Abstract

Rapid increase in interest and applications of through-focus (TF) or volumetric type of optical imaging in biology and other areas has resulted in the development of several TF image collection methods. Achieving quantitative results from images requires standardization and optimization of image acquisition protocols. Several standardization protocols are available for conventional optical microscopy where a best-focus image is used, but to date, rigorous testing protocols do not exist for TF optical imaging. In this paper, we present a method to determine the fidelity of the TF optical data using the TF scanning optical microscopy images.

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  50. F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).
  51. R. K. Attota, “Step beyond Kohler illumination analysis for far-field quantitative imaging: angular illumination asymmetry (ANILAS) maps,” Opt. Express 24(20), 22616–22627 (2016).
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2018 (4)

R. K. Attota, “Through-focus or volumetric type of optical imaging methods: a review,” J. Biomed. Opt. 23(7), 070901 (2018).

A. Azaripour, T. Lagerweij, C. Scharfbillig, A. E. Jadczak, B. V. Swaan, M. Molenaar, R. V. Waal, K. Kielbassa, W. Tigchelaar, D. I. Picavet, A. Jonker, E. M. L. Hendrikx, V. V. V. Hira, M. Khurshed, and C. J. F. V. Noorden, “Three-dimensional histochemistry and imaging of human gingiva,” Sci. Rep. 8(1), 1647 (2018).
[Crossref] [PubMed]

S. W. Park, G. Park, Y. Kim, J. H. Cho, J. Lee, and H. Kim, “Through-focus scanning optical microscopy with the Fourier modal method,” Opt. Express 26(9), 11649–11657 (2018).
[Crossref] [PubMed]

E. Agocs and R. K. Attota, “Enhancing optical microscopy illumination to enable quantitative imaging,” Sci. Rep. 8(1), 4782 (2018).
[Crossref] [PubMed]

2017 (4)

P. P. Zhao, C. Ataman, and H. Zappe, “Miniaturized variable-focus objective employing a liquid-filled tunable aspherical lens,” Opt. Eng. 56(10), 1 (2017).
[Crossref]

M. Žurauskas, O. Barnstedt, M. Frade-Rodriguez, S. Waddell, and M. J. Booth, “Rapid adaptive remote focusing microscope for sensing of volumetric neural activity,” Biomed. Opt. Express 8(10), 4369–4379 (2017).
[Crossref] [PubMed]

A. von Diezmann, Y. Shechtman, and W. E. Moerner, “Three-Dimensional Localization of Single Molecules for Super-Resolution Imaging and Single-Particle Tracking,” Chem. Rev. 117(11), 7244–7275 (2017).
[Crossref] [PubMed]

R. K. Attota and H. Park, “Optical microscope illumination analysis using through-focus scanning optical microscopy,” Opt. Lett. 42(12), 2306–2309 (2017).
[Crossref] [PubMed]

2016 (9)

R. K. Attota, P. Weck, J. A. Kramar, B. Bunday, and V. Vartanian, “Feasibility study on 3-D shape analysis of high-aspect-ratio features using through-focus scanning optical microscopy,” Opt. Express 24(15), 16574–16585 (2016).
[Crossref] [PubMed]

R. Attota, “Noise analysis for through-focus scanning optical microscopy,” Opt. Lett. 41(4), 745–748 (2016).
[Crossref] [PubMed]

N. Ji, J. Freeman, and S. L. Smith, “Technologies for imaging neural activity in large volumes,” Nat. Neurosci. 19(9), 1154–1164 (2016).
[Crossref] [PubMed]

J. H. Lee, J. H. Park, D. Jeong, E. J. Shin, and C. Park, “Tip/tilt-compensated through-focus scanning optical microscopy,” Proc. SPIE 10023, 100230P (2016).
[Crossref]

S. Abrahamsson, R. Ilic, J. Wisniewski, B. Mehl, L. Yu, L. Chen, M. Davanco, L. Oudjedi, J. B. Fiche, B. Hajj, X. Jin, J. Pulupa, C. Cho, M. Mir, M. El Beheiry, X. Darzacq, M. Nollmann, M. Dahan, C. Wu, T. Lionnet, J. A. Liddle, and C. I. Bargmann, “Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging,” Biomed. Opt. Express 7(3), 855–869 (2016).
[Crossref] [PubMed]

R. K. Attota, “Step beyond Kohler illumination analysis for far-field quantitative imaging: angular illumination asymmetry (ANILAS) maps,” Opt. Express 24(20), 22616–22627 (2016).
[Crossref] [PubMed]

R. Attota and J. Kramar, “Optimizing noise for defect analysis with through-focus scanning optical microscopy,” Proc SPIE Int Soc Opt Eng 9778, 977811 (2016).
[Crossref] [PubMed]

K. I. Mortensen and H. Flyvbjerg, “Calibration-on-the-spot”: How to calibrate an EMCCD camera from its images,” Sci. Rep. 628680 (2016).

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, 705–708 (2016).

2015 (3)

2014 (4)

R. Attota and R. G. Dixson, “Resolving three-dimensional shape of sub-50 nm wide lines with nanometer-scale sensitivity using conventional optical microscopes,” Appl. Phys. Lett. 105(4), 043101 (2014).
[Crossref]

A. Tahmasbi, S. Ram, J. Chao, A. V. Abraham, F. W. Tang, E. Sally Ward, and R. J. Ober, “Designing the focal plane spacing for multifocal plane microscopy,” Opt. Express 22(14), 16706–16721 (2014).
[Crossref] [PubMed]

M. Ryabko, S. Koptyaev, A. Shcherbakov, A. Lantsov, and S. Y. Oh, “Motion-free all optical inspection system for nanoscale topology control,” Opt. Express 22(12), 14958–14963 (2014).
[Crossref] [PubMed]

M. Halter, E. Bier, P. C. DeRose, G. A. Cooksey, S. J. Choquette, A. L. Plant, and J. T. Elliott, “An Automated Protocol for Performance Benchmarking a Widefield Fluorescence Microscope,” Cytometry A 85(11), 978–985 (2014).
[Crossref] [PubMed]

2013 (6)

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).

S. Usha, P. V. Shashikumar, G. C. Mohankumar, and S. S. Rao, “Through Focus Optical Imaging Technique To Analyze Variations In Nano-Scale Indents,” Int. J. Eng. Res. Technol. 2, 18 (2013).

M. V. Ryabko, S. N. Koptyaev, A. V. Shcherbakov, A. D. Lantsov, and S. Y. Oh, “Method for optical inspection of nanoscale objects based upon analysis of their defocused images and features of its practical implementation,” Opt. Express 21(21), 24483–24489 (2013).
[Crossref] [PubMed]

S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
[Crossref] [PubMed]

Z. Gan, S. Ram, R. J. Ober, and E. S. Ward, “Using multifocal plane microscopy to reveal novel trafficking processes in the recycling pathway,” J. Cell Sci. 126(5), 1176–1188 (2013).
[Crossref] [PubMed]

R. Attota, B. Bunday, and V. Vartanian, “Critical dimension metrology by through-focus scanning optical microscopy beyond the 22 nm node,” Appl. Phys. Lett. 102(22), 222107 (2013).
[Crossref]

2012 (1)

G. Katona, G. Szalay, P. Maák, A. Kaszás, M. Veress, D. Hillier, B. Chiovini, E. S. Vizi, B. Roska, and B. Rózsa, “Fast two-photon in vivo imaging with three-dimensional random-access scanning in large tissue volumes,” Nat. Methods 9(2), 201–208 (2012).
[Crossref] [PubMed]

2011 (4)

R. Attota and R. Silver, “Nanometrology using a through-focus scanning optical microscopy method,” Meas. Sci. Technol. 22(2), 024002 (2011).
[Crossref]

R. Attota, R. G. Dixson, J. A. Kramar, J. E. Potzick, A. E. Vladar, B. Bunday, E. Novak, and A. Rudack, “TSOM Method for Semiconductor Metrology,” Proc. SPIE 7971, 79710T (2011).
[Crossref]

J. M. Gineste, P. Macko, E. A. Patterson, and M. P. Whelan, “Three-dimensional automated nanoparticle tracking using Mie scattering in an optical microscope,” J. Microsc. 243(2), 172–178 (2011).
[Crossref] [PubMed]

K. M. Kedziora, J. H. M. Prehn, J. Dobrucki, and T. Bernas, “Method of calibration of a fluorescence microscope for quantitative studies,” J. Microsc. 244(1), 101–111 (2011).
[Crossref] [PubMed]

2010 (1)

2008 (2)

E. J. Botcherby, R. Juškaitis, M. J. Booth, and T. Wilson, “An optical technique for remote focusing in microscopy,” Opt. Commun. 281(4), 880–887 (2008).
[Crossref]

