/tsm25-10-d-b-632.html ,” 2019. [Online].

Auyeung, R. C. Y.

R. C. Y. Auyeung, H. Kim, N. A. Charipar, A. J. Birnbaum, S. A. Mathews, and A. Piqué, “Laser forward transfer based on a spatial light modulator,” Appl. Phys. A 102(1), 21–26 (2011).
[Crossref]

Balazs, C.

K. Smith, Y. Li, F. Piccinini, G. Csucs, C. Balazs, A. Bevilacqua, and P. Horvath, “CIDRE: an illumination-correction method for optical microscopy,” Nat. Methods 12(5), 404–406 (2015).
[Crossref]

Banterle, N.

D. Mahecic, D. Gambarotto, K. M. Douglass, D. Fortun, N. Banterle, M. L. Guennec, K. A. Ibrahim, P. Gönczy, V. Hamel, P. Guichard, and S. Manley, “Homogeneous multifocal excitation for high-throughput super-resolution imaging,” bioRxiv, 2020.

Bapty, R. A.

Bates, M.

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

Bestvater, F.

S.-Y. Chen, F. Bestvater, W. Schaufler, R. Heintzmann, and C. Cremer, “Patterned illumination single molecule localization microscopy (piSMLM): user defined blinking regions of interest,” Opt. Express 26(23), 30009–30020 (2018).
[Crossref]

M. Hausmann, E. Wagner, J.-H. Lee, G. Schrock, W. Schaufler, M. Krufczik, F. Papenfuß, M. Port, F. Bestvater, and H. Scherthan, “Super-resolution localization microscopy of radiation-induced histone H2AX-phosphorylation in relation to H3K9-trimethylation in HeLa cells,” Nanoscale 10(9), 4320–4331 (2018).
[Crossref]

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]

Bevilacqua, A.

K. Smith, Y. Li, F. Piccinini, G. Csucs, C. Balazs, A. Bevilacqua, and P. Horvath, “CIDRE: an illumination-correction method for optical microscopy,” Nat. Methods 12(5), 404–406 (2015).
[Crossref]

Bich, A.

Birnbaum, A. J.

R. C. Y. Auyeung, H. Kim, N. A. Charipar, A. J. Birnbaum, S. A. Mathews, and A. Piqué, “Laser forward transfer based on a spatial light modulator,” Appl. Phys. A 102(1), 21–26 (2011).
[Crossref]

Bischoff, C.

G. Račiukaitis, E. Stankevičius, P. Gečys, M. Gedvilas, C. Bischoff, E. Jäger, U. Umhoffer, and F. Völklein, “Laser processing by using diffractive optical laser beam shaping,” J. Laser Micro/Nanoeng. 6(1), 37–43 (2011).
[Crossref]

Blattner, P.

P. Blattner and R. Voelkel, “Homogenous monochromatic irradiance fields generated by microlens array,” in 10th International Conference on New Developments and Applications in Optical Radiometry (NEWRAD), Daejeon, 2008.

Bloom, K.

J. S. Verdaasdonk, J. Lawrimore, and K. Bloom, “Determining absolute protein numbers by quantitative fluorescence microscopy,” Methods Cell Biol. 123, 347–365 (2014).
[Crossref]

Bolton, P. R.

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]

Boone, J. M.

J. A. Seibert, J. M. Boone, and K. K. Lindfors, “Flat-field correction technique for digital detectors,” in SPIE Proceedings Volume 3336, Medical Imaging 1998: Physics of Medical Imaging, San Diego, 1998.

Bourg, N.

A. Mau, K. Friedl, C. Leterrier, N. Bourg, and S. Lévêque-Fort, “Fast scanned widefield scheme provides tunable and uniform illumination for optimized SMLM on large fields of view,” bioRxiv, 2020.

Boyd, R. W.

A. Schweinsberg, J. Kuper, and R. W. Boyd, “Loss of spatial coherence and limiting of focal plane intensity by small-scale laser-beam filamentation,” Phys. Rev. A 84(5), 053837 (2011).
[Crossref]

Bulanov, S.

