Abstract

Limited time-resolution in microscopy is an obstacle to many biological studies. Despite recent advances in hardware, digital cameras have limited operation modes that constrain frame-rate, integration time, and color sensing patterns. In this paper, we propose an approach to extend the temporal resolution of a conventional digital color camera by leveraging a multi-color illumination source. Our method allows for the imaging of single-hue objects at an increased frame-rate by trading spectral for temporal information (while retaining the ability to measure base hue). It also allows rapid switching to standard RGB acquisition. We evaluated the feasibility and performance of our method via experiments with mobile resolution targets. We observed a time-resolution increase by a factor 2.8 with a three-fold increase in temporal sampling rate. We further illustrate the use of our method to image the beating heart of a zebrafish larva, allowing the display of color or fast grayscale images. Our method is particularly well-suited to extend the capabilities of imaging systems where the flexibility of rapidly switching between high frame rate and color imaging are necessary.

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

Full Article  |  PDF Article
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References

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2017 (1)

2016 (1)

K. G. Chan, S. J. Streichan, L. A. Trinh, and M. Liebling, “Simultaneous temporal superresolution and denoising for cardiac fluorescence microscopy,” IEEE Trans. Comput. Imaging 2(3), 348–358 (2016).
[Crossref]

2015 (4)

T.-H. Tsai, P. Llull, X. Yuan, L. Carin, and D. J. Brady, “Spectral-temporal compressive imaging,” Opt. Lett. 40(17), 4054–4057 (2015).
[Crossref]

R. Koller, L. Schmid, N. Matsuda, T. Niederberger, L. Spinoulas, O. Cossairt, G. Schuster, and A. K. Katsaggelos, “High spatio-temporal resolution video with compressed sensing,” Opt. Express 23(12), 15992 (2015).
[Crossref]

J. B. Bosse, N. S. Tanneti, I. B. Hogue, and L. W. Enquist, “Open led illuminator: A simple and inexpensive LED illuminator for fast multicolor particle tracking in neurons,” PLoS One 10(11), e0143547 (2015).
[Crossref]

T. Li, X. He, Q. Teng, Z. Wang, and C. Ren, “Space-time super-resolution with patch group cuts prior,” Signal Process. 30, 147–165 (2015).
[Crossref]

2014 (3)

R. Pournaghi and X. Wu, “Coded Acquisition of High Frame Rate Video,” IEEE Trans. Image Process. 23(12), 5670–5682 (2014).
[Crossref]

A. Edelstein, M. Tsuchida, N. Amodaj, H. Pinkard, R. Vale, and N. Stuurman, “Advanced methods of microscope control using $\mu$μManager software,” J. Biol. Methods 1(2), 10 (2014).
[Crossref]

D. W. Staudt, J. Liu, K. S. Thorn, N. Stuurman, M. Liebling, and D. Y. R. Stainier, “High-resolution imaging of cardiomyocyte behavior reveals two distinct steps in ventricular trabeculation,” Development 141(3), 585–593 (2014).
[Crossref]

2013 (4)

S. S. Gorthi, D. Schaak, and E. Schonbrun, “Fluorescence imaging of flowing cells using a temporally coded excitation,” Opt. Express 21(4), 5164–5170 (2013).
[Crossref]

P. G. Pitrone, J. Schindelin, L. Stuyvenberg, S. Preibisch, M. Weber, K. W. Eliceiri, J. Huisken, and P. Tomancak, “OpenSPIM: an open-access light-sheet microscopy platform,” Nat. Methods 10(7), 598–599 (2013).
[Crossref]

E. J. Gualda, T. Vale, P. Almada, J. A. Feijó, G. G. Martins, and N. Moreno, “OpenSpin Microscopy: an open-source integrated microscopy platform,” Nat. Methods 10(7), 599–600 (2013).
[Crossref]

P. Llull, X. Liao, X. Yuan, J. Yang, D. Kittle, L. Carin, G. Sapiro, and D. J. Brady, “Coded aperture compressive temporal imaging,” Opt. Express 21(9), 10526–1306 (2013).
[Crossref]

2012 (2)

E. Mudry, K. Belkebir, J. Girard, J. Savatier, E. Le Moal, C. Nicoletti, M. Allain, and A. Sentenac, “Structured illumination microscopy using unknown speckle patterns,” Nat. Photonics 6(5), 312–315 (2012).
[Crossref]