R. Attota, T. A. Germer, and R. M. Silver, “Through-focus scanning-optical-microscope imaging method for nanoscale dimensional analysis,” Opt. Lett. 33(17), 1990–1992 (2008).
[Crossref] [PubMed]

2007 (3)

W. Göbel, B. M. Kampa, and F. Helmchen, “Imaging cellular network dynamics in three dimensions using fast 3D laser scanning,” Nat. Methods 4(1), 73–79 (2007).
[Crossref] [PubMed]

S. S. Kou and C. J. R. Sheppard, “Imaging in digital holographic microscopy,” Opt. Express 15(21), 13640–13648 (2007).
[Crossref] [PubMed]

P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, “Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(14), 5889–5894 (2007).
[Crossref] [PubMed]

2006 (2)

M. Levoy, R. Ng, A. Adams, M. Footer, and M. Horowitz, “Light field microscopy,” ACM Trans. Graph. 25(3), 924–934 (2006).
[Crossref]

R. M. Zucker, “Quality assessment of confocal microscopy slide-based systems: Instability,” Cytometry A 69A(7), 677–690 (2006).
[Crossref] [PubMed]

2004 (2)

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical Sectioning Deep Inside live Embryos by Selective Plane Illumination Microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

P. Prabhat, S. Ram, E. S. Ward, and R. J. Ober, “Simultaneous imaging of different focal planes in fluorescence microscopy for the study of cellular dynamics in three dimensions,” IEEE Trans. Nanobioscience 3(4), 237–242 (2004).
[Crossref] [PubMed]

2001 (2)

A. Kaplan, N. Friedman, and N. Davidson, “Acousto-optic lens with very fast focus scanning,” Opt. Lett. 26(14), 1078–1080 (2001).
[Crossref] [PubMed]

R. M. Zucker and O. Price, “Evaluation of confocal microscopy system performance,” Cytometry 44(4), 273–294 (2001).
[Crossref] [PubMed]

Abraham, A. V.

Abrahamsson, S.

S. Abrahamsson, R. Ilic, J. Wisniewski, B. Mehl, L. Yu, L. Chen, M. Davanco, L. Oudjedi, J. B. Fiche, B. Hajj, X. Jin, J. Pulupa, C. Cho, M. Mir, M. El Beheiry, X. Darzacq, M. Nollmann, M. Dahan, C. Wu, T. Lionnet, J. A. Liddle, and C. I. Bargmann, “Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging,” Biomed. Opt. Express 7(3), 855–869 (2016).
[Crossref] [PubMed]

S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
[Crossref] [PubMed]

Adams, A.

M. Levoy, R. Ng, A. Adams, M. Footer, and M. Horowitz, “Light field microscopy,” ACM Trans. Graph. 25(3), 924–934 (2006).
[Crossref]

Agard, D. A.

S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
[Crossref] [PubMed]

Agocs, E.

E. Agocs and R. K. Attota, “Enhancing optical microscopy illumination to enable quantitative imaging,” Sci. Rep. 8(1), 4782 (2018).
[Crossref] [PubMed]

Arceo, A.

A. Arceo, B. Bunday, and R. Attota, “Use of TSOM for sub-11 nm node pattern defect detection and HAR features,” Metrology, Inspection, and Process Control for Microlithography Xxvii8681, 86812G (2013).

Archetti, A.

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, 705–708 (2016).

Ataman, C.

P. P. Zhao, C. Ataman, and H. Zappe, “Miniaturized variable-focus objective employing a liquid-filled tunable aspherical lens,” Opt. Eng. 56(10), 1 (2017).
[Crossref]

Attota, R.

R. Attota and J. Kramar, “Optimizing noise for defect analysis with through-focus scanning optical microscopy,” Proc SPIE Int Soc Opt Eng 9778, 977811 (2016).
[Crossref] [PubMed]

R. Attota, “Noise analysis for through-focus scanning optical microscopy,” Opt. Lett. 41(4), 745–748 (2016).
[Crossref] [PubMed]

H. Kang, R. Attota, V. Tondare, A. E. Vladar, and P. Kavuri, “A method to determine the number of nanoparticles in a cluster using conventional optical microscopes,” Appl. Phys. Lett. 107(10), 103106 (2015).
[Crossref]

R. Attota and R. G. Dixson, “Resolving three-dimensional shape of sub-50 nm wide lines with nanometer-scale sensitivity using conventional optical microscopes,” Appl. Phys. Lett. 105(4), 043101 (2014).
[Crossref]

R. Attota, B. Bunday, and V. Vartanian, “Critical dimension metrology by through-focus scanning optical microscopy beyond the 22 nm node,” Appl. Phys. Lett. 102(22), 222107 (2013).
[Crossref]

R. Attota, R. G. Dixson, J. A. Kramar, J. E. Potzick, A. E. Vladar, B. Bunday, E. Novak, and A. Rudack, “TSOM Method for Semiconductor Metrology,” Proc. SPIE 7971, 79710T (2011).
[Crossref]

R. Attota and R. Silver, “Nanometrology using a through-focus scanning optical microscopy method,” Meas. Sci. Technol. 22(2), 024002 (2011).
[Crossref]

R. Attota, T. A. Germer, and R. M. Silver, “Through-focus scanning-optical-microscope imaging method for nanoscale dimensional analysis,” Opt. Lett. 33(17), 1990–1992 (2008).
[Crossref] [PubMed]

A. Arceo, B. Bunday, and R. Attota, “Use of TSOM for sub-11 nm node pattern defect detection and HAR features,” Metrology, Inspection, and Process Control for Microlithography Xxvii8681, 86812G (2013).

R. Attota, R. M. Silver, M. Stocker, E. Marx, J. Jun, M. Davidson, and R. Larrabee, “A new method to enhance overlay tool performance,” Metrology, Inspection, and Process Control for Microlithography Xvii5038, 428–436 (2003).

Attota, R. K.

Azaripour, A.

A. Azaripour, T. Lagerweij, C. Scharfbillig, A. E. Jadczak, B. V. Swaan, M. Molenaar, R. V. Waal, K. Kielbassa, W. Tigchelaar, D. I. Picavet, A. Jonker, E. M. L. Hendrikx, V. V. V. Hira, M. Khurshed, and C. J. F. V. Noorden, “Three-dimensional histochemistry and imaging of human gingiva,” Sci. Rep. 8(1), 1647 (2018).
[Crossref] [PubMed]

Baird, M. A.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).

Bargmann, C. I.

S. Abrahamsson, R. Ilic, J. Wisniewski, B. Mehl, L. Yu, L. Chen, M. Davanco, L. Oudjedi, J. B. Fiche, B. Hajj, X. Jin, J. Pulupa, C. Cho, M. Mir, M. El Beheiry, X. Darzacq, M. Nollmann, M. Dahan, C. Wu, T. Lionnet, J. A. Liddle, and C. I. Bargmann, “Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging,” Biomed. Opt. Express 7(3), 855–869 (2016).
[Crossref] [PubMed]

S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
[Crossref] [PubMed]

Barnstedt, O.

Bernas, T.

K. M. Kedziora, J. H. M. Prehn, J. Dobrucki, and T. Bernas, “Method of calibration of a fluorescence microscope for quantitative studies,” J. Microsc. 244(1), 101–111 (2011).
[Crossref] [PubMed]

Bewersdorf, J.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).

Bier, E.

M. Halter, E. Bier, P. C. DeRose, G. A. Cooksey, S. J. Choquette, A. L. Plant, and J. T. Elliott, “An Automated Protocol for Performance Benchmarking a Widefield Fluorescence Microscope,” Cytometry A 85(11), 978–985 (2014).
[Crossref] [PubMed]

Booth, M. J.

Botcherby, E. J.

E. J. Botcherby, R. Juškaitis, M. J. Booth, and T. Wilson, “An optical technique for remote focusing in microscopy,” Opt. Commun. 281(4), 880–887 (2008).
[Crossref]

Bunday, B.

R. K. Attota, P. Weck, J. A. Kramar, B. Bunday, and V. Vartanian, “Feasibility study on 3-D shape analysis of high-aspect-ratio features using through-focus scanning optical microscopy,” Opt. Express 24(15), 16574–16585 (2016).
[Crossref] [PubMed]

R. Attota, B. Bunday, and V. Vartanian, “Critical dimension metrology by through-focus scanning optical microscopy beyond the 22 nm node,” Appl. Phys. Lett. 102(22), 222107 (2013).
[Crossref]

R. Attota, R. G. Dixson, J. A. Kramar, J. E. Potzick, A. E. Vladar, B. Bunday, E. Novak, and A. Rudack, “TSOM Method for Semiconductor Metrology,” Proc. SPIE 7971, 79710T (2011).
[Crossref]

A. Arceo, B. Bunday, and R. Attota, “Use of TSOM for sub-11 nm node pattern defect detection and HAR features,” Metrology, Inspection, and Process Control for Microlithography Xxvii8681, 86812G (2013).

