Abstract

Recently, Fourier light field microscopy was proposed to overcome the limitations in conventional light field microscopy by placing a micro-lens array at the aperture stop of the microscope objective instead of the image plane. In this way, a collection of orthographic views from different perspectives are directly captured. When inspecting fluorescent samples, the sensitivity and noise of the sensors are a major concern and large sensor pixels are required to cope with low-light conditions, which implies under-sampling issues. In this context, we analyze the sampling patterns in Fourier light field microscopy to understand to what extent computational super-resolution can be triggered during deconvolution in order to improve the resolution of the 3D reconstruction of the imaged data.

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

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2020 (1)

2019 (4)

2018 (3)

2017 (1)

L. Cong, Z. Wang, Y. Chai, W. Hang, C. Shang, W. Yang, L. Bai, J. Du, K. Wang, and Q. Wen, “Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (Danio rerio),” eLife 6, e28158 (2017).
[Crossref]

2016 (2)

A. Llavador, J. Sola-Pikabea, G. Saavedra, B. Javidi, and M. Martínez-Corral, “Resolution improvements in integral microscopy with Fourier plane recording,” Opt. Express 24(18), 20792–20798 (2016).
[Crossref]

M. W. Tao, J. C. Su, T. C. Wang, J. Malik, and R. Ramamoorthi, “Depth Estimation and Specular Removal for Glossy Surfaces Using Point and Line Consistency with Light-Field Cameras,” IEEE Trans. Pattern Anal. Mach. Intell. 38(6), 1155–1169 (2016).
[Crossref]

2015 (2)

D. G. Dansereau, O. Pizarro, and S. B. Williams, “Linear Volumetric Focus for Light Field Cameras,” ACM Trans. Graph. 34(2), 1–20 (2015).
[Crossref]

C.-K. Liang and R. Ramamoorthi, “A Light Transport Framework for Lenslet Light Field Cameras,” ACM Trans. Graph. 34(2), 1–19 (2015).
[Crossref]

2014 (3)

R. Prevedel, Y. G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy,” Nat. Methods 11(7), 727–730 (2014).
[Crossref]

N. Cohen, S. Yang, A. Andalman, M. Broxton, L. Grosenick, K. Deisseroth, M. Horowitz, and M. Levoy, “Enhancing the performance of the light field microscope using wavefront coding,” Opt. Express 22(20), 24817–24839 (2014).
[Crossref]

S. Wanner and B. Goldluecke, “Variational light field analysis for disparity estimation and super-resolution,” IEEE Trans. Pattern Anal. Mach. Intell. 36(3), 606–619 (2014).
[Crossref]

2013 (2)

2012 (2)

T. Georgiev and A. Lumsdaine, “The multifocus plenoptic camera,” Proc. SPIE 8299, 829908–829911 (2012).
[Crossref]

T. E. Bishop and P. Favaro, “The light field camera: Extended depth of field, aliasing, and superresolution,” IEEE Trans. Pattern Anal. Mach. Intell. 34(5), 972–986 (2012).
[Crossref]

2011 (2)

2009 (2)

M. Martínez-Corral and G. Saavedra, “The Resolution Challenge in 3D Optical Microscopy,” Prog. Opt. 53, 1–67 (2009).
[Crossref]

M. Levoy, Z. Zhang, and I. McDowall, “Recording and controlling the 4D light field in a microscope using microlens arrays,” J. Microsc. 235(2), 144–162 (2009).
[Crossref]

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]

S. S. Young and R. G. Driggers, “Superresolution image reconstruction from a sequence of aliased imagery,” Appl. Opt. 45(21), 5073–5085 (2006).
[Crossref]

2004 (2)

S. Farsiu, D. Robinson, M. Elad, and P. Milanfar, “Advances and challenges in super-resolution,” Int. J. Imaging Syst. Technol. 14(2), 47–57 (2004).
[Crossref]

S.-H. Hong, J.-S. Jang, and B. Javidi, “Three-dimensional volumetric object reconstruction using computational integral imaging,” Opt. Express 12(3), 483–491 (2004).
[Crossref]

2003 (1)

M. G. Kang and S. Chaudhuri, “Super-resolution image reconstruction,” IEEE Signal Process. Mag. 20(3), 19–20 (2003).
[Crossref]

2002 (1)

S. Baker and T. Kanade, “Limits on super-resolution and how to break them,” IEEE Trans. Pattern Anal. Mach. Intell. 24(9), 1167–1183 (2002).
[Crossref]

1992 (1)

K. Grochenig, “Reconstruction Algorithms in Irregular Sampling,” Math. Comput. 59(199), 181–194 (1992).
[Crossref]

1987 (1)

K. D. Sauer and J. P. Allebach, “Iterative Reconstruction of Band Limited Images from Nonuniformly Spaced Samples,” IEEE Trans. Circuits Syst. 34(12), 1497–1506 (1987).
[Crossref]

1974 (1)

L. B. Lucy, “An iterative technique for the rectification of observed distributions,” The Astron. J. 79, 745 (1974).
[Crossref]

1972 (1)

1908 (1)

G. Lippmann, “Épreuves Réversibles Donnant La Sensation Du Relief,” J. Phys. Theor. Appl. 7(1), 821–825 (1908).
[Crossref]

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]

Adelson, E. H.

