Abstract

Confocal scanning microscopy is the de facto standard modality for fluorescence imaging. Point scanning, however, leads to a limited throughput and makes the technique unsuitable for fast multi-focal scanning over large areas. We propose an architecture for multi-focal fluorescence imaging that is scalable to large area imaging. The design is based on the concept of line scanning with continuous ‘push broom’ scanning. Instead of a line sensor, we use an area sensor that is tilted with respect to the optical axis to acquire image data from multiple depths inside the sample simultaneously. A multi-line illumination where the lines span a plane conjugate to the tilted sensor is created by means of a diffractive optics design, implemented on a spatial light modulator. In particular, we describe a design that uses higher order astigmatism to generate focal lines of substantially constant peak intensity along the lines. The proposed method is suitable for fast 3D image acquisition with unlimited field of view, it requires no moving components except for the sample scanning stage, and provides intrinsic alignment of the simultaneously scanned focal slices. As proof of concept, we have scanned 9 focal slices simultaneously over an area of 36 mm2 at 0.29 µm pixel size in object space. The projected ultimate throughput that can be realized with the proposed architecture is in excess of 100 Mpixel/s.

© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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References

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2019 (1)

B.-J. Chang, M. Kittisopikul, K. M. Dean, P. Roudot, E. S. Welf, and R. Fiolka, “Universal light-sheet generation with field synthesis,” Nat. Methods 16(3), 235–238 (2019).
[Crossref]

2018 (5)

2017 (1)

2016 (5)

A. Jesacher, S. Bernet, and M. Ritsch-Marte, “Colored point spread function engineering for parallel confocal microscopy,” Opt. Express 24(24), 27395–27402 (2016).
[Crossref]

L. Li, Q. Zhou, T. C. Voss, K. L. Quick, and D. V. LaBarbera, “High-throughput imaging: Focusing in on drug discovery in 3D,” Methods 96, 97–102 (2016).
[Crossref]

G. Bueno, M. M. Fernández-Carrobles, O. Deniz, and M. García-Rojo, “New Trends of Emerging Technologies in Digital Pathology,” Pathobiology 83(2-3), 61–69 (2016).
[Crossref]

C. Smith, M. Huisman, M. Siemons, D. Grünwald, and S. Stallinga, “Simultaneous measurement of emission color and 3D position of single molecules,” Opt. Express 24(5), 4996–5013 (2016).
[Crossref]

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[Crossref]

2015 (3)

2014 (4)

T. C. Schlichenmeyer, M. Wang, K. N. Elfer, and J. Q. Brown, “Video-rate structured illumination microscopy for high-throughput imaging of large tissue areas,” Biomed. Opt. Express 5(2), 366–377 (2014).
[Crossref]

Y. Shechtman, S. J. Sahl, A. S. Backer, and W. E. Moerner, “Optimal Point Spread Function Design for 3D Imaging,” Phys. Rev. Lett. 113(13), 133902 (2014).
[Crossref]

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref]

J. Broeken, B. Rieger, and S. Stallinga, “Simultaneous measurement of position and color of single fluorescent emitters using diffractive optics,” Opt. Lett. 39(11), 3352–3355 (2014).
[Crossref]

2013 (5)

H. L. Fu, J. L. Mueller, M. P. Javid, J. K. Mito, D. G. Kirsch, N. Ramanujam, and J. Q. Brown, “Optimization of a Widefield Structured Illumination Microscope for Non-Destructive Assessment and Quantification of Nuclear Features in Tumor Margins of a Primary Mouse Model of Sarcoma,” PLoS One 8(7), e68868 (2013).
[Crossref]

P. J. Cutler, M. D. Malik, S. Liu, J. M. Byars, D. S. Lidke, and K. A. Lidke, “Multi-Color Quantum Dot Tracking Using a High-Speed Hyperspectral Line-Scanning Microscope,” PLoS One 8(5), e64320 (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]

S. Roth, C. J. Sheppard, K. Wicker, and R. Heintzmann, “Optical photon reassignment microscopy (OPRA),” Opt. Nanoscopy 2(1), 5 (2013).
[Crossref]

G. M. De Luca, R. M. Breedijk, R. A. Brandt, C. H. Zeelenberg, B. E. de Jong, W. Timmermans, L. N. Azar, R. A. Hoebe, S. Stallinga, and E. M. Manders, “Re-scan confocal microscopy: scanning twice for better resolution,” Biomed. Opt. Express 4(11), 2644–2656 (2013).
[Crossref]

2012 (2)

E. Ronzitti, M. Guillon, V. de Sars, and V. Emiliani, “LCoS nematic SLM characterization and modeling for diffraction efficiency optimization, zero and ghost orders suppression,” Opt. Express 20(16), 17843–17855 (2012).
[Crossref]