Chao, J.

A. Tahmasbi, S. Ram, J. Chao, A. V. Abraham, F. W. Tang, E. Sally Ward, and R. J. Ober, “Designing the focal plane spacing for multifocal plane microscopy,” Opt. Express 22(14), 16706–16721 (2014).
[Crossref] [PubMed]

P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, “Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(14), 5889–5894 (2007).
[Crossref] [PubMed]

Chen, J.

S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
[Crossref] [PubMed]

Chen, L.

Chiovini, B.

G. Katona, G. Szalay, P. Maák, A. Kaszás, M. Veress, D. Hillier, B. Chiovini, E. S. Vizi, B. Roska, and B. Rózsa, “Fast two-photon in vivo imaging with three-dimensional random-access scanning in large tissue volumes,” Nat. Methods 9(2), 201–208 (2012).
[Crossref] [PubMed]

Cho, C.

Cho, J. H.

Choquette, S. J.

M. Halter, E. Bier, P. C. DeRose, G. A. Cooksey, S. J. Choquette, A. L. Plant, and J. T. Elliott, “An Automated Protocol for Performance Benchmarking a Widefield Fluorescence Microscope,” Cytometry A 85(11), 978–985 (2014).
[Crossref] [PubMed]

Cooksey, G. A.

M. Halter, E. Bier, P. C. DeRose, G. A. Cooksey, S. J. Choquette, A. L. Plant, and J. T. Elliott, “An Automated Protocol for Performance Benchmarking a Widefield Fluorescence Microscope,” Cytometry A 85(11), 978–985 (2014).
[Crossref] [PubMed]

Dahan, M.

S. Abrahamsson, R. Ilic, J. Wisniewski, B. Mehl, L. Yu, L. Chen, M. Davanco, L. Oudjedi, J. B. Fiche, B. Hajj, X. Jin, J. Pulupa, C. Cho, M. Mir, M. El Beheiry, X. Darzacq, M. Nollmann, M. Dahan, C. Wu, T. Lionnet, J. A. Liddle, and C. I. Bargmann, “Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging,” Biomed. Opt. Express 7(3), 855–869 (2016).
[Crossref] [PubMed]

S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
[Crossref] [PubMed]

Darzacq, C. D.

S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
[Crossref] [PubMed]

Darzacq, X.

S. Abrahamsson, R. Ilic, J. Wisniewski, B. Mehl, L. Yu, L. Chen, M. Davanco, L. Oudjedi, J. B. Fiche, B. Hajj, X. Jin, J. Pulupa, C. Cho, M. Mir, M. El Beheiry, X. Darzacq, M. Nollmann, M. Dahan, C. Wu, T. Lionnet, J. A. Liddle, and C. I. Bargmann, “Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging,” Biomed. Opt. Express 7(3), 855–869 (2016).
[Crossref] [PubMed]

S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
[Crossref] [PubMed]

Davanco, M.

Davidson, M.

R. Attota, R. M. Silver, M. Stocker, E. Marx, J. Jun, M. Davidson, and R. Larrabee, “A new method to enhance overlay tool performance,” Metrology, Inspection, and Process Control for Microlithography Xvii5038, 428–436 (2003).

Davidson, M. W.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).

Davidson, N.

Del Bene, F.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical Sectioning Deep Inside live Embryos by Selective Plane Illumination Microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

DeRose, P. C.

M. Halter, E. Bier, P. C. DeRose, G. A. Cooksey, S. J. Choquette, A. L. Plant, and J. T. Elliott, “An Automated Protocol for Performance Benchmarking a Widefield Fluorescence Microscope,” Cytometry A 85(11), 978–985 (2014).
[Crossref] [PubMed]

Diezmann, A.

Dixson, R. G.

R. Attota and R. G. Dixson, “Resolving three-dimensional shape of sub-50 nm wide lines with nanometer-scale sensitivity using conventional optical microscopes,” Appl. Phys. Lett. 105(4), 043101 (2014).
[Crossref]

R. Attota, R. G. Dixson, J. A. Kramar, J. E. Potzick, A. E. Vladar, B. Bunday, E. Novak, and A. Rudack, “TSOM Method for Semiconductor Metrology,” Proc. SPIE 7971, 79710T (2011).
[Crossref]

Dobrucki, J.

K. M. Kedziora, J. H. M. Prehn, J. Dobrucki, and T. Bernas, “Method of calibration of a fluorescence microscope for quantitative studies,” J. Microsc. 244(1), 101–111 (2011).
[Crossref] [PubMed]

Douglass, K. M.

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, 705–708 (2016).

Duim, W. C.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).

El Beheiry, M.

Elliott, J. T.

M. Halter, E. Bier, P. C. DeRose, G. A. Cooksey, S. J. Choquette, A. L. Plant, and J. T. Elliott, “An Automated Protocol for Performance Benchmarking a Widefield Fluorescence Microscope,” Cytometry A 85(11), 978–985 (2014).
[Crossref] [PubMed]

Fiche, J. B.

Flyvbjerg, H.

K. I. Mortensen and H. Flyvbjerg, “Calibration-on-the-spot”: How to calibrate an EMCCD camera from its images,” Sci. Rep. 628680 (2016).

Footer, M.

M. Levoy, R. Ng, A. Adams, M. Footer, and M. Horowitz, “Light field microscopy,” ACM Trans. Graph. 25(3), 924–934 (2006).
[Crossref]

Frade-Rodriguez, M.

Freeman, J.

N. Ji, J. Freeman, and S. L. Smith, “Technologies for imaging neural activity in large volumes,” Nat. Neurosci. 19(9), 1154–1164 (2016).
[Crossref] [PubMed]

Friedman, N.

Gan, Z.

Z. Gan, S. Ram, R. J. Ober, and E. S. Ward, “Using multifocal plane microscopy to reveal novel trafficking processes in the recycling pathway,” J. Cell Sci. 126(5), 1176–1188 (2013).
[Crossref] [PubMed]

P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, “Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(14), 5889–5894 (2007).
[Crossref] [PubMed]

Germer, T. A.

Gibbons, S.

P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, “Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(14), 5889–5894 (2007).
[Crossref] [PubMed]

Gineste, J. M.

J. M. Gineste, P. Macko, E. A. Patterson, and M. P. Whelan, “Three-dimensional automated nanoparticle tracking using Mie scattering in an optical microscope,” J. Microsc. 243(2), 172–178 (2011).
[Crossref] [PubMed]

Göbel, W.

W. Göbel, B. M. Kampa, and F. Helmchen, “Imaging cellular network dynamics in three dimensions using fast 3D laser scanning,” Nat. Methods 4(1), 73–79 (2007).
[Crossref] [PubMed]

Gustafsson, M. G. L.

S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
[Crossref] [PubMed]

Hajj, B.

S. Abrahamsson, R. Ilic, J. Wisniewski, B. Mehl, L. Yu, L. Chen, M. Davanco, L. Oudjedi, J. B. Fiche, B. Hajj, X. Jin, J. Pulupa, C. Cho, M. Mir, M. El Beheiry, X. Darzacq, M. Nollmann, M. Dahan, C. Wu, T. Lionnet, J. A. Liddle, and C. I. Bargmann, “Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging,” Biomed. Opt. Express 7(3), 855–869 (2016).
[Crossref] [PubMed]

S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
[Crossref] [PubMed]

Halter, M.

M. Halter, E. Bier, P. C. DeRose, G. A. Cooksey, S. J. Choquette, A. L. Plant, and J. T. Elliott, “An Automated Protocol for Performance Benchmarking a Widefield Fluorescence Microscope,” Cytometry A 85(11), 978–985 (2014).
[Crossref] [PubMed]

Hartwich, T. M. P.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).

Helmchen, F.

W. Göbel, B. M. Kampa, and F. Helmchen, “Imaging cellular network dynamics in three dimensions using fast 3D laser scanning,” Nat. Methods 4(1), 73–79 (2007).
[Crossref] [PubMed]

Hendrikx, E. M. L.

A. Azaripour, T. Lagerweij, C. Scharfbillig, A. E. Jadczak, B. V. Swaan, M. Molenaar, R. V. Waal, K. Kielbassa, W. Tigchelaar, D. I. Picavet, A. Jonker, E. M. L. Hendrikx, V. V. V. Hira, M. Khurshed, and C. J. F. V. Noorden, “Three-dimensional histochemistry and imaging of human gingiva,” Sci. Rep. 8(1), 1647 (2018).
[Crossref] [PubMed]

Hillier, D.