F. Orieux, E. Sepulveda, V. Loriette, B. Dubertret, and J. Olivo-Marin, “Bayesian estimation for optimized structured illumination microscopy,” IEEE Trans. Image Process. 21(2), 601–614 (2012).
[Crossref]

2011 (1)

A. Veeraraghavan, D. Reddy, and R. Raskar, “Coded strobing photography: Compressive sensing of high speed periodic videos,” IEEE Trans. Pattern Anal. Mach. Intell. 33(4), 671–686 (2011).
[Crossref]

2010 (3)

G. Bub, M. Tecza, M. Helmes, P. Lee, and P. Kohl, “Temporal pixel multiplexing for simultaneous high-speed, high-resolution imaging,” Nat. Methods 7(3), 209–211 (2010).
[Crossref]

A. Edelstein, N. Amodaj, K. Hoover, R. Vale, and N. Stuurman, “Computer control of microscopes using $\mu$μManager,” Curr. Protoc. Mol. Biol. 92(1), 1–17 (2010).
[Crossref]

I. Daubechies, R. Devore, M. Fornasier, and C. S. Gunturk, “Iteratively reweighted least squares minimization for sparse recovery,” Comm. Pure Appl. Math. 63(1), 1–38 (2010).
[Crossref]

2008 (1)

J. Vermot, S. E. Fraser, and M. Liebling, “Fast fluorescence microscopy for imaging the dynamics of embryonic development,” HFSP J. 2(3), 143–155 (2008).
[Crossref]

2006 (1)

R. Raskar, A. Agrawal, and J. Tumblin, “Coded exposure photography: Motion deblurring using fluttered shutter,” ACM Trans. Graph. 25(3), 795–804 (2006).
[Crossref]

2005 (1)

E. Shechtman, Y. Caspi, and M. Irani, “Space-time super-resolution,” IEEE Trans. Pattern Anal. Mach. Intell. 27(4), 531–545 (2005).
[Crossref]

2004 (1)

L. H. Schaefer, D. Schuster, and J. Schaffer, “Structured illumination microscopy: artefact analysis and reduction utilizing a parameter optimization approach,” J. Microsc. 216(2), 165–174 (2004).
[Crossref]

2003 (1)

T. Zimmermann, J. Rietdorf, and R. Pepperkok, “Spectral imaging and its applications in live cell microscopy,” FEBS Lett. 546(1), 87–92 (2003).
[Crossref]

2002 (1)

2000 (1)

M. G. L. Gustafsson, “Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy,” J. Microsc. 198(2), 82–87 (2000).
[Crossref]

1998 (1)

P. J. Verveer, Q. S. Hanley, P. W. Verbeek, L. J. Van Vliet, and T. M. Jovin, “Theory of confocal fluorescence imaging in the programmable array microscope (pam),” J. Microsc. 189(3), 192–198 (1998).
[Crossref]

1977 (1)

R. E. Welsch, “Robust regression using iteratively reweighted least-squares,” Commun. Stat. Theory. 6(9), 813–827 (1977).
[Crossref]

1967 (1)

1966 (1)

1893 (1)

A. Koehler, “Ein neues Beleuchtungsverfahren fur mikrophotographische Zwecke,” Zeitschrift für wissenschaftliche Mikroskopie und für Mikroskopische Technik 10, 433–440 (1893).

Agrawal, A.

R. Raskar, A. Agrawal, and J. Tumblin, “Coded exposure photography: Motion deblurring using fluttered shutter,” ACM Trans. Graph. 25(3), 795–804 (2006).
[Crossref]

A. Agrawal, M. Gupta, A. Veeraraghavan, and S. G. Narasimhan, “Optimal coded sampling for temporal super-resolution,” in CVPR, (2010), pp. 599–606.

Allain, M.

E. Mudry, K. Belkebir, J. Girard, J. Savatier, E. Le Moal, C. Nicoletti, M. Allain, and A. Sentenac, “Structured illumination microscopy using unknown speckle patterns,” Nat. Photonics 6(5), 312–315 (2012).
[Crossref]

Almada, P.