E. H. Adelson and J. Y. A. Wang, “Single Lens Stereo with a Plenoptic Camera,” Tech. Rep. 2 (1992).

Allebach, J. P.

K. D. Sauer and J. P. Allebach, “Iterative Reconstruction of Band Limited Images from Nonuniformly Spaced Samples,” IEEE Trans. Circuits Syst. 34(12), 1497–1506 (1987).
[Crossref]

Altshuller, Y.

Andalman, A.

Bai, L.

L. Cong, Z. Wang, Y. Chai, W. Hang, C. Shang, W. Yang, L. Bai, J. Du, K. Wang, and Q. Wen, “Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (Danio rerio),” eLife 6, e28158 (2017).
[Crossref]

Baker, S.

S. Baker and T. Kanade, “Limits on super-resolution and how to break them,” IEEE Trans. Pattern Anal. Mach. Intell. 24(9), 1167–1183 (2002).
[Crossref]

Balázs, B.

N. Wagner, N. Norlin, J. Gierten, G. de Medeiros, B. Balázs, J. Wittbrodt, L. Hufnagel, and R. Prevedel, “Instantaneous isotropic volumetric imaging of fast biological processes,” Nat. Methods 16(6), 497–500 (2019).
[Crossref]

Barreiro, J. C.

Berkner, K.

Bishop, T. E.

T. E. Bishop and P. Favaro, “The light field camera: Extended depth of field, aliasing, and superresolution,” IEEE Trans. Pattern Anal. Mach. Intell. 34(5), 972–986 (2012).
[Crossref]

T. E. Bishop, S. Zanetti, and P. Favaro, “Light field superresolution,” in 2009 IEEE International Conference on Computational Photography (ICCP), (2009), pp. 1–9.

Boyden, E. S.

R. Prevedel, Y. G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy,” Nat. Methods 11(7), 727–730 (2014).
[Crossref]

Brédif, M.

R. Ng, M. Levoy, M. Brédif, G. Duval, M. Horowitz, and P. Hanrahan, “Light Field Photography with a Hand-Held Plenoptic Camera – Stanford Tech Report CTSR 2005-02,” Tech. rep. (2005).

Brooker, G.

Broxton, M.

Chai, Y.

L. Cong, Z. Wang, Y. Chai, W. Hang, C. Shang, W. Yang, L. Bai, J. Du, K. Wang, and Q. Wen, “Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (Danio rerio),” eLife 6, e28158 (2017).
[Crossref]

Chan, W. S.

W. S. Chan, E. Y. Lam, M. K. Ng, and G. Y. Mak, “Super-resolution reconstruction in a computational compound-eye imaging system,” in Multidimensional Systems and Signal Processing, vol. 18 (2007), pp. 83–101.

Chaudhuri, S.

M. G. Kang and S. Chaudhuri, “Super-resolution image reconstruction,” IEEE Signal Process. Mag. 20(3), 19–20 (2003).
[Crossref]

Chen, Y.

Cohen, N.

Cong, L.

L. Cong, Z. Wang, Y. Chai, W. Hang, C. Shang, W. Yang, L. Bai, J. Du, K. Wang, and Q. Wen, “Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (Danio rerio),” eLife 6, e28158 (2017).
[Crossref]

Dansereau, D. G.

D. G. Dansereau, O. Pizarro, and S. B. Williams, “Linear Volumetric Focus for Light Field Cameras,” ACM Trans. Graph. 34(2), 1–20 (2015).
[Crossref]

de Medeiros, G.

N. Wagner, N. Norlin, J. Gierten, G. de Medeiros, B. Balázs, J. Wittbrodt, L. Hufnagel, and R. Prevedel, “Instantaneous isotropic volumetric imaging of fast biological processes,” Nat. Methods 16(6), 497–500 (2019).
[Crossref]

Deisseroth, K.

Driggers, R. G.

Du, J.

L. Cong, Z. Wang, Y. Chai, W. Hang, C. Shang, W. Yang, L. Bai, J. Du, K. Wang, and Q. Wen, “Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (Danio rerio),” eLife 6, e28158 (2017).
[Crossref]

Duval, G.

R. Ng, M. Levoy, M. Brédif, G. Duval, M. Horowitz, and P. Hanrahan, “Light Field Photography with a Hand-Held Plenoptic Camera – Stanford Tech Report CTSR 2005-02,” Tech. rep. (2005).

Elad, M.

S. Farsiu, D. Robinson, M. Elad, and P. Milanfar, “Advances and challenges in super-resolution,” Int. J. Imaging Syst. Technol. 14(2), 47–57 (2004).
[Crossref]

Farsiu, S.

S. Farsiu, D. Robinson, M. Elad, and P. Milanfar, “Advances and challenges in super-resolution,” Int. J. Imaging Syst. Technol. 14(2), 47–57 (2004).
[Crossref]

Favaro, P.

T. E. Bishop and P. Favaro, “The light field camera: Extended depth of field, aliasing, and superresolution,” IEEE Trans. Pattern Anal. Mach. Intell. 34(5), 972–986 (2012).
[Crossref]

T. E. Bishop, S. Zanetti, and P. Favaro, “Light field superresolution,” in 2009 IEEE International Conference on Computational Photography (ICCP), (2009), pp. 1–9.

Fleischer, J.