G. Katona, G. Szalay, P. Maák, A. Kaszás, M. Veress, D. Hillier, B. Chiovini, E. S. Vizi, B. Roska, and B. Rózsa, “Fast two-photon in vivo imaging with three-dimensional random-access scanning in large tissue volumes,” Nat. Methods 9(2), 201–208 (2012).
[Crossref] [PubMed]

Hira, V. V. V.

A. Azaripour, T. Lagerweij, C. Scharfbillig, A. E. Jadczak, B. V. Swaan, M. Molenaar, R. V. Waal, K. Kielbassa, W. Tigchelaar, D. I. Picavet, A. Jonker, E. M. L. Hendrikx, V. V. V. Hira, M. Khurshed, and C. J. F. V. Noorden, “Three-dimensional histochemistry and imaging of human gingiva,” Sci. Rep. 8(1), 1647 (2018).
[Crossref] [PubMed]

Horowitz, M.

M. Levoy, R. Ng, A. Adams, M. Footer, and M. Horowitz, “Light field microscopy,” ACM Trans. Graph. 25(3), 924–934 (2006).
[Crossref]

Huang, F.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).

Huisken, J.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical Sectioning Deep Inside live Embryos by Selective Plane Illumination Microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Ilic, R.

Isago, R.

Jadczak, A. E.

A. Azaripour, T. Lagerweij, C. Scharfbillig, A. E. Jadczak, B. V. Swaan, M. Molenaar, R. V. Waal, K. Kielbassa, W. Tigchelaar, D. I. Picavet, A. Jonker, E. M. L. Hendrikx, V. V. V. Hira, M. Khurshed, and C. J. F. V. Noorden, “Three-dimensional histochemistry and imaging of human gingiva,” Sci. Rep. 8(1), 1647 (2018).
[Crossref] [PubMed]

Jeong, D.

J. H. Lee, J. H. Park, D. Jeong, E. J. Shin, and C. Park, “Tip/tilt-compensated through-focus scanning optical microscopy,” Proc. SPIE 10023, 100230P (2016).
[Crossref]

Ji, N.

N. Ji, J. Freeman, and S. L. Smith, “Technologies for imaging neural activity in large volumes,” Nat. Neurosci. 19(9), 1154–1164 (2016).
[Crossref] [PubMed]

Jin, X.

Jonker, A.

A. Azaripour, T. Lagerweij, C. Scharfbillig, A. E. Jadczak, B. V. Swaan, M. Molenaar, R. V. Waal, K. Kielbassa, W. Tigchelaar, D. I. Picavet, A. Jonker, E. M. L. Hendrikx, V. V. V. Hira, M. Khurshed, and C. J. F. V. Noorden, “Three-dimensional histochemistry and imaging of human gingiva,” Sci. Rep. 8(1), 1647 (2018).
[Crossref] [PubMed]

Jun, J.

R. Attota, R. M. Silver, M. Stocker, E. Marx, J. Jun, M. Davidson, and R. Larrabee, “A new method to enhance overlay tool performance,” Metrology, Inspection, and Process Control for Microlithography Xvii5038, 428–436 (2003).

Juškaitis, R.

E. J. Botcherby, R. Juškaitis, M. J. Booth, and T. Wilson, “An optical technique for remote focusing in microscopy,” Opt. Commun. 281(4), 880–887 (2008).
[Crossref]

Kampa, B. M.

W. Göbel, B. M. Kampa, and F. Helmchen, “Imaging cellular network dynamics in three dimensions using fast 3D laser scanning,” Nat. Methods 4(1), 73–79 (2007).
[Crossref] [PubMed]

Kang, H.

H. Kang, R. Attota, V. Tondare, A. E. Vladar, and P. Kavuri, “A method to determine the number of nanoparticles in a cluster using conventional optical microscopes,” Appl. Phys. Lett. 107(10), 103106 (2015).
[Crossref]

Kaplan, A.

Kaszás, A.

G. Katona, G. Szalay, P. Maák, A. Kaszás, M. Veress, D. Hillier, B. Chiovini, E. S. Vizi, B. Roska, and B. Rózsa, “Fast two-photon in vivo imaging with three-dimensional random-access scanning in large tissue volumes,” Nat. Methods 9(2), 201–208 (2012).
[Crossref] [PubMed]

Katona, G.

G. Katona, G. Szalay, P. Maák, A. Kaszás, M. Veress, D. Hillier, B. Chiovini, E. S. Vizi, B. Roska, and B. Rózsa, “Fast two-photon in vivo imaging with three-dimensional random-access scanning in large tissue volumes,” Nat. Methods 9(2), 201–208 (2012).
[Crossref] [PubMed]

Katsov, A. Y.

S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
[Crossref] [PubMed]

Kavuri, P.

H. Kang, R. Attota, V. Tondare, A. E. Vladar, and P. Kavuri, “A method to determine the number of nanoparticles in a cluster using conventional optical microscopes,” Appl. Phys. Lett. 107(10), 103106 (2015).
[Crossref]

Kedziora, K. M.

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A. Azaripour, T. Lagerweij, C. Scharfbillig, A. E. Jadczak, B. V. Swaan, M. Molenaar, R. V. Waal, K. Kielbassa, W. Tigchelaar, D. I. Picavet, A. Jonker, E. M. L. Hendrikx, V. V. V. Hira, M. Khurshed, and C. J. F. V. Noorden, “Three-dimensional histochemistry and imaging of human gingiva,” Sci. Rep. 8(1), 1647 (2018).
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A. Azaripour, T. Lagerweij, C. Scharfbillig, A. E. Jadczak, B. V. Swaan, M. Molenaar, R. V. Waal, K. Kielbassa, W. Tigchelaar, D. I. Picavet, A. Jonker, E. M. L. Hendrikx, V. V. V. Hira, M. Khurshed, and C. J. F. V. Noorden, “Three-dimensional histochemistry and imaging of human gingiva,” Sci. Rep. 8(1), 1647 (2018).
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Koptyaev, S. N.

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R. Attota and J. Kramar, “Optimizing noise for defect analysis with through-focus scanning optical microscopy,” Proc SPIE Int Soc Opt Eng 9778, 977811 (2016).
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Kramar, J. A.

R. K. Attota, P. Weck, J. A. Kramar, B. Bunday, and V. Vartanian, “Feasibility study on 3-D shape analysis of high-aspect-ratio features using through-focus scanning optical microscopy,” Opt. Express 24(15), 16574–16585 (2016).
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R. Attota, R. G. Dixson, J. A. Kramar, J. E. Potzick, A. E. Vladar, B. Bunday, E. Novak, and A. Rudack, “TSOM Method for Semiconductor Metrology,” Proc. SPIE 7971, 79710T (2011).
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A. Azaripour, T. Lagerweij, C. Scharfbillig, A. E. Jadczak, B. V. Swaan, M. Molenaar, R. V. Waal, K. Kielbassa, W. Tigchelaar, D. I. Picavet, A. Jonker, E. M. L. Hendrikx, V. V. V. Hira, M. Khurshed, and C. J. F. V. Noorden, “Three-dimensional histochemistry and imaging of human gingiva,” Sci. Rep. 8(1), 1647 (2018).
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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, 705–708 (2016).

Lantsov, A.

Lantsov, A. D.

Larrabee, R.

R. Attota, R. M. Silver, M. Stocker, E. Marx, J. Jun, M. Davidson, and R. Larrabee, “A new method to enhance overlay tool performance,” Metrology, Inspection, and Process Control for Microlithography Xvii5038, 428–436 (2003).

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Lee, J. H.

J. H. Lee, J. H. Park, D. Jeong, E. J. Shin, and C. Park, “Tip/tilt-compensated through-focus scanning optical microscopy,” Proc. SPIE 10023, 100230P (2016).
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Long, J. J.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).

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G. Katona, G. Szalay, P. Maák, A. Kaszás, M. Veress, D. Hillier, B. Chiovini, E. S. Vizi, B. Roska, and B. Rózsa, “Fast two-photon in vivo imaging with three-dimensional random-access scanning in large tissue volumes,” Nat. Methods 9(2), 201–208 (2012).
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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, 705–708 (2016).

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R. Attota, R. M. Silver, M. Stocker, E. Marx, J. Jun, M. Davidson, and R. Larrabee, “A new method to enhance overlay tool performance,” Metrology, Inspection, and Process Control for Microlithography Xvii5038, 428–436 (2003).