E. J. Gualda, T. Vale, P. Almada, J. A. Feijó, G. G. Martins, and N. Moreno, “OpenSpin Microscopy: an open-source integrated microscopy platform,” Nat. Methods 10(7), 599–600 (2013).
[Crossref]

Amodaj, N.

A. Edelstein, M. Tsuchida, N. Amodaj, H. Pinkard, R. Vale, and N. Stuurman, “Advanced methods of microscope control using $\mu$μManager software,” J. Biol. Methods 1(2), 10 (2014).
[Crossref]

A. Edelstein, N. Amodaj, K. Hoover, R. Vale, and N. Stuurman, “Computer control of microscopes using $\mu$μManager,” Curr. Protoc. Mol. Biol. 92(1), 1–17 (2010).
[Crossref]

Belkebir, K.

E. Mudry, K. Belkebir, J. Girard, J. Savatier, E. Le Moal, C. Nicoletti, M. Allain, and A. Sentenac, “Structured illumination microscopy using unknown speckle patterns,” Nat. Photonics 6(5), 312–315 (2012).
[Crossref]

Bertero, M.

M. Bertero and P. Boccacci, Introduction to inverse problems in imaging (IOP Publishing, Bristol, UK, 1998).

Boccacci, P.

M. Bertero and P. Boccacci, Introduction to inverse problems in imaging (IOP Publishing, Bristol, UK, 1998).

Bosse, J. B.

J. B. Bosse, N. S. Tanneti, I. B. Hogue, and L. W. Enquist, “Open led illuminator: A simple and inexpensive LED illuminator for fast multicolor particle tracking in neurons,” PLoS One 10(11), e0143547 (2015).
[Crossref]

Brady, D. J.

Bub, G.

G. Bub, M. Tecza, M. Helmes, P. Lee, and P. Kohl, “Temporal pixel multiplexing for simultaneous high-speed, high-resolution imaging,” Nat. Methods 7(3), 209–211 (2010).
[Crossref]

Carin, L.

Caspi, Y.

E. Shechtman, Y. Caspi, and M. Irani, “Space-time super-resolution,” IEEE Trans. Pattern Anal. Mach. Intell. 27(4), 531–545 (2005).
[Crossref]

Chan, K. G.

K. G. Chan, S. J. Streichan, L. A. Trinh, and M. Liebling, “Simultaneous temporal superresolution and denoising for cardiac fluorescence microscopy,” IEEE Trans. Comput. Imaging 2(3), 348–358 (2016).
[Crossref]

Chartrand, R. L.

R. L. Chartrand and W. R. U. Yin, “Iterativery reweighted algorithms for compressive sensing,” in ICASSP, (2008), pp. 3869–3872.

Christensen, M. P.

Cossairt, O.

Cremer, C.

Daubechies, I.

I. Daubechies, R. Devore, M. Fornasier, and C. S. Gunturk, “Iteratively reweighted least squares minimization for sparse recovery,” Comm. Pure Appl. Math. 63(1), 1–38 (2010).
[Crossref]

Devore, R.

I. Daubechies, R. Devore, M. Fornasier, and C. S. Gunturk, “Iteratively reweighted least squares minimization for sparse recovery,” Comm. Pure Appl. Math. 63(1), 1–38 (2010).
[Crossref]

Dubertret, B.

F. Orieux, E. Sepulveda, V. Loriette, B. Dubertret, and J. Olivo-Marin, “Bayesian estimation for optimized structured illumination microscopy,” IEEE Trans. Image Process. 21(2), 601–614 (2012).
[Crossref]

Edelstein, A.

A. Edelstein, M. Tsuchida, N. Amodaj, H. Pinkard, R. Vale, and N. Stuurman, “Advanced methods of microscope control using $\mu$μManager software,” J. Biol. Methods 1(2), 10 (2014).
[Crossref]

A. Edelstein, N. Amodaj, K. Hoover, R. Vale, and N. Stuurman, “Computer control of microscopes using $\mu$μManager,” Curr. Protoc. Mol. Biol. 92(1), 1–17 (2010).
[Crossref]

Eliceiri, K. W.

P. G. Pitrone, J. Schindelin, L. Stuyvenberg, S. Preibisch, M. Weber, K. W. Eliceiri, J. Huisken, and P. Tomancak, “OpenSPIM: an open-access light-sheet microscopy platform,” Nat. Methods 10(7), 598–599 (2013).
[Crossref]

Enquist, L. W.