C.-H. Lu, S. Muenzel, and J. Fleischer, “High-Resolution Light-Field Microscopy,” in Imaging and Applied Optics, (2013), p. CTh3B.2.

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]

French, J. B.

Frohman, M. A.

Garcia-Sucerquia, J.

Georgiev, T.

T. Georgiev and A. Lumsdaine, “The multifocus plenoptic camera,” Proc. SPIE 8299, 829908–829911 (2012).
[Crossref]

A. Lumsdaine and T. Georgiev, “The focused plenoptic camera,” in 2009 IEEE International Conference on Computational Photography, ICCP 09, (IEEE, 2009), pp. 1–8.

Gierten, J.

N. Wagner, N. Norlin, J. Gierten, G. de Medeiros, B. Balázs, J. Wittbrodt, L. Hufnagel, and R. Prevedel, “Instantaneous isotropic volumetric imaging of fast biological processes,” Nat. Methods 16(6), 497–500 (2019).
[Crossref]

Goldluecke, B.

S. Wanner and B. Goldluecke, “Variational light field analysis for disparity estimation and super-resolution,” IEEE Trans. Pattern Anal. Mach. Intell. 36(3), 606–619 (2014).
[Crossref]

Greene, J.

Grochenig, K.

K. Grochenig, “Reconstruction Algorithms in Irregular Sampling,” Math. Comput. 59(199), 181–194 (1992).
[Crossref]

Gröchenig, K.

K. Gröchenig and T. Strohmer, “Numerical and Theoretical Aspects of Nonuniform Sampling of Band-Limited Images,” in F. Marvasti, (eds) Nonuniform Sampling. Information Technology: Transmission, Processing, and Storage (Springer, Boston, MA, 2001), pp. 283–324.

Grosenick, L.

Gu, M.

M. Gu, Advanced Optical Imaging Theory, vol. 75 (Springer, Berlin, Heidelberg, 1999).

Guo, C.

Hadap, S.

M. W. Tao, S. Hadap, J. Malik, and R. Ramamoorthi, “Depth from combining defocus and correspondence using light-field cameras,” in Proceedings of the IEEE International Conference on Computer Vision, (2013), pp. 673–680.

Hang, W.

L. Cong, Z. Wang, Y. Chai, W. Hang, C. Shang, W. Yang, L. Bai, J. Du, K. Wang, and Q. Wen, “Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (Danio rerio),” eLife 6, e28158 (2017).
[Crossref]

Hanrahan, P.

R. Ng, M. Levoy, M. Brédif, G. Duval, M. Horowitz, and P. Hanrahan, “Light Field Photography with a Hand-Held Plenoptic Camera – Stanford Tech Report CTSR 2005-02,” Tech. rep. (2005).

Hoffmann, M.

R. Prevedel, Y. G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy,” Nat. Methods 11(7), 727–730 (2014).
[Crossref]

Hong, S.-H.

Horowitz, M.

N. Cohen, S. Yang, A. Andalman, M. Broxton, L. Grosenick, K. Deisseroth, M. Horowitz, and M. Levoy, “Enhancing the performance of the light field microscope using wavefront coding,” Opt. Express 22(20), 24817–24839 (2014).
[Crossref]

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

R. Ng, M. Levoy, M. Brédif, G. Duval, M. Horowitz, and P. Hanrahan, “Light Field Photography with a Hand-Held Plenoptic Camera – Stanford Tech Report CTSR 2005-02,” Tech. rep. (2005).

Hua, X.

Hufnagel, L.

N. Wagner, N. Norlin, J. Gierten, G. de Medeiros, B. Balázs, J. Wittbrodt, L. Hufnagel, and R. Prevedel, “Instantaneous isotropic volumetric imaging of fast biological processes,” Nat. Methods 16(6), 497–500 (2019).
[Crossref]

Jang, J.-S.

Javidi, B.

Jia, S.

Jin, X.

Kanade, T.

S. Baker and T. Kanade, “Limits on super-resolution and how to break them,” IEEE Trans. Pattern Anal. Mach. Intell. 24(9), 1167–1183 (2002).
[Crossref]

Kang, M. G.

M. G. Kang and S. Chaudhuri, “Super-resolution image reconstruction,” IEEE Signal Process. Mag. 20(3), 19–20 (2003).
[Crossref]

Kato, S.

R. Prevedel, Y. G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy,” Nat. Methods 11(7), 727–730 (2014).
[Crossref]

Kim-Holzapfel, D.

Lam, E. Y.

W. S. Chan, E. Y. Lam, M. K. Ng, and G. Y. Mak, “Super-resolution reconstruction in a computational compound-eye imaging system,” in Multidimensional Systems and Signal Processing, vol. 18 (2007), pp. 83–101.

Lasser, T.

Lei Tian, A.

Levoy, M.

N. Cohen, S. Yang, A. Andalman, M. Broxton, L. Grosenick, K. Deisseroth, M. Horowitz, and M. Levoy, “Enhancing the performance of the light field microscope using wavefront coding,” Opt. Express 22(20), 24817–24839 (2014).
[Crossref]

M. Broxton, L. Grosenick, S. Yang, N. Cohen, A. Andalman, K. Deisseroth, and M. Levoy, “Wave optics theory and 3-D deconvolution for the light field microscope,” Opt. Express 21(21), 25418–25439 (2013).
[Crossref]

M. Levoy, Z. Zhang, and I. McDowall, “Recording and controlling the 4D light field in a microscope using microlens arrays,” J. Microsc. 235(2), 144–162 (2009).
[Crossref]

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

R. Ng, M. Levoy, M. Brédif, G. Duval, M. Horowitz, and P. Hanrahan, “Light Field Photography with a Hand-Held Plenoptic Camera – Stanford Tech Report CTSR 2005-02,” Tech. rep. (2005).