F. de Chaumont, S. Dallongeville, N. Chenouard, N. Hervé, S. Pop, T. Provoost, V. Meas-Yedid, P. Pankajakshan, T. Lecomte, Y. Le Montagner, T. Lagache, A. Dufour, and J.-C. Olivo-Marin, “Icy: an open bioimage informatics platform for extended reproducible research,” Nat. Methods 9(7), 690–696 (2012).
[Crossref]

2011 (1)

S. Abeytunge, Y. Li, B. Larson, R. Toledo-Crow, and M. Rajadhyaksha, “Rapid confocal imaging of large areas of excised tissue with strip mosaicing,” J. Biomed. Opt. 16(5), 050504 (2011).
[Crossref]

2010 (3)

I. Smal, M. Loog, W. Niessen, and E. Meijering, “Quantitative Comparison of Spot Detection Methods in Fluorescence Microscopy,” IEEE Trans. Med. Imaging 29(2), 282–301 (2010).
[Crossref]

C. B. Müller and J. Enderlein, “Image Scanning Microscopy,” Phys. Rev. Lett. 104(19), 198101 (2010).
[Crossref]

F. Zanella, J. B. Lorens, and W. Link, “High content screening: seeing is believing,” Trends Biotechnol. 28(5), 237–245 (2010).
[Crossref]

2008 (1)

2007 (1)

2006 (2)

R. Wolleschensky, B. Zimmermann, and M. Kempe, “High-speed confocal fluorescence imaging with a novel line scanning microscope,” J. Biomed. Opt. 11(6), 064011 (2006).
[Crossref]

A. Greengard, Y. Y. Schechner, and R. Piestun, “Depth from diffracted rotation,” Opt. Lett. 31(2), 181–183 (2006).
[Crossref]

2005 (3)

2002 (1)

1995 (1)

H. Netten, L. J. van Vliet, F. R. Boddeke, P. de Jong, and I. T. Young, “A fast scanner for fluorescence microscopy using a 2-D CCD and time delayed integration,” Bioimaging 3(2), 102 (1995).
[Crossref]

1988 (1)

C. Sheppard and X. Mao, “Confocal Microscopes with Slit Apertures,” J. Mod. Opt. 35(7), 1169–1185 (1988).
[Crossref]

1972 (1)

B. R. W. Gerchberg and W. O. Saxton, “A Practical Algorithm for the Determination of Phase from Image and Diffraction Plane Pictures,” Optik 35, 237–246 (1972).

Abeytunge, S.

S. Abeytunge, Y. Li, B. Larson, R. Toledo-Crow, and M. Rajadhyaksha, “Rapid confocal imaging of large areas of excised tissue with strip mosaicing,” J. Biomed. Opt. 16(5), 050504 (2011).
[Crossref]

Azar, L. N.

Babbey, C. M.

E. Wang, C. M. Babbey, and K. W. Dunn, “Performance comparison between the high-speed Yokogawa spinning disc confocal system and single-point scanning confocal systems,” J. Microsc. 218(2), 148–159 (2005).
[Crossref]

Backer, A. S.

Y. Shechtman, L. E. Weiss, A. S. Backer, M. Y. Lee, and W. E. Moerner, “Multicolour localization microscopy by point-spread-function engineering,” Nat. Photonics 10(9), 590–594 (2016).
[Crossref]

Y. Shechtman, S. J. Sahl, A. S. Backer, and W. E. Moerner, “Optimal Point Spread Function Design for 3D Imaging,” Phys. Rev. Lett. 113(13), 133902 (2014).
[Crossref]

Bembenek, J. N.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref]

Bernet, S.

Betzig, E.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref]

Bhattacharya, D.

Boddeke, F. R.

H. Netten, L. J. van Vliet, F. R. Boddeke, P. de Jong, and I. T. Young, “A fast scanner for fluorescence microscopy using a 2-D CCD and time delayed integration,” Bioimaging 3(2), 102 (1995).
[Crossref]

Böhme, R.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref]

Booth, M. J.

Boyaval, F.

L. van der Graaff, F. Boyaval, L. van Vliet, and S. Stallinga, “Fluorescence imaging for whole slide scanning using LED-based color sequential illumination,” Proc. SPIE 10679, 106790D (2018).
[Crossref]

Brady, D. J.

Brandt, R. A.

Breedijk, R. M.

Broeken, J.

Brown, J. Q.