J. B. Bosse, N. S. Tanneti, I. B. Hogue, and L. W. Enquist, “Open led illuminator: A simple and inexpensive LED illuminator for fast multicolor particle tracking in neurons,” PLoS One 10(11), e0143547 (2015).
[Crossref]

Feijó, J. A.

E. J. Gualda, T. Vale, P. Almada, J. A. Feijó, G. G. Martins, and N. Moreno, “OpenSpin Microscopy: an open-source integrated microscopy platform,” Nat. Methods 10(7), 599–600 (2013).
[Crossref]

Fornasier, M.

I. Daubechies, R. Devore, M. Fornasier, and C. S. Gunturk, “Iteratively reweighted least squares minimization for sparse recovery,” Comm. Pure Appl. Math. 63(1), 1–38 (2010).
[Crossref]

Fraser, S. E.

J. Vermot, S. E. Fraser, and M. Liebling, “Fast fluorescence microscopy for imaging the dynamics of embryonic development,” HFSP J. 2(3), 143–155 (2008).
[Crossref]

Furukawa, R.

Y. Shiba, S. Ono, R. Furukawa, S. Hiura, and H. Kawasaki, “Temporal shape super-resolution by intra-frame motion encoding using high-fps structured light,” ICCV (2017).

Girard, J.

E. Mudry, K. Belkebir, J. Girard, J. Savatier, E. Le Moal, C. Nicoletti, M. Allain, and A. Sentenac, “Structured illumination microscopy using unknown speckle patterns,” Nat. Photonics 6(5), 312–315 (2012).
[Crossref]

Golub, G. H.

G. H. Golub and C. F. Van Loan, Matrix Computations (The John Hopkins University Press, 1996), 3rd ed.

Gorthi, S. S.

Gualda, E. J.

E. J. Gualda, T. Vale, P. Almada, J. A. Feijó, G. G. Martins, and N. Moreno, “OpenSpin Microscopy: an open-source integrated microscopy platform,” Nat. Methods 10(7), 599–600 (2013).
[Crossref]

Gunturk, C. S.

I. Daubechies, R. Devore, M. Fornasier, and C. S. Gunturk, “Iteratively reweighted least squares minimization for sparse recovery,” Comm. Pure Appl. Math. 63(1), 1–38 (2010).
[Crossref]

Gupta, M.

A. Agrawal, M. Gupta, A. Veeraraghavan, and S. G. Narasimhan, “Optimal coded sampling for temporal super-resolution,” in CVPR, (2010), pp. 599–606.

Gustafsson, M. G. L.

M. G. L. Gustafsson, “Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy,” J. Microsc. 198(2), 82–87 (2000).
[Crossref]

Hanley, Q. S.

P. J. Verveer, Q. S. Hanley, P. W. Verbeek, L. J. Van Vliet, and T. M. Jovin, “Theory of confocal fluorescence imaging in the programmable array microscope (pam),” J. Microsc. 189(3), 192–198 (1998).
[Crossref]

He, X.

T. Li, X. He, Q. Teng, Z. Wang, and C. Ren, “Space-time super-resolution with patch group cuts prior,” Signal Process. 30, 147–165 (2015).
[Crossref]

Heintzmann, R.

Helmes, M.

G. Bub, M. Tecza, M. Helmes, P. Lee, and P. Kohl, “Temporal pixel multiplexing for simultaneous high-speed, high-resolution imaging,” Nat. Methods 7(3), 209–211 (2010).
[Crossref]

Hiura, S.

Y. Shiba, S. Ono, R. Furukawa, S. Hiura, and H. Kawasaki, “Temporal shape super-resolution by intra-frame motion encoding using high-fps structured light,” ICCV (2017).

Hogue, I. B.

J. B. Bosse, N. S. Tanneti, I. B. Hogue, and L. W. Enquist, “Open led illuminator: A simple and inexpensive LED illuminator for fast multicolor particle tracking in neurons,” PLoS One 10(11), e0143547 (2015).
[Crossref]

Hoover, K.

A. Edelstein, N. Amodaj, K. Hoover, R. Vale, and N. Stuurman, “Computer control of microscopes using $\mu$μManager,” Curr. Protoc. Mol. Biol. 92(1), 1–17 (2010).
[Crossref]

Huisken, J.