Li, H.

Li, W.

Liang, C.-K.

C.-K. Liang and R. Ramamoorthi, “A Light Transport Framework for Lenslet Light Field Cameras,” ACM Trans. Graph. 34(2), 1–19 (2015).
[Crossref]

Lippmann, G.

G. Lippmann, “Épreuves Réversibles Donnant La Sensation Du Relief,” J. Phys. Theor. Appl. 7(1), 821–825 (1908).
[Crossref]

Liu, W.

Llavador, A.

Lu, C.-H.

C.-H. Lu, S. Muenzel, and J. Fleischer, “High-Resolution Light-Field Microscopy,” in Imaging and Applied Optics, (2013), p. CTh3B.2.

Lucy, L. B.

L. B. Lucy, “An iterative technique for the rectification of observed distributions,” The Astron. J. 79, 745 (1974).
[Crossref]

Lumsdaine, A.

T. Georgiev and A. Lumsdaine, “The multifocus plenoptic camera,” Proc. SPIE 8299, 829908–829911 (2012).
[Crossref]

A. Lumsdaine and T. Georgiev, “The focused plenoptic camera,” in 2009 IEEE International Conference on Computational Photography, ICCP 09, (IEEE, 2009), pp. 1–8.

Ma, K. K.

J. Tian and K. K. Ma, “A survey on super-resolution imaging,” Signal, Image Video Process. 5(3), 329–342 (2011).
[Crossref]

Mak, G. Y.

W. S. Chan, E. Y. Lam, M. K. Ng, and G. Y. Mak, “Super-resolution reconstruction in a computational compound-eye imaging system,” in Multidimensional Systems and Signal Processing, vol. 18 (2007), pp. 83–101.

Malik, J.

M. W. Tao, J. C. Su, T. C. Wang, J. Malik, and R. Ramamoorthi, “Depth Estimation and Specular Removal for Glossy Surfaces Using Point and Line Consistency with Light-Field Cameras,” IEEE Trans. Pattern Anal. Mach. Intell. 38(6), 1155–1169 (2016).
[Crossref]

M. W. Tao, S. Hadap, J. Malik, and R. Ramamoorthi, “Depth from combining defocus and correspondence using light-field cameras,” in Proceedings of the IEEE International Conference on Computer Vision, (2013), pp. 673–680.

Martinez-Corral, M.

Martínez-Corral, M.

McDowall, I.

M. Levoy, Z. Zhang, and I. McDowall, “Recording and controlling the 4D light field in a microscope using microlens arrays,” J. Microsc. 235(2), 144–162 (2009).
[Crossref]

Meng, Y.

Milanfar, P.

S. Farsiu, D. Robinson, M. Elad, and P. Milanfar, “Advances and challenges in super-resolution,” Int. J. Imaging Syst. Technol. 14(2), 47–57 (2004).
[Crossref]

Muenzel, S.

C.-H. Lu, S. Muenzel, and J. Fleischer, “High-Resolution Light-Field Microscopy,” in Imaging and Applied Optics, (2013), p. CTh3B.2.

Ng, M. K.

W. S. Chan, E. Y. Lam, M. K. Ng, and G. Y. Mak, “Super-resolution reconstruction in a computational compound-eye imaging system,” in Multidimensional Systems and Signal Processing, vol. 18 (2007), pp. 83–101.

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]

R. Ng, M. Levoy, M. Brédif, G. Duval, M. Horowitz, and P. Hanrahan, “Light Field Photography with a Hand-Held Plenoptic Camera – Stanford Tech Report CTSR 2005-02,” Tech. rep. (2005).

R. Ng, “Fourier slice photography,” in ACM SIGGRAPH 2005 Papers on - SIGGRAPH ’05, (2005), pp. 735–744.

Norlin, N.

N. Wagner, N. Norlin, J. Gierten, G. de Medeiros, B. Balázs, J. Wittbrodt, L. Hufnagel, and R. Prevedel, “Instantaneous isotropic volumetric imaging of fast biological processes,” Nat. Methods 16(6), 497–500 (2019).
[Crossref]

Page, J.

Pak, N.

R. Prevedel, Y. G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy,” Nat. Methods 11(7), 727–730 (2014).
[Crossref]

Perwass, C.

C. Perwass and L. Wietzke, “Single lens 3D-camera with extended depth-of-field,” (2012), p. 829108.

Pizarro, O.

D. G. Dansereau, O. Pizarro, and S. B. Williams, “Linear Volumetric Focus for Light Field Cameras,” ACM Trans. Graph. 34(2), 1–20 (2015).
[Crossref]

Prevedel, R.

N. Wagner, N. Norlin, J. Gierten, G. de Medeiros, B. Balázs, J. Wittbrodt, L. Hufnagel, and R. Prevedel, “Instantaneous isotropic volumetric imaging of fast biological processes,” Nat. Methods 16(6), 497–500 (2019).
[Crossref]

R. Prevedel, Y. G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy,” Nat. Methods 11(7), 727–730 (2014).
[Crossref]

Ramamoorthi, R.