T. C. Schlichenmeyer, M. Wang, K. N. Elfer, and J. Q. Brown, “Video-rate structured illumination microscopy for high-throughput imaging of large tissue areas,” Biomed. Opt. Express 5(2), 366–377 (2014).
[Crossref]

H. L. Fu, J. L. Mueller, M. P. Javid, J. K. Mito, D. G. Kirsch, N. Ramanujam, and J. Q. Brown, “Optimization of a Widefield Structured Illumination Microscope for Non-Destructive Assessment and Quantification of Nuclear Features in Tumor Margins of a Primary Mouse Model of Sarcoma,” PLoS One 8(7), e68868 (2013).
[Crossref]

Bueno, G.

G. Bueno, M. M. Fernández-Carrobles, O. Deniz, and M. García-Rojo, “New Trends of Emerging Technologies in Digital Pathology,” Pathobiology 83(2-3), 61–69 (2016).
[Crossref]

Byars, J. M.

P. J. Cutler, M. D. Malik, S. Liu, J. M. Byars, D. S. Lidke, and K. A. Lidke, “Multi-Color Quantum Dot Tracking Using a High-Speed Hyperspectral Line-Scanning Microscope,” PLoS One 8(5), e64320 (2013).
[Crossref]

Cattin, M.-E.

T. Dorval, B. Chanrion, M.-E. Cattin, and J. P. Stephan, “Filling the drug discovery gap: is high-content screening the missing link?” Curr. Opin. Pharmacol. 42, 40–45 (2018).
[Crossref]

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]

Chang, B.-J.

B.-J. Chang, M. Kittisopikul, K. M. Dean, P. Roudot, E. S. Welf, and R. Fiolka, “Universal light-sheet generation with field synthesis,” Nat. Methods 16(3), 235–238 (2019).
[Crossref]

Chanrion, B.

T. Dorval, B. Chanrion, M.-E. Cattin, and J. P. Stephan, “Filling the drug discovery gap: is high-content screening the missing link?” Curr. Opin. Pharmacol. 42, 40–45 (2018).
[Crossref]

Chen, B.-C.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
[Crossref]

Chen, M.

Chenouard, N.

F. de Chaumont, S. Dallongeville, N. Chenouard, N. Hervé, S. Pop, T. Provoost, V. Meas-Yedid, P. Pankajakshan, T. Lecomte, Y. Le Montagner, T. Lagache, A. Dufour, and J.-C. Olivo-Marin, “Icy: an open bioimage informatics platform for extended reproducible research,” Nat. Methods 9(7), 690–696 (2012).
[Crossref]

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Olivo-Marin, J.-C.

F. de Chaumont, S. Dallongeville, N. Chenouard, N. Hervé, S. Pop, T. Provoost, V. Meas-Yedid, P. Pankajakshan, T. Lecomte, Y. Le Montagner, T. Lagache, A. Dufour, and J.-C. Olivo-Marin, “Icy: an open bioimage informatics platform for extended reproducible research,” Nat. Methods 9(7), 690–696 (2012).
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Otsuki, S.

Pankajakshan, P.

F. de Chaumont, S. Dallongeville, N. Chenouard, N. Hervé, S. Pop, T. Provoost, V. Meas-Yedid, P. Pankajakshan, T. Lecomte, Y. Le Montagner, T. Lagache, A. Dufour, and J.-C. Olivo-Marin, “Icy: an open bioimage informatics platform for extended reproducible research,” Nat. Methods 9(7), 690–696 (2012).
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F. de Chaumont, S. Dallongeville, N. Chenouard, N. Hervé, S. Pop, T. Provoost, V. Meas-Yedid, P. Pankajakshan, T. Lecomte, Y. Le Montagner, T. Lagache, A. Dufour, and J.-C. Olivo-Marin, “Icy: an open bioimage informatics platform for extended reproducible research,” Nat. Methods 9(7), 690–696 (2012).
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L. Li, Q. Zhou, T. C. Voss, K. L. Quick, and D. V. LaBarbera, “High-throughput imaging: Focusing in on drug discovery in 3D,” Methods 96, 97–102 (2016).
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Rajadhyaksha, M.

S. Abeytunge, Y. Li, B. Larson, R. Toledo-Crow, and M. Rajadhyaksha, “Rapid confocal imaging of large areas of excised tissue with strip mosaicing,” J. Biomed. Opt. 16(5), 050504 (2011).
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Ramanujam, N.

H. L. Fu, J. L. Mueller, M. P. Javid, J. K. Mito, D. G. Kirsch, N. Ramanujam, and J. Q. Brown, “Optimization of a Widefield Structured Illumination Microscope for Non-Destructive Assessment and Quantification of Nuclear Features in Tumor Margins of a Primary Mouse Model of Sarcoma,” PLoS One 8(7), e68868 (2013).
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B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
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Ritter, A. T.

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
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B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
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B.-J. Chang, M. Kittisopikul, K. M. Dean, P. Roudot, E. S. Welf, and R. Fiolka, “Universal light-sheet generation with field synthesis,” Nat. Methods 16(3), 235–238 (2019).
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B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
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Shang, Z.