Chandris, P.

A. G. York, P. Chandris, D. D. Nogare, J. Head, P. Wawrzusin, R. S. Fischer, A. Chitnis, and H. Shroff, “Instant super-resolution imaging in live cells and embryos via analog image processing,” Nat. Methods 10(11), 1122–1126 (2013).
[Crossref]

Charipar, N. A.

R. C. Y. Auyeung, H. Kim, N. A. Charipar, A. J. Birnbaum, S. A. Mathews, and A. Piqué, “Laser forward transfer based on a spatial light modulator,” Appl. Phys. A 102(1), 21–26 (2011).
[Crossref]

Chen, S.-Y.

Chitnis, A.

A. G. York, P. Chandris, D. D. Nogare, J. Head, P. Wawrzusin, R. S. Fischer, A. Chitnis, and H. Shroff, “Instant super-resolution imaging in live cells and embryos via analog image processing,” Nat. Methods 10(11), 1122–1126 (2013).
[Crossref]

Chitnis, A. B.

A. G. York, S. H. Parekh, D. D. Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
[Crossref]

Choudhury, A.

Coherent,

Coherent, “Efficient transformation of Gaussian beams into uniform, rectangular intensity distributions,” [Online]. Available: https://www.coherent.com/assets/pdf/Efficient-Transformation-of-Gaussian-Beams-into-Uniform-Rectangular-Intensity-Distributions_FORMFIRST.pdf . [Accessed 1 June 2020].

Collier, J. L.

Combs, C. A.

A. G. York, S. H. Parekh, D. D. Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
[Crossref]

Cowling, J. J.

J. J. Toriz-Garcia, G. L. Williams, R. McWilliam, N. L. Seed, A. Purvis, F. B. Soulard, J. J. Cowling, and P. A. Ivey, “Vertical tracks on the sidewall of a silicon die using 3D holographic photolithography,” J. Micromech. Microeng. 21(8), 085034 (2011).
[Crossref]

Cremer, C.

Croop, B.

Csucs, G.

K. Smith, Y. Li, F. Piccinini, G. Csucs, C. Balazs, A. Bevilacqua, and P. Horvath, “CIDRE: an illumination-correction method for optical microscopy,” Nat. Methods 12(5), 404–406 (2015).
[Crossref]

Cullmann, E.

Daido, H.

Daito, I.

Dändliker, R.

R. Völkel, H. P. Herzig, P. Nussbaum, and R. Dändliker, “Microlens array imaging system for photolithography,” Opt. Eng. 35(11), 3323–3330 (1996).
[Crossref]

Dannberg, P.

P. Schreiber, S. Kudaev, P. Dannberg, and U. D. Zeitner, “Homogeneous LED-illumination using microlens arrays,” in SPIE Proceedings Volume 5942, Nonimaging Optics and Efficient Illumination Systems II, San Diego, 2005.

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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).
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D. Mahecic, D. Gambarotto, K. M. Douglass, D. Fortun, N. Banterle, M. L. Guennec, K. A. Ibrahim, P. Gönczy, V. Hamel, P. Guichard, and S. Manley, “Homogeneous multifocal excitation for high-throughput super-resolution imaging,” bioRxiv, 2020.

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D. Mahecic, D. Gambarotto, K. M. Douglass, D. Fortun, N. Banterle, M. L. Guennec, K. A. Ibrahim, P. Gönczy, V. Hamel, P. Guichard, and S. Manley, “Homogeneous multifocal excitation for high-throughput super-resolution imaging,” bioRxiv, 2020.

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D. Mahecic, D. Gambarotto, K. M. Douglass, D. Fortun, N. Banterle, M. L. Guennec, K. A. Ibrahim, P. Gönczy, V. Hamel, P. Guichard, and S. Manley, “Homogeneous multifocal excitation for high-throughput super-resolution imaging,” bioRxiv, 2020.