M. W. Tao, J. C. Su, T. C. Wang, J. Malik, and R. Ramamoorthi, “Depth Estimation and Specular Removal for Glossy Surfaces Using Point and Line Consistency with Light-Field Cameras,” IEEE Trans. Pattern Anal. Mach. Intell. 38(6), 1155–1169 (2016).
[Crossref]

C.-K. Liang and R. Ramamoorthi, “A Light Transport Framework for Lenslet Light Field Cameras,” ACM Trans. Graph. 34(2), 1–19 (2015).
[Crossref]

M. W. Tao, S. Hadap, J. Malik, and R. Ramamoorthi, “Depth from combining defocus and correspondence using light-field cameras,” in Proceedings of the IEEE International Conference on Computer Vision, (2013), pp. 673–680.

Raskar, R.

R. Prevedel, Y. G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy,” Nat. Methods 11(7), 727–730 (2014).
[Crossref]

Richardson, W. H.

Robinson, D.

S. Farsiu, D. Robinson, M. Elad, and P. Milanfar, “Advances and challenges in super-resolution,” Int. J. Imaging Syst. Technol. 14(2), 47–57 (2004).
[Crossref]

Rosen, J.

Saavedra, G.

Sanchez-Ortiga, E.

Sauer, K. D.

K. D. Sauer and J. P. Allebach, “Iterative Reconstruction of Band Limited Images from Nonuniformly Spaced Samples,” IEEE Trans. Circuits Syst. 34(12), 1497–1506 (1987).
[Crossref]

Schrödel, T.

R. Prevedel, Y. G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy,” Nat. Methods 11(7), 727–730 (2014).
[Crossref]

Schroeder, B.

Scrofani, G.

Shang, C.

L. Cong, Z. Wang, Y. Chai, W. Hang, C. Shang, W. Yang, L. Bai, J. Du, K. Wang, and Q. Wen, “Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (Danio rerio),” eLife 6, e28158 (2017).
[Crossref]

Shroff, S. A.

Siegel, N.

Simpkins, J.

J. Simpkins and R. Stevenson, “An Introduction to Super-Resolution Imaging,” in Mathematical Optics (CRC Press, 2012), pp. 555–580.

Sola-Pikabea, J.

Stefanoiu, A.

Stevenson, R.

J. Simpkins and R. Stevenson, “An Introduction to Super-Resolution Imaging,” in Mathematical Optics (CRC Press, 2012), pp. 555–580.

Strohmer, T.

K. Gröchenig and T. Strohmer, “Numerical and Theoretical Aspects of Nonuniform Sampling of Band-Limited Images,” in F. Marvasti, (eds) Nonuniform Sampling. Information Technology: Transmission, Processing, and Storage (Springer, Boston, MA, 2001), pp. 283–324.

Su, J. C.

M. W. Tao, J. C. Su, T. C. Wang, J. Malik, and R. Ramamoorthi, “Depth Estimation and Specular Removal for Glossy Surfaces Using Point and Line Consistency with Light-Field Cameras,” IEEE Trans. Pattern Anal. Mach. Intell. 38(6), 1155–1169 (2016).
[Crossref]

Symvoulidis, P.

Takamaru, K.-I.

Tao, M. W.

M. W. Tao, J. C. Su, T. C. Wang, J. Malik, and R. Ramamoorthi, “Depth Estimation and Specular Removal for Glossy Surfaces Using Point and Line Consistency with Light-Field Cameras,” IEEE Trans. Pattern Anal. Mach. Intell. 38(6), 1155–1169 (2016).
[Crossref]

M. W. Tao, S. Hadap, J. Malik, and R. Ramamoorthi, “Depth from combining defocus and correspondence using light-field cameras,” in Proceedings of the IEEE International Conference on Computer Vision, (2013), pp. 673–680.

Tian, J.

J. Tian and K. K. Ma, “A survey on super-resolution imaging,” Signal, Image Video Process. 5(3), 329–342 (2011).
[Crossref]

Vaziri, A.

R. Prevedel, Y. G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy,” Nat. Methods 11(7), 727–730 (2014).
[Crossref]

Voelz, D. G.

D. G. Voelz, Computational Fourier Optics: A MATLAB® Tutorial (SPIE, 2011).

Wagner, N.

N. Wagner, N. Norlin, J. Gierten, G. de Medeiros, B. Balázs, J. Wittbrodt, L. Hufnagel, and R. Prevedel, “Instantaneous isotropic volumetric imaging of fast biological processes,” Nat. Methods 16(6), 497–500 (2019).
[Crossref]

Wang, J. Y. A.

E. H. Adelson and J. Y. A. Wang, “Single Lens Stereo with a Plenoptic Camera,” Tech. Rep. 2 (1992).

Wang, K.

L. Cong, Z. Wang, Y. Chai, W. Hang, C. Shang, W. Yang, L. Bai, J. Du, K. Wang, and Q. Wen, “Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (Danio rerio),” eLife 6, e28158 (2017).
[Crossref]

Wang, T. C.