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B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
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B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
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B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
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Wang, P.-H.

Wang, X.

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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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Y. Shechtman, L. E. Weiss, A. S. Backer, M. Y. Lee, and W. E. Moerner, “Multicolour localization microscopy by point-spread-function engineering,” Nat. Photonics 10(9), 590–594 (2016).
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B.-J. Chang, M. Kittisopikul, K. M. Dean, P. Roudot, E. S. Welf, and R. Fiolka, “Universal light-sheet generation with field synthesis,” Nat. Methods 16(3), 235–238 (2019).
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S. Roth, C. J. Sheppard, K. Wicker, and R. Heintzmann, “Optical photon reassignment microscopy (OPRA),” Opt. Nanoscopy 2(1), 5 (2013).
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B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
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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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H. Netten, L. J. van Vliet, F. R. Boddeke, P. de Jong, and I. T. Young, “A fast scanner for fluorescence microscopy using a 2-D CCD and time delayed integration,” Bioimaging 3(2), 102 (1995).
[Crossref]

Yuan, J.

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F. Zanella, J. B. Lorens, and W. Link, “High content screening: seeing is believing,” Trends Biotechnol. 28(5), 237–245 (2010).
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Zeelenberg, C. H.

Zeng, S.

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Zhong, J.

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L. Li, Q. Zhou, T. C. Voss, K. L. Quick, and D. V. LaBarbera, “High-throughput imaging: Focusing in on drug discovery in 3D,” Methods 96, 97–102 (2016).
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R. Wolleschensky, B. Zimmermann, and M. Kempe, “High-speed confocal fluorescence imaging with a novel line scanning microscope,” J. Biomed. Opt. 11(6), 064011 (2006).
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Appl. Opt. (2)

Bioimaging (1)

H. Netten, L. J. van Vliet, F. R. Boddeke, P. de Jong, and I. T. Young, “A fast scanner for fluorescence microscopy using a 2-D CCD and time delayed integration,” Bioimaging 3(2), 102 (1995).
[Crossref]

Biomed. Opt. Express (3)

Curr. Opin. Pharmacol. (1)

T. Dorval, B. Chanrion, M.-E. Cattin, and J. P. Stephan, “Filling the drug discovery gap: is high-content screening the missing link?” Curr. Opin. Pharmacol. 42, 40–45 (2018).
[Crossref]

IEEE Trans. Med. Imaging (1)

I. Smal, M. Loog, W. Niessen, and E. Meijering, “Quantitative Comparison of Spot Detection Methods in Fluorescence Microscopy,” IEEE Trans. Med. Imaging 29(2), 282–301 (2010).
[Crossref]

J. Biomed. Opt. (2)

R. Wolleschensky, B. Zimmermann, and M. Kempe, “High-speed confocal fluorescence imaging with a novel line scanning microscope,” J. Biomed. Opt. 11(6), 064011 (2006).
[Crossref]

S. Abeytunge, Y. Li, B. Larson, R. Toledo-Crow, and M. Rajadhyaksha, “Rapid confocal imaging of large areas of excised tissue with strip mosaicing,” J. Biomed. Opt. 16(5), 050504 (2011).
[Crossref]

J. Microsc. (1)

E. Wang, C. M. Babbey, and K. W. Dunn, “Performance comparison between the high-speed Yokogawa spinning disc confocal system and single-point scanning confocal systems,” J. Microsc. 218(2), 148–159 (2005).
[Crossref]

J. Mod. Opt. (1)

C. Sheppard and X. Mao, “Confocal Microscopes with Slit Apertures,” J. Mod. Opt. 35(7), 1169–1185 (1988).
[Crossref]

Methods (1)

L. Li, Q. Zhou, T. C. Voss, K. L. Quick, and D. V. LaBarbera, “High-throughput imaging: Focusing in on drug discovery in 3D,” Methods 96, 97–102 (2016).
[Crossref]

Nat. Methods (3)

B.-J. Chang, M. Kittisopikul, K. M. Dean, P. Roudot, E. S. Welf, and R. Fiolka, “Universal light-sheet generation with field synthesis,” Nat. Methods 16(3), 235–238 (2019).
[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]

F. de Chaumont, S. Dallongeville, N. Chenouard, N. Hervé, S. Pop, T. Provoost, V. Meas-Yedid, P. Pankajakshan, T. Lecomte, Y. Le Montagner, T. Lagache, A. Dufour, and J.-C. Olivo-Marin, “Icy: an open bioimage informatics platform for extended reproducible research,” Nat. Methods 9(7), 690–696 (2012).
[Crossref]

Nat. Photonics (1)