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S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
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A. von Diezmann, Y. Shechtman, and W. E. Moerner, “Three-Dimensional Localization of Single Molecules for Super-Resolution Imaging and Single-Particle Tracking,” Chem. Rev. 117(11), 7244–7275 (2017).
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A. Azaripour, T. Lagerweij, C. Scharfbillig, A. E. Jadczak, B. V. Swaan, M. Molenaar, R. V. Waal, K. Kielbassa, W. Tigchelaar, D. I. Picavet, A. Jonker, E. M. L. Hendrikx, V. V. V. Hira, M. Khurshed, and C. J. F. V. Noorden, “Three-dimensional histochemistry and imaging of human gingiva,” Sci. Rep. 8(1), 1647 (2018).
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F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).

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S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
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F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).

Nakamura, K.

Ng, R.

M. Levoy, R. Ng, A. Adams, M. Footer, and M. Horowitz, “Light field microscopy,” ACM Trans. Graph. 25(3), 924–934 (2006).
[Crossref]

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Noorden, C. J. F. V.

A. Azaripour, T. Lagerweij, C. Scharfbillig, A. E. Jadczak, B. V. Swaan, M. Molenaar, R. V. Waal, K. Kielbassa, W. Tigchelaar, D. I. Picavet, A. Jonker, E. M. L. Hendrikx, V. V. V. Hira, M. Khurshed, and C. J. F. V. Noorden, “Three-dimensional histochemistry and imaging of human gingiva,” Sci. Rep. 8(1), 1647 (2018).
[Crossref] [PubMed]

Novak, E.

R. Attota, R. G. Dixson, J. A. Kramar, J. E. Potzick, A. E. Vladar, B. Bunday, E. Novak, and A. Rudack, “TSOM Method for Semiconductor Metrology,” Proc. SPIE 7971, 79710T (2011).
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A. Tahmasbi, S. Ram, J. Chao, A. V. Abraham, F. W. Tang, E. Sally Ward, and R. J. Ober, “Designing the focal plane spacing for multifocal plane microscopy,” Opt. Express 22(14), 16706–16721 (2014).
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Z. Gan, S. Ram, R. J. Ober, and E. S. Ward, “Using multifocal plane microscopy to reveal novel trafficking processes in the recycling pathway,” J. Cell Sci. 126(5), 1176–1188 (2013).
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P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, “Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(14), 5889–5894 (2007).
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P. Prabhat, S. Ram, E. S. Ward, and R. J. Ober, “Simultaneous imaging of different focal planes in fluorescence microscopy for the study of cellular dynamics in three dimensions,” IEEE Trans. Nanobioscience 3(4), 237–242 (2004).
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Oudjedi, L.

Park, C.

J. H. Lee, J. H. Park, D. Jeong, E. J. Shin, and C. Park, “Tip/tilt-compensated through-focus scanning optical microscopy,” Proc. SPIE 10023, 100230P (2016).
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Park, H.

Park, J. H.

J. H. Lee, J. H. Park, D. Jeong, E. J. Shin, and C. Park, “Tip/tilt-compensated through-focus scanning optical microscopy,” Proc. SPIE 10023, 100230P (2016).
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Park, S. W.

Patterson, E. A.

J. M. Gineste, P. Macko, E. A. Patterson, and M. P. Whelan, “Three-dimensional automated nanoparticle tracking using Mie scattering in an optical microscope,” J. Microsc. 243(2), 172–178 (2011).
[Crossref] [PubMed]

Picavet, D. I.

A. Azaripour, T. Lagerweij, C. Scharfbillig, A. E. Jadczak, B. V. Swaan, M. Molenaar, R. V. Waal, K. Kielbassa, W. Tigchelaar, D. I. Picavet, A. Jonker, E. M. L. Hendrikx, V. V. V. Hira, M. Khurshed, and C. J. F. V. Noorden, “Three-dimensional histochemistry and imaging of human gingiva,” Sci. Rep. 8(1), 1647 (2018).
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R. Attota, R. G. Dixson, J. A. Kramar, J. E. Potzick, A. E. Vladar, B. Bunday, E. Novak, and A. Rudack, “TSOM Method for Semiconductor Metrology,” Proc. SPIE 7971, 79710T (2011).
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P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, “Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(14), 5889–5894 (2007).
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P. Prabhat, S. Ram, E. S. Ward, and R. J. Ober, “Simultaneous imaging of different focal planes in fluorescence microscopy for the study of cellular dynamics in three dimensions,” IEEE Trans. Nanobioscience 3(4), 237–242 (2004).
[Crossref] [PubMed]

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K. M. Kedziora, J. H. M. Prehn, J. Dobrucki, and T. Bernas, “Method of calibration of a fluorescence microscope for quantitative studies,” J. Microsc. 244(1), 101–111 (2011).
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A. Tahmasbi, S. Ram, J. Chao, A. V. Abraham, F. W. Tang, E. Sally Ward, and R. J. Ober, “Designing the focal plane spacing for multifocal plane microscopy,” Opt. Express 22(14), 16706–16721 (2014).
[Crossref] [PubMed]

Z. Gan, S. Ram, R. J. Ober, and E. S. Ward, “Using multifocal plane microscopy to reveal novel trafficking processes in the recycling pathway,” J. Cell Sci. 126(5), 1176–1188 (2013).
[Crossref] [PubMed]

P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, “Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(14), 5889–5894 (2007).
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P. Prabhat, S. Ram, E. S. Ward, and R. J. Ober, “Simultaneous imaging of different focal planes in fluorescence microscopy for the study of cellular dynamics in three dimensions,” IEEE Trans. Nanobioscience 3(4), 237–242 (2004).
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S. Usha, P. V. Shashikumar, G. C. Mohankumar, and S. S. Rao, “Through Focus Optical Imaging Technique To Analyze Variations In Nano-Scale Indents,” Int. J. Eng. Res. Technol. 2, 18 (2013).

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F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).

Roska, B.

G. Katona, G. Szalay, P. Maák, A. Kaszás, M. Veress, D. Hillier, B. Chiovini, E. S. Vizi, B. Roska, and B. Rózsa, “Fast two-photon in vivo imaging with three-dimensional random-access scanning in large tissue volumes,” Nat. Methods 9(2), 201–208 (2012).
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G. Katona, G. Szalay, P. Maák, A. Kaszás, M. Veress, D. Hillier, B. Chiovini, E. S. Vizi, B. Roska, and B. Rózsa, “Fast two-photon in vivo imaging with three-dimensional random-access scanning in large tissue volumes,” Nat. Methods 9(2), 201–208 (2012).
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Rudack, A.

R. Attota, R. G. Dixson, J. A. Kramar, J. E. Potzick, A. E. Vladar, B. Bunday, E. Novak, and A. Rudack, “TSOM Method for Semiconductor Metrology,” Proc. SPIE 7971, 79710T (2011).
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Ryabko, M. V.

Sally Ward, E.

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A. Azaripour, T. Lagerweij, C. Scharfbillig, A. E. Jadczak, B. V. Swaan, M. Molenaar, R. V. Waal, K. Kielbassa, W. Tigchelaar, D. I. Picavet, A. Jonker, E. M. L. Hendrikx, V. V. V. Hira, M. Khurshed, and C. J. F. V. Noorden, “Three-dimensional histochemistry and imaging of human gingiva,” Sci. Rep. 8(1), 1647 (2018).
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S. Usha, P. V. Shashikumar, G. C. Mohankumar, and S. S. Rao, “Through Focus Optical Imaging Technique To Analyze Variations In Nano-Scale Indents,” Int. J. Eng. Res. Technol. 2, 18 (2013).

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Shcherbakov, A.

Shcherbakov, A. V.

Shechtman, Y.

A. von Diezmann, Y. Shechtman, and W. E. Moerner, “Three-Dimensional Localization of Single Molecules for Super-Resolution Imaging and Single-Particle Tracking,” Chem. Rev. 117(11), 7244–7275 (2017).
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Shin, E. J.

J. H. Lee, J. H. Park, D. Jeong, E. J. Shin, and C. Park, “Tip/tilt-compensated through-focus scanning optical microscopy,” Proc. SPIE 10023, 100230P (2016).
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Sieben, C.

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, 705–708 (2016).

Silver, R.

R. Attota and R. Silver, “Nanometrology using a through-focus scanning optical microscopy method,” Meas. Sci. Technol. 22(2), 024002 (2011).
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R. Attota, T. A. Germer, and R. M. Silver, “Through-focus scanning-optical-microscope imaging method for nanoscale dimensional analysis,” Opt. Lett. 33(17), 1990–1992 (2008).
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R. Attota, R. M. Silver, M. Stocker, E. Marx, J. Jun, M. Davidson, and R. Larrabee, “A new method to enhance overlay tool performance,” Metrology, Inspection, and Process Control for Microlithography Xvii5038, 428–436 (2003).