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J. J. Toriz-Garcia, G. L. Williams, R. McWilliam, N. L. Seed, A. Purvis, F. B. Soulard, J. J. Cowling, and P. A. Ivey, “Vertical tracks on the sidewall of a silicon die using 3D holographic photolithography,” J. Micromech. Microeng. 21(8), 085034 (2011).
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K. M. Douglass, C. Sieben, A. Archetti, A. Lambert, and S. Manley, “Super-resolution imaging of multiple cells by optimized flat-field epi-illumination,” Nat. Photonics 10(11), 705–708 (2016).
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A. Laskin, V. Laskin, and A. Ostrun, “Beam shaping for holographic techniques,” in SPIE Proceedings Volume 9200, Photonic Fiber and Crystal Devices: Advances in Materials and Innovations in Device Applications VIII, San Diego, 2014.

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A. Mau, K. Friedl, C. Leterrier, N. Bourg, and S. Lévêque-Fort, “Fast scanned widefield scheme provides tunable and uniform illumination for optimized SMLM on large fields of view,” bioRxiv, 2020.

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K. Smith, Y. Li, F. Piccinini, G. Csucs, C. Balazs, A. Bevilacqua, and P. Horvath, “CIDRE: an illumination-correction method for optical microscopy,” Nat. Methods 12(5), 404–406 (2015).
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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).
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D. Mahecic, D. Gambarotto, K. M. Douglass, D. Fortun, N. Banterle, M. L. Guennec, K. A. Ibrahim, P. Gönczy, V. Hamel, P. Guichard, and S. Manley, “Homogeneous multifocal excitation for high-throughput super-resolution imaging,” bioRxiv, 2020.

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A. Archetti, E. Glushkov, C. Sieben, A. Stroganov, A. Radenovic, and S. Manley, “Waveguide-PAINT offers an open platform for large field-of-view super-resolution imaging,” Nat. Commun. 10(1), 1267 (2019).
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K. M. Douglass, C. Sieben, A. Archetti, A. Lambert, and S. Manley, “Super-resolution imaging of multiple cells by optimized flat-field epi-illumination,” Nat. Photonics 10(11), 705–708 (2016).
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J. J. Toriz-Garcia, G. L. Williams, R. McWilliam, N. L. Seed, A. Purvis, F. B. Soulard, J. J. Cowling, and P. A. Ivey, “Vertical tracks on the sidewall of a silicon die using 3D holographic photolithography,” J. Micromech. Microeng. 21(8), 085034 (2011).
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C. J. Rowlands, F. Ströhl, P. P. V. Ramirez, K. M. Scherer, and C. F. Kaminski, “Flat-field super-resolution localization microscopy with a low-cost refractive beam-shaping element,” Sci. Rep. 8(1), 5630 (2018).
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C. J. Rowlands, F. Ströhl, P. P. V. Ramirez, K. M. Scherer, and C. F. Kaminski, “Flat-field super-resolution localization microscopy with a low-cost refractive beam-shaping element,” Sci. Rep. 8(1), 5630 (2018).
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M. Hausmann, E. Wagner, J.-H. Lee, G. Schrock, W. Schaufler, M. Krufczik, F. Papenfuß, M. Port, F. Bestvater, and H. Scherthan, “Super-resolution localization microscopy of radiation-induced histone H2AX-phosphorylation in relation to H3K9-trimethylation in HeLa cells,” Nanoscale 10(9), 4320–4331 (2018).
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P. Schreiber, S. Kudaev, P. Dannberg, and U. D. Zeitner, “Homogeneous LED-illumination using microlens arrays,” in SPIE Proceedings Volume 5942, Nonimaging Optics and Efficient Illumination Systems II, San Diego, 2005.

Schrock, G.