M. W. Tao, J. C. Su, T. C. Wang, J. Malik, and R. Ramamoorthi, “Depth Estimation and Specular Removal for Glossy Surfaces Using Point and Line Consistency with Light-Field Cameras,” IEEE Trans. Pattern Anal. Mach. Intell. 38(6), 1155–1169 (2016).
[Crossref]

Wang, Z.

L. Cong, Z. Wang, Y. Chai, W. Hang, C. Shang, W. Yang, L. Bai, J. Du, K. Wang, and Q. Wen, “Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (Danio rerio),” eLife 6, e28158 (2017).
[Crossref]

Wanner, S.

S. Wanner and B. Goldluecke, “Variational light field analysis for disparity estimation and super-resolution,” IEEE Trans. Pattern Anal. Mach. Intell. 36(3), 606–619 (2014).
[Crossref]

Wen, Q.

L. Cong, Z. Wang, Y. Chai, W. Hang, C. Shang, W. Yang, L. Bai, J. Du, K. Wang, and Q. Wen, “Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (Danio rerio),” eLife 6, e28158 (2017).
[Crossref]

Westmeyer, G. G.

Wetzstein, G.

R. Prevedel, Y. G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy,” Nat. Methods 11(7), 727–730 (2014).
[Crossref]

Wietzke, L.

C. Perwass and L. Wietzke, “Single lens 3D-camera with extended depth-of-field,” (2012), p. 829108.

Williams, S. B.

D. G. Dansereau, O. Pizarro, and S. B. Williams, “Linear Volumetric Focus for Light Field Cameras,” ACM Trans. Graph. 34(2), 1–20 (2015).
[Crossref]

Wittbrodt, J.

N. Wagner, N. Norlin, J. Gierten, G. de Medeiros, B. Balázs, J. Wittbrodt, L. Hufnagel, and R. Prevedel, “Instantaneous isotropic volumetric imaging of fast biological processes,” Nat. Methods 16(6), 497–500 (2019).
[Crossref]

Wolberg, G.

G. Wolberg, “Sampling, Reconstruction, and Antialiasing,” in Digital Image Warping (CRC Press, 2004), pp. 1–32.

Xiong, B. O.

Xue, Y.

Yang, S.

Yang, W.

L. Cong, Z. Wang, Y. Chai, W. Hang, C. Shang, W. Yang, L. Bai, J. Du, K. Wang, and Q. Wen, “Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (Danio rerio),” eLife 6, e28158 (2017).
[Crossref]

Yoon, Y. G.

R. Prevedel, Y. G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy,” Nat. Methods 11(7), 727–730 (2014).
[Crossref]

Young, S. S.

Zanetti, S.

T. E. Bishop, S. Zanetti, and P. Favaro, “Light field superresolution,” in 2009 IEEE International Conference on Computational Photography (ICCP), (2009), pp. 1–9.

Zhang, Z.

M. Levoy, Z. Zhang, and I. McDowall, “Recording and controlling the 4D light field in a microscope using microlens arrays,” J. Microsc. 235(2), 144–162 (2009).
[Crossref]

Zimmer, M.

R. Prevedel, Y. G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy,” Nat. Methods 11(7), 727–730 (2014).
[Crossref]

ACM Trans. Graph. (3)

D. G. Dansereau, O. Pizarro, and S. B. Williams, “Linear Volumetric Focus for Light Field Cameras,” ACM Trans. Graph. 34(2), 1–20 (2015).
[Crossref]

C.-K. Liang and R. Ramamoorthi, “A Light Transport Framework for Lenslet Light Field Cameras,” ACM Trans. Graph. 34(2), 1–19 (2015).
[Crossref]

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

Adv. Opt. Photonics (1)

M. Martinez-Corral and B. Javidi, “Fundamentals of 3D imaging and displays: a tutorial on integral imaging, light-field, and plenoptic systems,” Adv. Opt. Photonics 10(3), 512–566 (2018).
[Crossref]

Appl. Opt. (2)

Biomed. Opt. Express (3)

eLife (1)

L. Cong, Z. Wang, Y. Chai, W. Hang, C. Shang, W. Yang, L. Bai, J. Du, K. Wang, and Q. Wen, “Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (Danio rerio),” eLife 6, e28158 (2017).
[Crossref]

IEEE Signal Process. Mag. (1)

M. G. Kang and S. Chaudhuri, “Super-resolution image reconstruction,” IEEE Signal Process. Mag. 20(3), 19–20 (2003).
[Crossref]

IEEE Trans. Circuits Syst. (1)

K. D. Sauer and J. P. Allebach, “Iterative Reconstruction of Band Limited Images from Nonuniformly Spaced Samples,” IEEE Trans. Circuits Syst. 34(12), 1497–1506 (1987).
[Crossref]

IEEE Trans. Pattern Anal. Mach. Intell. (4)

S. Baker and T. Kanade, “Limits on super-resolution and how to break them,” IEEE Trans. Pattern Anal. Mach. Intell. 24(9), 1167–1183 (2002).
[Crossref]

M. W. Tao, J. C. Su, T. C. Wang, J. Malik, and R. Ramamoorthi, “Depth Estimation and Specular Removal for Glossy Surfaces Using Point and Line Consistency with Light-Field Cameras,” IEEE Trans. Pattern Anal. Mach. Intell. 38(6), 1155–1169 (2016).
[Crossref]

S. Wanner and B. Goldluecke, “Variational light field analysis for disparity estimation and super-resolution,” IEEE Trans. Pattern Anal. Mach. Intell. 36(3), 606–619 (2014).
[Crossref]