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N. Ji, J. Freeman, and S. L. Smith, “Technologies for imaging neural activity in large volumes,” Nat. Neurosci. 19(9), 1154–1164 (2016).
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S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
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S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
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J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical Sectioning Deep Inside live Embryos by Selective Plane Illumination Microscopy,” Science 305(5686), 1007–1009 (2004).
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Stocker, M.

R. Attota, R. M. Silver, M. Stocker, E. Marx, J. Jun, M. Davidson, and R. Larrabee, “A new method to enhance overlay tool performance,” Metrology, Inspection, and Process Control for Microlithography Xvii5038, 428–436 (2003).

Swaan, B. V.

A. Azaripour, T. Lagerweij, C. Scharfbillig, A. E. Jadczak, B. V. Swaan, M. Molenaar, R. V. Waal, K. Kielbassa, W. Tigchelaar, D. I. Picavet, A. Jonker, E. M. L. Hendrikx, V. V. V. Hira, M. Khurshed, and C. J. F. V. Noorden, “Three-dimensional histochemistry and imaging of human gingiva,” Sci. Rep. 8(1), 1647 (2018).
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G. Katona, G. Szalay, P. Maák, A. Kaszás, M. Veress, D. Hillier, B. Chiovini, E. S. Vizi, B. Roska, and B. Rózsa, “Fast two-photon in vivo imaging with three-dimensional random-access scanning in large tissue volumes,” Nat. Methods 9(2), 201–208 (2012).
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Tang, F. W.

Tigchelaar, W.

A. Azaripour, T. Lagerweij, C. Scharfbillig, A. E. Jadczak, B. V. Swaan, M. Molenaar, R. V. Waal, K. Kielbassa, W. Tigchelaar, D. I. Picavet, A. Jonker, E. M. L. Hendrikx, V. V. V. Hira, M. Khurshed, and C. J. F. V. Noorden, “Three-dimensional histochemistry and imaging of human gingiva,” Sci. Rep. 8(1), 1647 (2018).
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H. Kang, R. Attota, V. Tondare, A. E. Vladar, and P. Kavuri, “A method to determine the number of nanoparticles in a cluster using conventional optical microscopes,” Appl. Phys. Lett. 107(10), 103106 (2015).
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F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).

Uchil, P. D.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).

Usha, S.

S. Usha, P. V. Shashikumar, G. C. Mohankumar, and S. S. Rao, “Through Focus Optical Imaging Technique To Analyze Variations In Nano-Scale Indents,” Int. J. Eng. Res. Technol. 2, 18 (2013).

Vaccaro, C.

P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, “Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(14), 5889–5894 (2007).
[Crossref] [PubMed]

Vartanian, V.

R. K. Attota, P. Weck, J. A. Kramar, B. Bunday, and V. Vartanian, “Feasibility study on 3-D shape analysis of high-aspect-ratio features using through-focus scanning optical microscopy,” Opt. Express 24(15), 16574–16585 (2016).
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R. Attota, B. Bunday, and V. Vartanian, “Critical dimension metrology by through-focus scanning optical microscopy beyond the 22 nm node,” Appl. Phys. Lett. 102(22), 222107 (2013).
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G. Katona, G. Szalay, P. Maák, A. Kaszás, M. Veress, D. Hillier, B. Chiovini, E. S. Vizi, B. Roska, and B. Rózsa, “Fast two-photon in vivo imaging with three-dimensional random-access scanning in large tissue volumes,” Nat. Methods 9(2), 201–208 (2012).
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Vizi, E. S.

G. Katona, G. Szalay, P. Maák, A. Kaszás, M. Veress, D. Hillier, B. Chiovini, E. S. Vizi, B. Roska, and B. Rózsa, “Fast two-photon in vivo imaging with three-dimensional random-access scanning in large tissue volumes,” Nat. Methods 9(2), 201–208 (2012).
[Crossref] [PubMed]

Vladar, A. E.

H. Kang, R. Attota, V. Tondare, A. E. Vladar, and P. Kavuri, “A method to determine the number of nanoparticles in a cluster using conventional optical microscopes,” Appl. Phys. Lett. 107(10), 103106 (2015).
[Crossref]

R. Attota, R. G. Dixson, J. A. Kramar, J. E. Potzick, A. E. Vladar, B. Bunday, E. Novak, and A. Rudack, “TSOM Method for Semiconductor Metrology,” Proc. SPIE 7971, 79710T (2011).
[Crossref]

von Diezmann, A.

A. von Diezmann, Y. Shechtman, and W. E. Moerner, “Three-Dimensional Localization of Single Molecules for Super-Resolution Imaging and Single-Particle Tracking,” Chem. Rev. 117(11), 7244–7275 (2017).
[Crossref] [PubMed]

Waal, R. V.

A. Azaripour, T. Lagerweij, C. Scharfbillig, A. E. Jadczak, B. V. Swaan, M. Molenaar, R. V. Waal, K. Kielbassa, W. Tigchelaar, D. I. Picavet, A. Jonker, E. M. L. Hendrikx, V. V. V. Hira, M. Khurshed, and C. J. F. V. Noorden, “Three-dimensional histochemistry and imaging of human gingiva,” Sci. Rep. 8(1), 1647 (2018).
[Crossref] [PubMed]

Waddell, S.

Ward, E. S.

Z. Gan, S. Ram, R. J. Ober, and E. S. Ward, “Using multifocal plane microscopy to reveal novel trafficking processes in the recycling pathway,” J. Cell Sci. 126(5), 1176–1188 (2013).
[Crossref] [PubMed]

P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, “Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(14), 5889–5894 (2007).
[Crossref] [PubMed]

P. Prabhat, S. Ram, E. S. Ward, and R. J. Ober, “Simultaneous imaging of different focal planes in fluorescence microscopy for the study of cellular dynamics in three dimensions,” IEEE Trans. Nanobioscience 3(4), 237–242 (2004).
[Crossref] [PubMed]

Weck, P.

Whelan, M. P.

J. M. Gineste, P. Macko, E. A. Patterson, and M. P. Whelan, “Three-dimensional automated nanoparticle tracking using Mie scattering in an optical microscope,” J. Microsc. 243(2), 172–178 (2011).
[Crossref] [PubMed]

Wilson, T.

E. J. Botcherby, R. Juškaitis, M. J. Booth, and T. Wilson, “An optical technique for remote focusing in microscopy,” Opt. Commun. 281(4), 880–887 (2008).
[Crossref]

Wisniewski, J.

S. Abrahamsson, R. Ilic, J. Wisniewski, B. Mehl, L. Yu, L. Chen, M. Davanco, L. Oudjedi, J. B. Fiche, B. Hajj, X. Jin, J. Pulupa, C. Cho, M. Mir, M. El Beheiry, X. Darzacq, M. Nollmann, M. Dahan, C. Wu, T. Lionnet, J. A. Liddle, and C. I. Bargmann, “Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging,” Biomed. Opt. Express 7(3), 855–869 (2016).
[Crossref] [PubMed]

S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
[Crossref] [PubMed]

Wittbrodt, J.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical Sectioning Deep Inside live Embryos by Selective Plane Illumination Microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Wu, C.

S. Abrahamsson, R. Ilic, J. Wisniewski, B. Mehl, L. Yu, L. Chen, M. Davanco, L. Oudjedi, J. B. Fiche, B. Hajj, X. Jin, J. Pulupa, C. Cho, M. Mir, M. El Beheiry, X. Darzacq, M. Nollmann, M. Dahan, C. Wu, T. Lionnet, J. A. Liddle, and C. I. Bargmann, “Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging,” Biomed. Opt. Express 7(3), 855–869 (2016).
[Crossref] [PubMed]

S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
[Crossref] [PubMed]

Yu, L.

Zappe, H.

P. P. Zhao, C. Ataman, and H. Zappe, “Miniaturized variable-focus objective employing a liquid-filled tunable aspherical lens,” Opt. Eng. 56(10), 1 (2017).
[Crossref]

Zhao, P. P.

P. P. Zhao, C. Ataman, and H. Zappe, “Miniaturized variable-focus objective employing a liquid-filled tunable aspherical lens,” Opt. Eng. 56(10), 1 (2017).
[Crossref]

Zucker, R. M.

R. M. Zucker, “Quality assessment of confocal microscopy slide-based systems: Instability,” Cytometry A 69A(7), 677–690 (2006).
[Crossref] [PubMed]

R. M. Zucker and O. Price, “Evaluation of confocal microscopy system performance,” Cytometry 44(4), 273–294 (2001).
[Crossref] [PubMed]

Žurauskas, M.