M. Hausmann, E. Wagner, J.-H. Lee, G. Schrock, W. Schaufler, M. Krufczik, F. Papenfuß, M. Port, F. Bestvater, and H. Scherthan, “Super-resolution localization microscopy of radiation-induced histone H2AX-phosphorylation in relation to H3K9-trimethylation in HeLa cells,” Nanoscale 10(9), 4320–4331 (2018).
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F. Stehr, J. Stein, F. Schueder, P. Schwille, and R. Jungmann, “Flat-top TIRF illumination boosts DNA-PAINT imaging and quantification,” Nat. Commun. 10(1), 1268 (2019).
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C. Eggeling, A. Volkmer, and C. A. M. Seidel, “Molecular photobleaching kinetics of Rhodamine 6G by one- and two-photon induced confocal fluorescence microscopy,” ChemPhysChem 6(5), 791–804 (2005).
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Shroff, H.

A. G. York, P. Chandris, D. D. Nogare, J. Head, P. Wawrzusin, R. S. Fischer, A. Chitnis, and H. Shroff, “Instant super-resolution imaging in live cells and embryos via analog image processing,” Nat. Methods 10(11), 1122–1126 (2013).
[Crossref]

A. G. York, S. H. Parekh, D. D. Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
[Crossref]

Sieben, C.

A. Archetti, E. Glushkov, C. Sieben, A. Stroganov, A. Radenovic, and S. Manley, “Waveguide-PAINT offers an open platform for large field-of-view super-resolution imaging,” Nat. Commun. 10(1), 1267 (2019).
[Crossref]

K. M. Douglass, C. Sieben, A. Archetti, A. Lambert, and S. Manley, “Super-resolution imaging of multiple cells by optimized flat-field epi-illumination,” Nat. Photonics 10(11), 705–708 (2016).
[Crossref]

Smith, K.

K. Smith, Y. Li, F. Piccinini, G. Csucs, C. Balazs, A. Bevilacqua, and P. Horvath, “CIDRE: an illumination-correction method for optical microscopy,” Nat. Methods 12(5), 404–406 (2015).
[Crossref]

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]

Soulard, F. B.

J. J. Toriz-Garcia, G. L. Williams, R. McWilliam, N. L. Seed, A. Purvis, F. B. Soulard, J. J. Cowling, and P. A. Ivey, “Vertical tracks on the sidewall of a silicon die using 3D holographic photolithography,” J. Micromech. Microeng. 21(8), 085034 (2011).
[Crossref]

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G. Račiukaitis, E. Stankevičius, P. Gečys, M. Gedvilas, C. Bischoff, E. Jäger, U. Umhoffer, and F. Völklein, “Laser processing by using diffractive optical laser beam shaping,” J. Laser Micro/Nanoeng. 6(1), 37–43 (2011).
[Crossref]

Stehr, F.

F. Stehr, J. Stein, F. Schueder, P. Schwille, and R. Jungmann, “Flat-top TIRF illumination boosts DNA-PAINT imaging and quantification,” Nat. Commun. 10(1), 1268 (2019).
[Crossref]

Stein, J.

F. Stehr, J. Stein, F. Schueder, P. Schwille, and R. Jungmann, “Flat-top TIRF illumination boosts DNA-PAINT imaging and quantification,” Nat. Commun. 10(1), 1268 (2019).
[Crossref]

Stroganov, A.

A. Archetti, E. Glushkov, C. Sieben, A. Stroganov, A. Radenovic, and S. Manley, “Waveguide-PAINT offers an open platform for large field-of-view super-resolution imaging,” Nat. Commun. 10(1), 1267 (2019).
[Crossref]

Ströhl, F.

C. J. Rowlands, F. Ströhl, P. P. V. Ramirez, K. M. Scherer, and C. F. Kaminski, “Flat-field super-resolution localization microscopy with a low-cost refractive beam-shaping element,” Sci. Rep. 8(1), 5630 (2018).
[Crossref]

Stuerzebecher, L.

Sugiyama, A.

Suzuki, M.

Taghizadeh, M. R.

Tajima, T.

Tanaka, M.

Tanbakuchi, A.

Tang, J.

Tanoue, M.

Temprine, K.

A. G. York, S. H. Parekh, D. D. Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
[Crossref]

Toriz-Garcia, J. J.