Y. Shechtman, L. E. Weiss, A. S. Backer, M. Y. Lee, and W. E. Moerner, “Multicolour localization microscopy by point-spread-function engineering,” Nat. Photonics 10(9), 590–594 (2016).
[Crossref]

Opt. Express (9)

M. Siemons, C. N. Hulleman, R. Ø. Thorsen, C. S. Smith, and S. Stallinga, “High precision wavefront control in point spread function engineering for single emitter localization,” Opt. Express 26(7), 8397–8416 (2018).
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C. Smith, M. Huisman, M. Siemons, D. Grünwald, and S. Stallinga, “Simultaneous measurement of emission color and 3D position of single molecules,” Opt. Express 24(5), 4996–5013 (2016).
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S. M. Shakeri, B. Hulsken, L. J. van Vliet, and S. Stallinga, “Optical quality assessment of whole slide imaging systems for digital pathology,” Opt. Express 23(2), 1319–1336 (2015).
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M. E. Gehm, M. S. Kim, C. Fernandez, and D. J. Brady, “High-throughput, multiplexed pushbroom hyperspectral microscopy,” Opt. Express 16(15), 11032–11043 (2008).
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A. Jesacher, S. Bernet, and M. Ritsch-Marte, “Colored point spread function engineering for parallel confocal microscopy,” Opt. Express 24(24), 27395–27402 (2016).
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Opt. Nanoscopy (1)

S. Roth, C. J. Sheppard, K. Wicker, and R. Heintzmann, “Optical photon reassignment microscopy (OPRA),” Opt. Nanoscopy 2(1), 5 (2013).
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Optica (1)

Optik (1)

B. R. W. Gerchberg and W. O. Saxton, “A Practical Algorithm for the Determination of Phase from Image and Diffraction Plane Pictures,” Optik 35, 237–246 (1972).

Pathobiology (1)

G. Bueno, M. M. Fernández-Carrobles, O. Deniz, and M. García-Rojo, “New Trends of Emerging Technologies in Digital Pathology,” Pathobiology 83(2-3), 61–69 (2016).
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Y. Shechtman, S. J. Sahl, A. S. Backer, and W. E. Moerner, “Optimal Point Spread Function Design for 3D Imaging,” Phys. Rev. Lett. 113(13), 133902 (2014).
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C. B. Müller and J. Enderlein, “Image Scanning Microscopy,” Phys. Rev. Lett. 104(19), 198101 (2010).
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PLoS One (2)

P. J. Cutler, M. D. Malik, S. Liu, J. M. Byars, D. S. Lidke, and K. A. Lidke, “Multi-Color Quantum Dot Tracking Using a High-Speed Hyperspectral Line-Scanning Microscope,” PLoS One 8(5), e64320 (2013).
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H. L. Fu, J. L. Mueller, M. P. Javid, J. K. Mito, D. G. Kirsch, N. Ramanujam, and J. Q. Brown, “Optimization of a Widefield Structured Illumination Microscope for Non-Destructive Assessment and Quantification of Nuclear Features in Tumor Margins of a Primary Mouse Model of Sarcoma,” PLoS One 8(7), e68868 (2013).
[Crossref]

Proc. SPIE (1)

L. van der Graaff, F. Boyaval, L. van Vliet, and S. Stallinga, “Fluorescence imaging for whole slide scanning using LED-based color sequential illumination,” Proc. SPIE 10679, 106790D (2018).
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Science (1)

B.-C. Chen, W. R. Legant, K. Wang, L. Shao, D. E. Milkie, M. W. Davidson, C. Janetopoulos, X. S. Wu, J. A. Hammer, Z. Liu, B. P. English, Y. Mimori-Kiyosue, D. P. Romero, A. T. Ritter, J. Lippincott-Schwartz, L. Fritz-Laylin, R. D. Mullins, D. M. Mitchell, J. N. Bembenek, A.-C. Reymann, R. Böhme, S. W. Grill, J. T. Wang, G. Seydoux, U. S. Tulu, D. P. Kiehart, and E. Betzig, “Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution,” Science 346(6208), 1257998 (2014).
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F. Zanella, J. B. Lorens, and W. Link, “High content screening: seeing is believing,” Trends Biotechnol. 28(5), 237–245 (2010).
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Supplementary Material (2)

NameDescription
» Visualization 1       A 400 Mpixel maximum intensity projection of a 9 layer multi-focal scan of a tissue micro array (TMA) section labeled using FISH, shown over 100 length scales.
» Visualization 2       3D visualisations of a 9 layer multi-focal scan of a tissue micro array (TMA) section labeled using FISH.