ACM Trans. Graph. (1)

M. Levoy, R. Ng, A. Adams, M. Footer, and M. Horowitz, “Light field microscopy,” ACM Trans. Graph. 25(3), 924–934 (2006).
[Crossref]

Appl. Phys. Lett. (3)

R. Attota, B. Bunday, and V. Vartanian, “Critical dimension metrology by through-focus scanning optical microscopy beyond the 22 nm node,” Appl. Phys. Lett. 102(22), 222107 (2013).
[Crossref]

H. Kang, R. Attota, V. Tondare, A. E. Vladar, and P. Kavuri, “A method to determine the number of nanoparticles in a cluster using conventional optical microscopes,” Appl. Phys. Lett. 107(10), 103106 (2015).
[Crossref]

R. Attota and R. G. Dixson, “Resolving three-dimensional shape of sub-50 nm wide lines with nanometer-scale sensitivity using conventional optical microscopes,” Appl. Phys. Lett. 105(4), 043101 (2014).
[Crossref]

Biomed. Opt. Express (2)

Chem. Rev. (1)

A. von Diezmann, Y. Shechtman, and W. E. Moerner, “Three-Dimensional Localization of Single Molecules for Super-Resolution Imaging and Single-Particle Tracking,” Chem. Rev. 117(11), 7244–7275 (2017).
[Crossref] [PubMed]

Cytometry (1)

R. M. Zucker and O. Price, “Evaluation of confocal microscopy system performance,” Cytometry 44(4), 273–294 (2001).
[Crossref] [PubMed]

Cytometry A (2)

R. M. Zucker, “Quality assessment of confocal microscopy slide-based systems: Instability,” Cytometry A 69A(7), 677–690 (2006).
[Crossref] [PubMed]

M. Halter, E. Bier, P. C. DeRose, G. A. Cooksey, S. J. Choquette, A. L. Plant, and J. T. Elliott, “An Automated Protocol for Performance Benchmarking a Widefield Fluorescence Microscope,” Cytometry A 85(11), 978–985 (2014).
[Crossref] [PubMed]

IEEE Trans. Nanobioscience (1)

P. Prabhat, S. Ram, E. S. Ward, and R. J. Ober, “Simultaneous imaging of different focal planes in fluorescence microscopy for the study of cellular dynamics in three dimensions,” IEEE Trans. Nanobioscience 3(4), 237–242 (2004).
[Crossref] [PubMed]

Int. J. Eng. Res. Technol. (1)

S. Usha, P. V. Shashikumar, G. C. Mohankumar, and S. S. Rao, “Through Focus Optical Imaging Technique To Analyze Variations In Nano-Scale Indents,” Int. J. Eng. Res. Technol. 2, 18 (2013).

J. Biomed. Opt. (1)

R. K. Attota, “Through-focus or volumetric type of optical imaging methods: a review,” J. Biomed. Opt. 23(7), 070901 (2018).

J. Cell Sci. (1)

Z. Gan, S. Ram, R. J. Ober, and E. S. Ward, “Using multifocal plane microscopy to reveal novel trafficking processes in the recycling pathway,” J. Cell Sci. 126(5), 1176–1188 (2013).
[Crossref] [PubMed]

J. Microsc. (2)

J. M. Gineste, P. Macko, E. A. Patterson, and M. P. Whelan, “Three-dimensional automated nanoparticle tracking using Mie scattering in an optical microscope,” J. Microsc. 243(2), 172–178 (2011).
[Crossref] [PubMed]

K. M. Kedziora, J. H. M. Prehn, J. Dobrucki, and T. Bernas, “Method of calibration of a fluorescence microscope for quantitative studies,” J. Microsc. 244(1), 101–111 (2011).
[Crossref] [PubMed]

Meas. Sci. Technol. (1)

R. Attota and R. Silver, “Nanometrology using a through-focus scanning optical microscopy method,” Meas. Sci. Technol. 22(2), 024002 (2011).
[Crossref]

Nat. Methods (4)

G. Katona, G. Szalay, P. Maák, A. Kaszás, M. Veress, D. Hillier, B. Chiovini, E. S. Vizi, B. Roska, and B. Rózsa, “Fast two-photon in vivo imaging with three-dimensional random-access scanning in large tissue volumes,” Nat. Methods 9(2), 201–208 (2012).
[Crossref] [PubMed]

W. Göbel, B. M. Kampa, and F. Helmchen, “Imaging cellular network dynamics in three dimensions using fast 3D laser scanning,” Nat. Methods 4(1), 73–79 (2007).
[Crossref] [PubMed]

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10, 653–658 (2013).

S. Abrahamsson, J. Chen, B. Hajj, S. Stallinga, A. Y. Katsov, J. Wisniewski, G. Mizuguchi, P. Soule, F. Mueller, C. D. Darzacq, X. Darzacq, C. Wu, C. I. Bargmann, D. A. Agard, M. Dahan, and M. G. L. Gustafsson, “Fast multicolor 3D imaging using aberration-corrected multifocus microscopy,” Nat. Methods 10(1), 60–63 (2013).
[Crossref] [PubMed]

Nat. Neurosci. (1)

N. Ji, J. Freeman, and S. L. Smith, “Technologies for imaging neural activity in large volumes,” Nat. Neurosci. 19(9), 1154–1164 (2016).
[Crossref] [PubMed]

Nat. Photonics (1)

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, 705–708 (2016).

Opt. Commun. (1)

E. J. Botcherby, R. Juškaitis, M. J. Booth, and T. Wilson, “An optical technique for remote focusing in microscopy,” Opt. Commun. 281(4), 880–887 (2008).
[Crossref]

Opt. Eng. (1)

P. P. Zhao, C. Ataman, and H. Zappe, “Miniaturized variable-focus objective employing a liquid-filled tunable aspherical lens,” Opt. Eng. 56(10), 1 (2017).
[Crossref]

Opt. Express (9)

D. Koyama, R. Isago, and K. Nakamura, “Compact, high-speed variable-focus liquid lens using acoustic radiation force,” Opt. Express 18(24), 25158–25169 (2010).
[Crossref] [PubMed]

M. V. Ryabko, S. N. Koptyaev, A. V. Shcherbakov, A. D. Lantsov, and S. Y. Oh, “Method for optical inspection of nanoscale objects based upon analysis of their defocused images and features of its practical implementation,” Opt. Express 21(21), 24483–24489 (2013).
[Crossref] [PubMed]

M. Ryabko, A. Shchekin, S. Koptyaev, A. Lantsov, A. Medvedev, A. Shcherbakov, and S. Y. Oh, “Through-focus scanning optical microscopy (TSOM) considering optical aberrations: practical implementation,” Opt. Express 23(25), 32215–32221 (2015).
[Crossref] [PubMed]

A. Tahmasbi, S. Ram, J. Chao, A. V. Abraham, F. W. Tang, E. Sally Ward, and R. J. Ober, “Designing the focal plane spacing for multifocal plane microscopy,” Opt. Express 22(14), 16706–16721 (2014).
[Crossref] [PubMed]

S. W. Park, G. Park, Y. Kim, J. H. Cho, J. Lee, and H. Kim, “Through-focus scanning optical microscopy with the Fourier modal method,” Opt. Express 26(9), 11649–11657 (2018).
[Crossref] [PubMed]

M. Ryabko, S. Koptyaev, A. Shcherbakov, A. Lantsov, and S. Y. Oh, “Motion-free all optical inspection system for nanoscale topology control,” Opt. Express 22(12), 14958–14963 (2014).
[Crossref] [PubMed]

R. K. Attota, P. Weck, J. A. Kramar, B. Bunday, and V. Vartanian, “Feasibility study on 3-D shape analysis of high-aspect-ratio features using through-focus scanning optical microscopy,” Opt. Express 24(15), 16574–16585 (2016).
[Crossref] [PubMed]

S. S. Kou and C. J. R. Sheppard, “Imaging in digital holographic microscopy,” Opt. Express 15(21), 13640–13648 (2007).
[Crossref] [PubMed]

R. K. Attota, “Step beyond Kohler illumination analysis for far-field quantitative imaging: angular illumination asymmetry (ANILAS) maps,” Opt. Express 24(20), 22616–22627 (2016).
[Crossref] [PubMed]

Opt. Lett. (4)

Optica (1)

Proc SPIE Int Soc Opt Eng (1)

R. Attota and J. Kramar, “Optimizing noise for defect analysis with through-focus scanning optical microscopy,” Proc SPIE Int Soc Opt Eng 9778, 977811 (2016).
[Crossref] [PubMed]