J. J. Toriz-Garcia, G. L. Williams, R. McWilliam, N. L. Seed, A. Purvis, F. B. Soulard, J. J. Cowling, and P. A. Ivey, “Vertical tracks on the sidewall of a silicon die using 3D holographic photolithography,” J. Micromech. Microeng. 21(8), 085034 (2011).
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Umhoffer, U.

G. Račiukaitis, E. Stankevičius, P. Gečys, M. Gedvilas, C. Bischoff, E. Jäger, U. Umhoffer, and F. Völklein, “Laser processing by using diffractive optical laser beam shaping,” J. Laser Micro/Nanoeng. 6(1), 37–43 (2011).
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R. Voelkel, U. Vogler, A. Bich, P. Pernet, K. J. Weible, M. Hornung, R. Zoberbier, E. Cullmann, L. Stuerzebecher, T. Harzendorf, and U. D. Zeitner, “Advanced mask aligner lithography: new illumination system,” Opt. Express 18(20), 20968–20978 (2010).
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M. Hausmann, E. Wagner, J.-H. Lee, G. Schrock, W. Schaufler, M. Krufczik, F. Papenfuß, M. Port, F. Bestvater, and H. Scherthan, “Super-resolution localization microscopy of radiation-induced histone H2AX-phosphorylation in relation to H3K9-trimethylation in HeLa cells,” Nanoscale 10(9), 4320–4331 (2018).
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R. Voelkel, U. Vogler, A. Bich, P. Pernet, K. J. Weible, M. Hornung, R. Zoberbier, E. Cullmann, L. Stuerzebecher, T. Harzendorf, and U. D. Zeitner, “Advanced mask aligner lithography: new illumination system,” Opt. Express 18(20), 20968–20978 (2010).
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J. J. Toriz-Garcia, G. L. Williams, R. McWilliam, N. L. Seed, A. Purvis, F. B. Soulard, J. J. Cowling, and P. A. Ivey, “Vertical tracks on the sidewall of a silicon die using 3D holographic photolithography,” J. Micromech. Microeng. 21(8), 085034 (2011).
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Xin, B.

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A. G. York, P. Chandris, D. D. Nogare, J. Head, P. Wawrzusin, R. S. Fischer, A. Chitnis, and H. Shroff, “Instant super-resolution imaging in live cells and embryos via analog image processing,” Nat. Methods 10(11), 1122–1126 (2013).
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A. G. York, S. H. Parekh, D. D. Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
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R. Voelkel, U. Vogler, A. Bich, P. Pernet, K. J. Weible, M. Hornung, R. Zoberbier, E. Cullmann, L. Stuerzebecher, T. Harzendorf, and U. D. Zeitner, “Advanced mask aligner lithography: new illumination system,” Opt. Express 18(20), 20968–20978 (2010).
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M. Zimmermann, N. Lindlein, R. Voelkel, and K. J. Weible, “Microlens laser beam homogenizer: from theory to application,” in SPIE Proceedings Volume 6663, Laser Beam Shaping VIII, San Diego, 2007.

Zimmermann, T.

R. Gräf, J. Rietdorf, and T. Zimmermann, “Live Cell Spinning Disk Microscopy,” in Microscopy Techniques95 (Springer, Berlin, Heidelberg, 2005) 57–75.

Zoberbier, R.

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M. Hausmann, E. Wagner, J.-H. Lee, G. Schrock, W. Schaufler, M. Krufczik, F. Papenfuß, M. Port, F. Bestvater, and H. Scherthan, “Super-resolution localization microscopy of radiation-induced histone H2AX-phosphorylation in relation to H3K9-trimethylation in HeLa cells,” Nanoscale 10(9), 4320–4331 (2018).
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A. Archetti, E. Glushkov, C. Sieben, A. Stroganov, A. Radenovic, and S. Manley, “Waveguide-PAINT offers an open platform for large field-of-view super-resolution imaging,” Nat. Commun. 10(1), 1267 (2019).
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K. Smith, Y. Li, F. Piccinini, G. Csucs, C. Balazs, A. Bevilacqua, and P. Horvath, “CIDRE: an illumination-correction method for optical microscopy,” Nat. Methods 12(5), 404–406 (2015).
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A. G. York, S. H. Parekh, D. D. Nogare, R. S. Fischer, K. Temprine, M. Mione, A. B. Chitnis, C. A. Combs, and H. Shroff, “Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy,” Nat. Methods 9(7), 749–754 (2012).
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M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
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K. M. Douglass, C. Sieben, A. Archetti, A. Lambert, and S. Manley, “Super-resolution imaging of multiple cells by optimized flat-field epi-illumination,” Nat. Photonics 10(11), 705–708 (2016).
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Opt. Eng. (1)