T. E. Bishop and P. Favaro, “The light field camera: Extended depth of field, aliasing, and superresolution,” IEEE Trans. Pattern Anal. Mach. Intell. 34(5), 972–986 (2012).
[Crossref]

Int. J. Imaging Syst. Technol. (1)

S. Farsiu, D. Robinson, M. Elad, and P. Milanfar, “Advances and challenges in super-resolution,” Int. J. Imaging Syst. Technol. 14(2), 47–57 (2004).
[Crossref]

J. Microsc. (1)

M. Levoy, Z. Zhang, and I. McDowall, “Recording and controlling the 4D light field in a microscope using microlens arrays,” J. Microsc. 235(2), 144–162 (2009).
[Crossref]

J. Opt. Soc. Am. (1)

J. Phys. Theor. Appl. (1)

G. Lippmann, “Épreuves Réversibles Donnant La Sensation Du Relief,” J. Phys. Theor. Appl. 7(1), 821–825 (1908).
[Crossref]

Math. Comput. (1)

K. Grochenig, “Reconstruction Algorithms in Irregular Sampling,” Math. Comput. 59(199), 181–194 (1992).
[Crossref]

Nat. Methods (2)

R. Prevedel, Y. G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E. S. Boyden, and A. Vaziri, “Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy,” Nat. Methods 11(7), 727–730 (2014).
[Crossref]

N. Wagner, N. Norlin, J. Gierten, G. de Medeiros, B. Balázs, J. Wittbrodt, L. Hufnagel, and R. Prevedel, “Instantaneous isotropic volumetric imaging of fast biological processes,” Nat. Methods 16(6), 497–500 (2019).
[Crossref]

Opt. Express (7)

OSA Continuum (1)

Proc. SPIE (1)

T. Georgiev and A. Lumsdaine, “The multifocus plenoptic camera,” Proc. SPIE 8299, 829908–829911 (2012).
[Crossref]

Prog. Opt. (1)

M. Martínez-Corral and G. Saavedra, “The Resolution Challenge in 3D Optical Microscopy,” Prog. Opt. 53, 1–67 (2009).
[Crossref]

Signal, Image Video Process. (1)

J. Tian and K. K. Ma, “A survey on super-resolution imaging,” Signal, Image Video Process. 5(3), 329–342 (2011).
[Crossref]

The Astron. J. (1)

L. B. Lucy, “An iterative technique for the rectification of observed distributions,” The Astron. J. 79, 745 (1974).
[Crossref]

Other (14)

M. Gu, Advanced Optical Imaging Theory, vol. 75 (Springer, Berlin, Heidelberg, 1999).

J. Simpkins and R. Stevenson, “An Introduction to Super-Resolution Imaging,” in Mathematical Optics (CRC Press, 2012), pp. 555–580.

W. S. Chan, E. Y. Lam, M. K. Ng, and G. Y. Mak, “Super-resolution reconstruction in a computational compound-eye imaging system,” in Multidimensional Systems and Signal Processing, vol. 18 (2007), pp. 83–101.

K. Gröchenig and T. Strohmer, “Numerical and Theoretical Aspects of Nonuniform Sampling of Band-Limited Images,” in F. Marvasti, (eds) Nonuniform Sampling. Information Technology: Transmission, Processing, and Storage (Springer, Boston, MA, 2001), pp. 283–324.

G. Wolberg, “Sampling, Reconstruction, and Antialiasing,” in Digital Image Warping (CRC Press, 2004), pp. 1–32.

C. Perwass and L. Wietzke, “Single lens 3D-camera with extended depth-of-field,” (2012), p. 829108.

R. Ng, “Fourier slice photography,” in ACM SIGGRAPH 2005 Papers on - SIGGRAPH ’05, (2005), pp. 735–744.

T. E. Bishop, S. Zanetti, and P. Favaro, “Light field superresolution,” in 2009 IEEE International Conference on Computational Photography (ICCP), (2009), pp. 1–9.

M. W. Tao, S. Hadap, J. Malik, and R. Ramamoorthi, “Depth from combining defocus and correspondence using light-field cameras,” in Proceedings of the IEEE International Conference on Computer Vision, (2013), pp. 673–680.

E. H. Adelson and J. Y. A. Wang, “Single Lens Stereo with a Plenoptic Camera,” Tech. Rep. 2 (1992).

R. Ng, M. Levoy, M. Brédif, G. Duval, M. Horowitz, and P. Hanrahan, “Light Field Photography with a Hand-Held Plenoptic Camera – Stanford Tech Report CTSR 2005-02,” Tech. rep. (2005).

A. Lumsdaine and T. Georgiev, “The focused plenoptic camera,” in 2009 IEEE International Conference on Computational Photography, ICCP 09, (IEEE, 2009), pp. 1–8.

C.-H. Lu, S. Muenzel, and J. Fleischer, “High-Resolution Light-Field Microscopy,” in Imaging and Applied Optics, (2013), p. CTh3B.2.