P. G. Pitrone, J. Schindelin, L. Stuyvenberg, S. Preibisch, M. Weber, K. W. Eliceiri, J. Huisken, and P. Tomancak, “OpenSPIM: an open-access light-sheet microscopy platform,” Nat. Methods 10(7), 598–599 (2013).
[Crossref]

Irani, M.

E. Shechtman, Y. Caspi, and M. Irani, “Space-time super-resolution,” IEEE Trans. Pattern Anal. Mach. Intell. 27(4), 531–545 (2005).
[Crossref]

Jovin, T. M.

R. Heintzmann, T. M. Jovin, and C. Cremer, “Saturated patterned excitation microscopy—a concept for optical resolution improvement,” J. Opt. Soc. Am. A 19(8), 1599–1609 (2002).
[Crossref]

P. J. Verveer, Q. S. Hanley, P. W. Verbeek, L. J. Van Vliet, and T. M. Jovin, “Theory of confocal fluorescence imaging in the programmable array microscope (pam),” J. Microsc. 189(3), 192–198 (1998).
[Crossref]

Katsaggelos, A. K.

Kawasaki, H.

Y. Shiba, S. Ono, R. Furukawa, S. Hiura, and H. Kawasaki, “Temporal shape super-resolution by intra-frame motion encoding using high-fps structured light,” ICCV (2017).

Kittle, D.

Koehler, A.

A. Koehler, “Ein neues Beleuchtungsverfahren fur mikrophotographische Zwecke,” Zeitschrift für wissenschaftliche Mikroskopie und für Mikroskopische Technik 10, 433–440 (1893).

Kohl, P.

G. Bub, M. Tecza, M. Helmes, P. Lee, and P. Kohl, “Temporal pixel multiplexing for simultaneous high-speed, high-resolution imaging,” Nat. Methods 7(3), 209–211 (2010).
[Crossref]

Koller, R.

Le Moal, E.

E. Mudry, K. Belkebir, J. Girard, J. Savatier, E. Le Moal, C. Nicoletti, M. Allain, and A. Sentenac, “Structured illumination microscopy using unknown speckle patterns,” Nat. Photonics 6(5), 312–315 (2012).
[Crossref]

Lee, P.

G. Bub, M. Tecza, M. Helmes, P. Lee, and P. Kohl, “Temporal pixel multiplexing for simultaneous high-speed, high-resolution imaging,” Nat. Methods 7(3), 209–211 (2010).
[Crossref]

Li, T.

T. Li, X. He, Q. Teng, Z. Wang, and C. Ren, “Space-time super-resolution with patch group cuts prior,” Signal Process. 30, 147–165 (2015).
[Crossref]

Liao, X.

Liebling, M.

K. G. Chan, S. J. Streichan, L. A. Trinh, and M. Liebling, “Simultaneous temporal superresolution and denoising for cardiac fluorescence microscopy,” IEEE Trans. Comput. Imaging 2(3), 348–358 (2016).
[Crossref]

D. W. Staudt, J. Liu, K. S. Thorn, N. Stuurman, M. Liebling, and D. Y. R. Stainier, “High-resolution imaging of cardiomyocyte behavior reveals two distinct steps in ventricular trabeculation,” Development 141(3), 585–593 (2014).
[Crossref]

J. Vermot, S. E. Fraser, and M. Liebling, “Fast fluorescence microscopy for imaging the dynamics of embryonic development,” HFSP J. 2(3), 143–155 (2008).
[Crossref]

Liu, J.

D. W. Staudt, J. Liu, K. S. Thorn, N. Stuurman, M. Liebling, and D. Y. R. Stainier, “High-resolution imaging of cardiomyocyte behavior reveals two distinct steps in ventricular trabeculation,” Development 141(3), 585–593 (2014).
[Crossref]

Llull, P.

Loriette, V.

F. Orieux, E. Sepulveda, V. Loriette, B. Dubertret, and J. Olivo-Marin, “Bayesian estimation for optimized structured illumination microscopy,” IEEE Trans. Image Process. 21(2), 601–614 (2012).
[Crossref]

Lukosz, W.

Martins, G. G.