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Figures (15)

Fig. 1.
Fig. 1. Schematic side view of the architecture for a multi-line fluorescence scanning microscope for multi-focal imaging with an unlimited field of view. For clarity we illustrate the concept using only two focal layers. The imaging path is shown in green, the illumination path is shown in blue. A diffractive optical element (DOE) is used for generating a set of parallel scan lines, focused at equidistant planes. Note that in this side view, the lines are orthogonal to the drawing. (a) The tube lens and objective lens form a telecentric optical system such that the tilted sensor has a tilted conjugate plane in object space. The rows on the area sensor conjugate to the line foci are used to capture the image data from the different focal slices scanned by the line foci simultaneously. (b) The sample is scanned in a continuous ‘push broom’ scanning fashion to obtain a multi-focal image with a field of view that is in principle unlimited.
Fig. 2.
Fig. 2. Demonstration of grating with tilt and defocus. (a) The zone function with $\Delta y = 10\lambda$ and $\Delta{z} = 10\lambda$. These numbers are chosen for demonstration purpose, and do not represent a realistic scenario. (b) The profile function optimized for 9 lines. (c) The resulting distribution of power over the diffraction orders. (d) The corresponding aberration function.
Fig. 3.
Fig. 3. Illustration of the proposed geometry for the aspherical cylindrical lens design. (a) In the back focal plane, we have an circular aperture which is illuminated by a beam profile $A\left ( \rho _{x},\rho _{y} \right )$. We introduce an astigmatic aberration function $W$ such that every strip in the back focal plane there is a corresponding strip in the front focal plane (red boxes in all subfigures). (b) Side view of the optical system, with the back focal plane (bfp), the objective lens (obj) and the front focal plane (ffp). (c) The strips in the front focal plane have a non-constant width $dx$. By changing the shape of the $W$, $dx$ can be modified to obtain a uniform distribution of power.
Fig. 4.
Fig. 4. Calculated intensities in the focal plane using 2D scalar diffraction. A value $l = 256 \lambda /\textrm {NA}{}$ was used. The aperture is assumed to be circular. The red lines indicate one airy unit. (a) A line created using a parabolic aberration function. (b) A line created using an aberration function with higher order astigmatism optimized for uniformity conform Eq. (17). The yellow boxes correspond to the detailed images given in c-e. (c) Close to the edge of the line profile ringing is present. (d) This ringing has disappeared around $x = - 220 \lambda /\textrm {NA}{}$. Here the line width is within one Airy unit. (e) In the center of the line pattern, the line has the smallest line width. The peak is constant over the line.
Fig. 5.
Fig. 5. Schematic illustration of the multi-focal line confocal scanner prototype. The polarization of the laser beam is aligned to the SLM using a half wave plate (HWP) and filtered using a polarizer (POL). The beam is expanded and projected onto the SLM. The diffracted light is coupled into the objective lens using a filter cube consisting of an excitation filter (EX), emission filter (EM) and a dichroic mirror (DIC) and imaged in the back focal plane of the objective. The fluorescence light is imaged onto the CMOS sensor using the tube lens. Focal lengths $F$ are given in mm. (b). The measured impact on the photon detection efficiency of tilting the camera with respect to the optical axis. For a tilt of 20° the detection efficiency is reduced with 53 % with respect to orthogonal incidence.
Fig. 6.
Fig. 6. Results of the image based calibration of the SLM response curve. (a) Measured ratio between the first and zeroth diffraction order as a function of the gray levels $\epsilon _{1}$ and $\epsilon _{2}$ of the binary grating structure. (b) Modeled diffraction order ratio for the found fit parameters. (c) The induced phase change as a function of the digital gray level. The red boxes indicate the gray values that are used to create the lookup table and correspond to a $2\pi$ phase change.
Fig. 7.
Fig. 7. Illustration of the alignment calibration using a spot grid. (a-c) image data for three different $B$ values. (d-f) The found spot positions (blue circles) and the fitted model (red crosses). (g-h) The change in the $x$ and $y$ spot coordinate with respect to their average value as a function of $B$ (blue) and the fitted change in position (red).
Fig. 8.
Fig. 8. (a) Example showing the measurements performed to minimize vertical astigmatism. Four measurements where required to coarsely find the optimum (blue circles). From these measurements a fine estimation of the optimum was calculated using parabolic interpolation (yellow). (b) Graph showing the contributions of the Zernike polynomials to the total aberration. The error bars indicate two standard deviations. (c) The raw image data underlying the vertical astigmatism measurement. (d) The depth averaged illumination spot without any corrections, after minimizing the contribution of $Z_{20}$, and after aberration correction. The red circles indicate one Airy unit.
Fig. 9.