D. G. Voelz, Computational Fourier Optics: A MATLAB® Tutorial (SPIE, 2011).

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Figures (5)

Fig. 1.
Fig. 1. Reconstruction of the USAF 1951 resolution target. Top: (a) Raw elemental image of the resolution target acquired with our experimental FiMic (shown is a close up on groups 6 and 7 of the central elemental image). (b) The post-acquisition refocused image using the popular algorithm of shifting views and summing up [23]. (c) The deconvolved image at sensor resolution. (d) The reconstructed image at a 3x super-sampling of the object space, exploiting complementary multi-view aliasing in the elemental images. Bottom: Line profiles through the elements 6.4 to 7.3 of the images above. While the elemental image (a) and the refocused image (b) resolve up to element 6.4 (11 $\mu m$), the deconvolution resolves up to element 6.6 (8.8 $\mu m$) in (c) and element 7.1 (7.8 $\mu m$) in the computationally super-resolved image (d).
Fig. 2.
Fig. 2. Image formation in FLFM. (a) Ray diagram: light field propagation through the Fourier integral microscope. The FiMic depicted here makes use of an optical relay system (RL1 and RL2 with focal lengths $f_1$ and $f_2$, respectively) which conjugate the back aperture of the microscope objective (MO) with the MLA plane. The reason for the relay is that the back aperture is usually not accessible in conventional commercial MOs. A source point $\textbf {o}(o_x, o_y, z = f_{obj} + \Delta z)$ in front of the MO has a conjugate image by the first relay lens (RL1) at $z'$. RL2 picks up this image and magnified images are recorded behind each micro-lens as the light reaches the camera sensor. $f_{obj}$ denotes the MO focal length and $\Delta z$ represents the axial offset from the native object plane. (b) The field stop (FS) controls the size of the elemental images (EIs) as well as the size of the microscope’s field of view. See Eq. (1) and Eq. (2). (c) Overlapping images of the USAF resolution target when the FS is too large.
Fig. 3.
Fig. 3. Aliasing and EI sampling rates. a) The EIs formed behind off-axis micro-lenses are shifted with respect to the centers of the micro-lenses. b) FiMic image of the USAF 1951 resolution target placed at $\Delta z = -100 \mu m$. c) Zoomed-in regions of the EIs in b) showing distinct aliasing patterns in areas with high frequency features as highlighted by the arrows. The micro-lens centers (red dots) and the EI centers (dark blue dots) are mismatched for the off-axis EIs. d) The EIs exhibit different shift pattern with object depth. e) EIs offsets in pixels from the micro-lens centers with respect to a reference EI (closest to the optical axis) for objects placed at $\Delta z$ = [-120, 120] $\mu m$. The $\mu _{lens}$ index $= 0$ refers to the central micro-lens (closest to the OA). f) Sub-pixel shifts of the EIs with respect to the reference EI over depth. It is these sub-pixel shifts between the captured views that record complementary aliased information and motivate computational super-resolution.
Fig. 4.
Fig. 4. Reconstruction of the USAF 1951 target imaged at $\Delta z$ = [-120, 120] $\mu m$. a) Example central EI of the FiMic image (green), the refocused image (yellow), the deconvolved image at sensor resolution (red), the deconvolved image at 3x sensor resolution (blue) for arbitrarily picked axial positions $\Delta z = \{0,-20,-50, -100\}$. When compared to the raw and refocused images, the deconvolved images appear to better resolve details through deblurring. Element 7.1 appears resolved in the super-resolved image (blue oval). b) Contrast of the USAF element 7.1 over $\Delta z$ = [-120, 120] $\mu m$ is generally constant for all the methods in a). As expected, the super-resolved deconvolution shows the best contrast.
Fig. 5.
Fig. 5. 3D reconstruction of cotton fibers. a) Raw image acquired with our experimental FiMic setup and zoomed-in regions of an EI for details. b) Maximum intensity projections (MIPs) and zoomed-in regions of the 3D reconstructed sample ($\Delta z$ = [-150,150]$\mu m$) using our proposed method at sensor resolution ($s = 1$). c) MIPs of the super-resolved 3D reconstruction at 4x sensor resolution ($s = 4$). The deconvolved images resolve structures structures that do not show in the EI. The close-ups in b) and c) clearly shows that the super-resolved reconstruction recovers fine details in the sample, that are not resolved in the normal deconvolution.

Equations (12)

Equations on this page are rendered with MathJax. Learn more.

r F S = r m l f 2 / f m l .
r F O V = r F S f o b j / f 1 .
δ d i f f = N λ 2 N A o b j ,
δ s e n s o r = 2 ρ p x M F i M i c .
δ s u p e r = δ s e n s o r s .
U 0 ( x , y ; o ) = ( A / r ) e i k r ( sign ( Δ z o ) ) ,
U A S ( r a s ; o ) = 0 α U 0 ( θ ; o ) J 0 ( k r a s sin ( θ ) ) sin ( θ ) d θ ,
U M L A ( x m l a , y m l a ; o ) = U A S ( x m l a M r e l a y , y m l a M r e l a y ; o ) ,
U M L A + ( x m l a , y m l a ; o ) = U M L A ( x m l a , y m l a ; o ) T ( x m l a , y m l a ) .
U s e n s ( x s , y s ; o ) = F 1 { F { U M L A + ( x s , y s ; o ) } H r s ( f X , f Y ) } ,
H r s ( f X , f Y ) = e ( i k f m l 1 ( λ f X ) 2 ( λ f Y ) 2 ) .
v q + 1 = v q A T 1 [ A T m A v q ] ,