E. J. Gualda, T. Vale, P. Almada, J. A. Feijó, G. G. Martins, and N. Moreno, “OpenSpin Microscopy: an open-source integrated microscopy platform,” Nat. Methods 10(7), 599–600 (2013).
[Crossref]

Matsuda, N.

Milojkovic, P.

Moreno, N.

E. J. Gualda, T. Vale, P. Almada, J. A. Feijó, G. G. Martins, and N. Moreno, “OpenSpin Microscopy: an open-source integrated microscopy platform,” Nat. Methods 10(7), 599–600 (2013).
[Crossref]

Mudry, E.

E. Mudry, K. Belkebir, J. Girard, J. Savatier, E. Le Moal, C. Nicoletti, M. Allain, and A. Sentenac, “Structured illumination microscopy using unknown speckle patterns,” Nat. Photonics 6(5), 312–315 (2012).
[Crossref]

Narasimhan, S. G.

A. Agrawal, M. Gupta, A. Veeraraghavan, and S. G. Narasimhan, “Optimal coded sampling for temporal super-resolution,” in CVPR, (2010), pp. 599–606.

Nicoletti, C.

E. Mudry, K. Belkebir, J. Girard, J. Savatier, E. Le Moal, C. Nicoletti, M. Allain, and A. Sentenac, “Structured illumination microscopy using unknown speckle patterns,” Nat. Photonics 6(5), 312–315 (2012).
[Crossref]

Niederberger, T.

Olivo-Marin, J.

F. Orieux, E. Sepulveda, V. Loriette, B. Dubertret, and J. Olivo-Marin, “Bayesian estimation for optimized structured illumination microscopy,” IEEE Trans. Image Process. 21(2), 601–614 (2012).
[Crossref]

Ono, S.

Y. Shiba, S. Ono, R. Furukawa, S. Hiura, and H. Kawasaki, “Temporal shape super-resolution by intra-frame motion encoding using high-fps structured light,” ICCV (2017).

Orieux, F.

F. Orieux, E. Sepulveda, V. Loriette, B. Dubertret, and J. Olivo-Marin, “Bayesian estimation for optimized structured illumination microscopy,” IEEE Trans. Image Process. 21(2), 601–614 (2012).
[Crossref]

Pepperkok, R.

T. Zimmermann, J. Rietdorf, and R. Pepperkok, “Spectral imaging and its applications in live cell microscopy,” FEBS Lett. 546(1), 87–92 (2003).
[Crossref]

Pinkard, H.

A. Edelstein, M. Tsuchida, N. Amodaj, H. Pinkard, R. Vale, and N. Stuurman, “Advanced methods of microscope control using $\mu$μManager software,” J. Biol. Methods 1(2), 10 (2014).
[Crossref]

Pitrone, P. G.

P. G. Pitrone, J. Schindelin, L. Stuyvenberg, S. Preibisch, M. Weber, K. W. Eliceiri, J. Huisken, and P. Tomancak, “OpenSPIM: an open-access light-sheet microscopy platform,” Nat. Methods 10(7), 598–599 (2013).
[Crossref]

Pournaghi, R.

R. Pournaghi and X. Wu, “Coded Acquisition of High Frame Rate Video,” IEEE Trans. Image Process. 23(12), 5670–5682 (2014).
[Crossref]

Preibisch, S.

P. G. Pitrone, J. Schindelin, L. Stuyvenberg, S. Preibisch, M. Weber, K. W. Eliceiri, J. Huisken, and P. Tomancak, “OpenSPIM: an open-access light-sheet microscopy platform,” Nat. Methods 10(7), 598–599 (2013).
[Crossref]

Rangarajan, P.

Raskar, R.

A. Veeraraghavan, D. Reddy, and R. Raskar, “Coded strobing photography: Compressive sensing of high speed periodic videos,” IEEE Trans. Pattern Anal. Mach. Intell. 33(4), 671–686 (2011).
[Crossref]

R. Raskar, A. Agrawal, and J. Tumblin, “Coded exposure photography: Motion deblurring using fluttered shutter,” ACM Trans. Graph. 25(3), 795–804 (2006).
[Crossref]

Reddy, D.

A. Veeraraghavan, D. Reddy, and R. Raskar, “Coded strobing photography: Compressive sensing of high speed periodic videos,” IEEE Trans. Pattern Anal. Mach. Intell. 33(4), 671–686 (2011).
[Crossref]

Ren, C.