Fig. 9. The illumination PSF measured using a thin uniformly fluorescent test slide. (a). The full illumination PSF. The scale bar represents 100 µm. The focal lines are labeled with their diffraction order number $m$ and with aranging from blue for $m = - 4$ to yellow for $m = 4.$ The red lines indicate the width of the regions of interest (ROIs) that are used for imaging. The design line length $2l = 488$ µm is indicated by green lines. Further indicated are the SLM’s zeroth order spot (A), the first alias to the right of the central pattern (B), and higher order focal lines ($\left | m \right |\;>\;4)$ that are folded back into the central domain due to undersampling (C). These are minor artifacts that are blocked by the spatial slit filter in the digital domain. (b) The intensity distribution over the lines. The higher order astigmatism successfully prevents a zero rim intensity. A decrease of intensity is observed around $x = 0$ µm which is caused by an uneven illumination of the SLM. (c) The full width at half maximum (FWHM) of the focal lines. The center lines are in focus and approach the theoretical limit (full black line), a bit broader than the height of a ROI for four line TDI (dashed black line). The lines in (b) and (c) correspond to the diffraction orders as indicated at the left side of the figure, the width of the $x$-axis is scaled to the design length $2l$, and the red lines indicate the ROI width.
Fig. 10.
Fig. 10. Confocal detection of a uniform fluorescent plane. The top row (a, b, c) shows the signal as a function of the sample position in air, for the 9 illumination lines. The bottom row (d, e, f) shows the corresponding axial FWHM. The focal lines are labeled with their diffraction order number $m$ and with aranging from blue for $m = - 4$ to yellow for $m = 4.$ (a, b) The measured signal, while a single row on the sensor is used as a confocal detection. (c, d), The measured response for a four-row confocal detection. (e, f) The simulated response for a four-row confocal detection.
Fig. 11.
Fig. 11. Assessment of illumination PSF in a thick fluorescent material. (a) Through focus stack averaged along the $x$ direction. The red crosses mark the focal points. Thebars below the images indicate the intensity value mapping that is adjusted to cover the full dynamic range in each image. (b) The focal points plotted in the $(y,\;z)$ plane (blue circles) including a linear fit through the focal points (blue) which overlaps the object plane (red dashed curve).
Fig. 12.
Fig. 12. A 400 Mpixel maximum intensity projection of a 9 layer multi-focal scan of a tissue micro array (TMA) section labeled using FISH. Every figure zooms in a factor of five, such that the images are shown over a factor of 125 different length scales. The scan is made using an exposure time of 1 ms and four TDI lines. A gamma of 0.7 is used for an enhanced dynamic range. This image is also shown over 100 length scales in Visualization 1. (a) Whole slide scan. The white boxes indicate two regions that displayed in more detail. (b, d) 5$\times$ enlarged. (c, e) 25$\times$ enlarged. (f) 125$\times$ enlarged.
Fig. 13.
Fig. 13. 3D visualizations of a 9 layer multi-focal scan of a tissue micro array (TMA) section labeled using FISH. The scan is made using an exposure time of 10 ms and a single line detector. (a) A frame from a 3D visualization using the Icy software [37] (see Visualization 2). The white line grid has a 10 µm spacing. (b) A maximum intensity projection, where pixels have a assigned according to the layer of maximum intensity, ranging from −5.2 µm (blue) to 5.2 µm (yellow). The FISH probes can be observed to have different positions in $z$. The scale bar represents 10 µm.
Fig. 14.
Fig. 14. A single lane, 9 layer multi-focal scan of an immunofluorescently labeled human rectum tissue section. The scan is made using an exposure time of 10 ms and a single line digital spatial filter. (a) Central layer of the scan, showing the full width of a scan lane. The white box indicates the area that is showed in detail. (b) Detailed view. The white box marks the area displayed in (c-k), which provides a through focus stack of all layers, demonstrating the optical sectioning capability. Although this is a thick tissue section, a high contrast is observed in the central layers.
Fig. 15.
Fig. 15. Determination of the peak signal to noise ratio (pSNR), the peak signal to background ratio (pSBR), and the lateral and axial resolution expressed using the full width at half maximum (FWHM). (a) Maximum intensity projection of the image data of a scan of the FISH slide made using 1 ms exposure time and a four-line TDI acquisition. The scale bar indicates 100 µm. A gamma correction of 0.7 is applied. Three locations are highlighted. (b-d) A zoomed in view to the highlighted areas. The layer with best focus is displayed. The spots location are given including their peak intensity in photo electrons (e). The scale bar indicates 2 µm. The yellow ellipses have a horizontal and vertical diameter equal to the FWHM along the and direction respectively. (e) The image data was classified as background (black) and non-background values (green) or part of a spot. In total, 109 spots where segmented and their location is indicated with a yellow dot. (f-j) Histograms of the pSNR, pSBR and the FWHM along the $x$, and $y$ direction. The red line indicates the mean and the red dashed lines the 5th and 95th percentile respectively. In (h-j) a black line is included indicating the FWHM of the imaging PSF.