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

P. Prabhat, Z. Gan, J. Chao, S. Ram, C. Vaccaro, S. Gibbons, R. J. Ober, and E. S. Ward, “Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(14), 5889–5894 (2007).
[Crossref] [PubMed]

Proc. SPIE (2)

R. Attota, R. G. Dixson, J. A. Kramar, J. E. Potzick, A. E. Vladar, B. Bunday, E. Novak, and A. Rudack, “TSOM Method for Semiconductor Metrology,” Proc. SPIE 7971, 79710T (2011).
[Crossref]

J. H. Lee, J. H. Park, D. Jeong, E. J. Shin, and C. Park, “Tip/tilt-compensated through-focus scanning optical microscopy,” Proc. SPIE 10023, 100230P (2016).
[Crossref]

Sci. Rep. (3)

A. Azaripour, T. Lagerweij, C. Scharfbillig, A. E. Jadczak, B. V. Swaan, M. Molenaar, R. V. Waal, K. Kielbassa, W. Tigchelaar, D. I. Picavet, A. Jonker, E. M. L. Hendrikx, V. V. V. Hira, M. Khurshed, and C. J. F. V. Noorden, “Three-dimensional histochemistry and imaging of human gingiva,” Sci. Rep. 8(1), 1647 (2018).
[Crossref] [PubMed]

E. Agocs and R. K. Attota, “Enhancing optical microscopy illumination to enable quantitative imaging,” Sci. Rep. 8(1), 4782 (2018).
[Crossref] [PubMed]

K. I. Mortensen and H. Flyvbjerg, “Calibration-on-the-spot”: How to calibrate an EMCCD camera from its images,” Sci. Rep. 628680 (2016).

Science (1)

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical Sectioning Deep Inside live Embryos by Selective Plane Illumination Microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Other (6)

G. Popescu, Quantitative phase imaging of cells and tissues, McGraw-Hill biophotonics (McGraw-Hill, New York, 2011), pp. xx, 362 p.

R. Attota, R. M. Silver, M. Stocker, E. Marx, J. Jun, M. Davidson, and R. Larrabee, “A new method to enhance overlay tool performance,” Metrology, Inspection, and Process Control for Microlithography Xvii5038, 428–436 (2003).

J. C. Waters and T. Wittmann, Quantitative Imaging in Cell Biology, First ed., Methods in Cell Biology (Elsevier, 2014), Vol. 123.

K. F. Tehrani, M. K. Sun, L. Karumbaiah, and L. J. Mortensen, “Fast axial scanning for 2-photon microscopy using liquid lens technology,” in SPIE BiOS, (SPIE, 2017), 6.

A. Arceo, B. Bunday, and R. Attota, “Use of TSOM for sub-11 nm node pattern defect detection and HAR features,” Metrology, Inspection, and Process Control for Microlithography Xxvii8681, 86812G (2013).

S. N. Koptyaev, M. V. Ryabko, A. V. Hcherbakov, and A. D. Lantsov, “Optical measuring system and method of measuring critical size,” (2014).

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Figures (13)

Fig. 1
Fig. 1 Animation depicting a typical TSOM image construction process.
Fig. 2
Fig. 2 (a) A typical top-down optical image of the selected line. (b) The relative lateral displacement of the target image in the X-direction for the selected three conditions indicated at the top of the figure. Condition 1: the camera exposure time was 1 ms with simulated vibrations transmitted to the microscope from a running fan placed on the microscope. Condition 2: the camera exposure time was 1 ms without the fan. Condition 3: the camera exposure time was 500 ms without the fan. The measured standard deviations of the lateral movement under the three conditions are shown at the bottom.
Fig. 3
Fig. 3 (a) TSOM image of the selected line target at 100 nm step size. (b) Figure depicting relative orientations of the optical and the TSOM images.
Fig. 4
Fig. 4 D-TSOM images representing (a) typical non-mechanical sources of noise, and (b) zero noise. Numbers in the inset are MAV/OIR values.
Fig. 5
Fig. 5 Effect of the simulated random mechanical lateral stage vibrations of different magnitudes during TF image collection. (a), (b), and (c) Typical TSOM images with 100 nm step size for lateral stage vibrations of 0 nm to ± 20 nm, ± 40 nm, and ± 80 nm, respectively. (a1), (b1), and (c1) Typical D-TSOM images between two TSOM images generated similar to (a), (b), and (c), respectively. (d), (e), and (f) Typical TSOM images with 250 nm step size for lateral stage vibrations of 0 to ± 20 nm, ± 40 nm, and ± 80 nm, respectively. (d1), (e1), and (f1) Typical D-TSOM images between two TSOM images generated similar to (d), (e), and (f), respectively. Numbers in the inset of (a) to (f) indicate lateral maximum vibrations and focus step size. Numbers in the inset of (a1) to (f1) indicate mean MAV/OIR values from 20 repeats.
Fig. 6
Fig. 6 Mean D-TSOM image noise levels as extracted by (a) MAV, and (b) OIR, for different simulated maximum lateral vibrations at two focus steps sizes of 100 nm and 250 nm. ‘Self’ indicates D-TSOM image obtained using random lateral vibrations applied on the same TSOM image. ‘Repeat’ indicates D-TSOM image obtained using random lateral vibrations applied on repeated collections of the TSOM images from the same line target. Error bars represent one standard deviation using 20 data points.
Fig. 7
Fig. 7 One standard deviation of the noise extracted using MAV and OIR metrics as a percentage of the mean values obtained from repeating the process 20 times for (a) lateral, and (b) axial vibrations. The D-TSOM images were extracted using random vibrations applied to the same (‘self’) TSOM image.
Fig. 8
Fig. 8 Effect of the simulated random mechanical stage vibrations in the focus (axial) direction of different magnitudes during TF image collection. (a), (b), and (c) Typical TSOM images with 100 nm step size for axial stage vibrations of 0 nm to ± 20 nm ± 40 nm, and ± 80 nm, respectively. (a1), (b1), and (c1) Typical D-TSOM images between two TSOM images generated similar to (a), (b), and (c), respectively. (d), (e), and (f) Typical TSOM images with 250 nm step size for axial stage vibrations of 0 to ± 20 nm, ± 40 nm, and ± 80 nm, respectively. (d1), (e1), and (f1) Typical D-TSOM images between two TSOM images generated similar to (d), (e), and (f), respectively. Numbers in the inset of (a) to (f) indicate axial maximum vibrations and focus step size. Numbers in the inset of (a1) to (f1) indicate mean MAV/OIR values from 20 repeats.
Fig. 9
Fig. 9 Mean D-TSOM image noise levels as extracted by (a) MAV, and (b) OIR, for the different simulated maximum axial vibrations at two focus steps sizes of 100 nm and 250 nm. ‘Self’ indicates D-TSOM image obtained using random axial vibrations applied on the same TSOM image twice. ‘Repeat’ indicates D-TSOM image obtained using random axial vibrations applied on repeated collections of TSOM images from the same line target. Error bars represent one standard deviation using 20 data points.
Fig. 10
Fig. 10 Mean D-TSOM image noise levels as extracted by (a) MAV, and (b) OIR, for the different simulated maximum lateral and axial vibrations together at two focus steps sizes of 100 nm and 250 nm. ‘Self’ indicates D-TSOM image obtained using random lateral and axial vibrations applied on the same TSOM image twice. ‘Repeat’ indicates D-TSOM image obtained using random lateral and axial vibrations applied on repeated collections of TSOM images from the same line target. Error bars represent one standard deviation using 20 data points.
Fig. 11
Fig. 11 Effect of the increased camera exposure time on the natural mechanical stage vibrations detected during TF image collection. (a), (b), (c) and (d) Typical TSOM images with 100 nm step size for different camera exposure. (a1), (b1), (c1) and (d1) Typical D-TSOM images between two TSOM images generated similar to (a), (b), (c) and (d), respectively. Numbers in the inset of (a) to (d) indicate camera exposure time and activation condition of the computer cooling fan placed on the microscope. Numbers in the inset of (a1) to (d1) indicate mean MAV/OIR values from 20 repeats.
Fig. 12
Fig. 12 Mean noise as measured by MAV/OIR with increased camera exposure time. The error bars represent one standard deviation using 20 measurements.
Fig. 13
Fig. 13 Tilt in the TSOM axis shown by dashed lines due to (a) the stage unidirectional lateral movement (in this case 10 nm lateral shift to the right for each focus step), and (b) misalignment of the aperture diaphragm (reproduced from [15]).

Equations (1)

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MAV= 1 n k=1 n | DTSOM | k

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