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Opt. Express (7)

R. Voelkel, U. Vogler, A. Bich, P. Pernet, K. J. Weible, M. Hornung, R. Zoberbier, E. Cullmann, L. Stuerzebecher, T. Harzendorf, and U. D. Zeitner, “Advanced mask aligner lithography: new illumination system,” Opt. Express 18(20), 20968–20978 (2010).
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R. Gräf, J. Rietdorf, and T. Zimmermann, “Live Cell Spinning Disk Microscopy,” in Microscopy Techniques95 (Springer, Berlin, Heidelberg, 2005) 57–75.

A. Laskin, V. Laskin, and A. Ostrun, “Beam shaping for holographic techniques,” in SPIE Proceedings Volume 9200, Photonic Fiber and Crystal Devices: Advances in Materials and Innovations in Device Applications VIII, San Diego, 2014.

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Figures (4)

Fig. 1.
Fig. 1. Greyscale images of different conditions for the input illumination and the corresponding outputs produced by each of the three beam shapers. (A) Low quality input beam deviates from a Gaussian profile. (B-D) Flat-field outputs produced by the (B) Köhler integrator, (C) PiShaper and (D) Top shape, using a low quality input beam (A). (E) Spatial filtering produces a smoother Gaussian profile. (F-H) Flat-field outputs produced by the (F) Köhler integrator, (G) PiShaper and (H) TopShape, using the filtered Gaussian input beam (E). (I) The input beam is cropped in half. (J-L) Flat-field outputs for the (J) Köhler integrator, (K) PiShaper and (L) TopShape, using the cropped beam as input (I). Images (B,C) were taken before the introduction of a beam de-expander to the system. Scale bar, 1.5 mm.
Fig. 2.
Fig. 2. Uniform greyscale images obtained from the three flat-topping systems under widefield illumination and their corresponding intensity profiles and histograms. (A) Köhler integrator. (B) PiShaper. (C) TopShape. The colored lines show the two locations where the intensity profiles are taken and then averaged. (D) Superimposed intensity profiles (here shown for the vertical line profile from A-C) of the three beam shapers. (E) Superimposed image (A-C) pixel grey-value histograms of the three beam shapers. The black bars represent the full-widths at half-maximum which are used to calculate the plateau uniformity. Scale bar, 1.5 mm.
Fig. 3.
Fig. 3. Variation of the ISO standard values at varying propagation distance from the intended sample plane of each beam shaper. (A) Köhler integrator images are taken at positive and negative displacements from the focal plane where the flat-top is produced. (B) PiShaper and TopShape images are taken at increasing distances from their output apertures. (C-E) Plateau uniformity, edge steepness and flatness factor as a function of the displacement from the defined flat-field plane for the (C) Köhler integrator, (D) PiShaper and (E) TopShape. Scale bar, 1.5 mm.
Fig. 4.
Fig. 4. Images of the multifocal illumination output of the three beam shapers, colored to represent quantitative variation. The three rows display the variation in intensity, pitch (spacing between points), and point width, respectively, with each column a different beam shaper. Scale bar, 1 mm.

Tables (3)

Tables Icon

Table 1. Overview and qualitative evaluation of hardware flat-fielding methods. €: <1k, €€: 1k-5k, €€€: >10k.

Tables Icon

Table 2. Specifications of the flat-fielding systems.

Tables Icon

Table 3. Summary of results. Results in bold indicate the best quantitative performance, where applicable. NSF: non-spatially-filtered, SF: spatially-filtered, MF: multifocal.