Equations (37)

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W ( ρ ) = f ( mod [ K ( ρ ) λ ] ) ,
C m = 0 1 d t exp ( 2 π i m t ) exp ( 2 π i f ( t ) λ ) ,
W m ( ρ ) = m K ( ρ ) ,
K ( ρ ) = Δ y NA ρ y λ + Δ z n 2 NA 2 | ρ | 2 λ ,
f ( t ) = n = 1 N a n cos ( 2 π n t ) ,
Z ( a 0 , , a N ) = m = M M ( | C m | 2 η m ) 2 ,
W ( ρ ) = W y z ( ρ x , ρ y ) + W x ( ρ x ) ,
sin α = 1 R d W x d ρ x .
x = F sin α = 1 NA d W x d ρ x ,
d x = d ( F sin α ) d ρ x d ρ x = 1 NA d 2 W x d ρ x 2 d ρ x .
I f ( x , y ) = ( 1 NA d 2 W x d ρ x 2 ) 1 | U f ( x , y ) | 2 ,
U f ( x , y ) = NA λ 1 ρ x 2 1 ρ x 2 d ρ y A ( ρ x , ρ y ) exp ( 2 π i ρ y y NA λ ) ,
U f ( x , y ) = 2 A NA λ 1 ρ x 2 sinc ( 2 π 1 ρ x 2 y NA λ ) ,
I f ( x , y ) = ( 1 NA d 2 W x d ρ x 2 ) 1 4 A 2 NA 2 λ 2 ( 1 ρ x 2 ) [ sinc ( 2 π 1 ρ x 2 y NA λ ) ] 2 .
I f ( x , y ) = 4 A 2 NA 3 a λ 2 ( 1 [ NA x a ] 2 ) sinc ( 2 π 1 [ NA x a ] 2 y NA λ ) 2 .
d 2 W x d ρ x 2 1 ρ x 2 .
W x ( ρ x ) = 3 4 w NA [ ρ x 2 1 6 ρ x 4 ] ,
x = 3 2 l [ ρ x 1 3 ρ x 3 ] .
ρ x = 2 cos ( π 3 + 1 3 arccos ( x l ) ) .
d 2 W x d ρ x 2 d y | U f ( x , y ) | 2 1 ρ x 2 ,
W x ( ρ x ) = w 2 NA π [ ρ x arcsin ( ρ x ) 1 3 ( 1 ρ x 2 ) 3 2 + 1 ρ x 2 ]
H i l l ( x , y , z ) = m H e x ( y m Δ y , z m Δ z ) ,
I ( M x , M y , y s ) = d x d y d z H e m ( x x , y y , z + Δ z Δ y y ) F ( x , y + y s , z ) H i l l ( x , y , z ) ,
I ( M x , M y , y s ) = m I m ( x , y m Δ y , y s ) ,
I m ( x , y , y s ) = d x d y d z H e m ( x x , y y + y s , z + Δ z Δ y y ) H e x ( y y s , z ) × F ( x , y + m Δ y , z + m Δ z ) ,
I m ( x , y , y s ) = d x d y d z H e m ( x x , y y + y s , z ) H e x ( y y s , z ) × F ( x , y + m Δ y , z + m Δ z ) .
J m ( x i , y i ) = d y I m ( x i , y i , y i + y ) = d x d y d z H ( x i x , y i y , z ) F ( x , y + m Δ y , z + m Δ z ) ,
H ( x , y , z ) = H e m ( x , y , z ) [ d y H e x ( y + y , z ) ]
B ( z ) = d x d y H ( x , y , z ) ,
I m ( x , y , z ) = d x d y H e m ( x x , y y , m Δ z z ) H e x ( y , z m Δ z ) ,
T m ( y , z ) = d x d y d z H e m ( x x , y , z z ) H e x ( y , z ) ,
FOV i l l = 2 F 0 sin η = N 2 λ NA i l l .
z c = s l 1 tan α i l l tan β tan α i l l + tan α d e t .
R ( ϵ 1 , ϵ 2 ) = sin ( 1 2 [ ϕ ( ϵ 1 ) ϕ ( ϵ 2 ) ] ) cos ( 1 2 [ ϕ ( ϵ 1 ) ϕ ( ϵ 2 ) ] ) + C ,
ρ = [ cos θ sin θ sin θ cos θ ] [ M x 0 0 M y ] ( σ σ 0 ) ,
W = g ( mod [ 1 λ A σ x R s ] ) + g ( mod [ 1 λ A σ y R s ] ) + 1 2 B | σ | 2 R S 2 ,
x k l m = F 0 R s [ cos θ sin θ sin θ cos θ ] [ 1 / M x 0 0 1 / M y ] ( A [ k l ] + m Δ B σ 0 R s ) + x 0 ,