T. Li, X. He, Q. Teng, Z. Wang, and C. Ren, “Space-time super-resolution with patch group cuts prior,” Signal Process. 30, 147–165 (2015).
[Crossref]

Rietdorf, J.

T. Zimmermann, J. Rietdorf, and R. Pepperkok, “Spectral imaging and its applications in live cell microscopy,” FEBS Lett. 546(1), 87–92 (2003).
[Crossref]

Sapiro, G.

Savatier, J.

E. Mudry, K. Belkebir, J. Girard, J. Savatier, E. Le Moal, C. Nicoletti, M. Allain, and A. Sentenac, “Structured illumination microscopy using unknown speckle patterns,” Nat. Photonics 6(5), 312–315 (2012).
[Crossref]

Schaak, D.

Schaefer, L. H.

L. H. Schaefer, D. Schuster, and J. Schaffer, “Structured illumination microscopy: artefact analysis and reduction utilizing a parameter optimization approach,” J. Microsc. 216(2), 165–174 (2004).
[Crossref]

Schaffer, J.

L. H. Schaefer, D. Schuster, and J. Schaffer, “Structured illumination microscopy: artefact analysis and reduction utilizing a parameter optimization approach,” J. Microsc. 216(2), 165–174 (2004).
[Crossref]

Schindelin, J.

P. G. Pitrone, J. Schindelin, L. Stuyvenberg, S. Preibisch, M. Weber, K. W. Eliceiri, J. Huisken, and P. Tomancak, “OpenSPIM: an open-access light-sheet microscopy platform,” Nat. Methods 10(7), 598–599 (2013).
[Crossref]

Schmid, L.

Schonbrun, E.

Schuster, D.

L. H. Schaefer, D. Schuster, and J. Schaffer, “Structured illumination microscopy: artefact analysis and reduction utilizing a parameter optimization approach,” J. Microsc. 216(2), 165–174 (2004).
[Crossref]

Schuster, G.

Sentenac, A.

E. Mudry, K. Belkebir, J. Girard, J. Savatier, E. Le Moal, C. Nicoletti, M. Allain, and A. Sentenac, “Structured illumination microscopy using unknown speckle patterns,” Nat. Photonics 6(5), 312–315 (2012).
[Crossref]

Sepulveda, E.

F. Orieux, E. Sepulveda, V. Loriette, B. Dubertret, and J. Olivo-Marin, “Bayesian estimation for optimized structured illumination microscopy,” IEEE Trans. Image Process. 21(2), 601–614 (2012).
[Crossref]

Shechtman, E.

E. Shechtman, Y. Caspi, and M. Irani, “Space-time super-resolution,” IEEE Trans. Pattern Anal. Mach. Intell. 27(4), 531–545 (2005).
[Crossref]

Shiba, Y.

Y. Shiba, S. Ono, R. Furukawa, S. Hiura, and H. Kawasaki, “Temporal shape super-resolution by intra-frame motion encoding using high-fps structured light,” ICCV (2017).

Sinharoy, I.

Spinoulas, L.

Stainier, D. Y. R.

D. W. Staudt, J. Liu, K. S. Thorn, N. Stuurman, M. Liebling, and D. Y. R. Stainier, “High-resolution imaging of cardiomyocyte behavior reveals two distinct steps in ventricular trabeculation,” Development 141(3), 585–593 (2014).
[Crossref]

Staudt, D. W.

D. W. Staudt, J. Liu, K. S. Thorn, N. Stuurman, M. Liebling, and D. Y. R. Stainier, “High-resolution imaging of cardiomyocyte behavior reveals two distinct steps in ventricular trabeculation,” Development 141(3), 585–593 (2014).
[Crossref]

Streichan, S. J.

K. G. Chan, S. J. Streichan, L. A. Trinh, and M. Liebling, “Simultaneous temporal superresolution and denoising for cardiac fluorescence microscopy,” IEEE Trans. Comput. Imaging 2(3), 348–358 (2016).
[Crossref]

Stuurman, N.

A. Edelstein, M. Tsuchida, N. Amodaj, H. Pinkard, R. Vale, and N. Stuurman, “Advanced methods of microscope control using $\mu$μManager software,” J. Biol. Methods 1(2), 10 (2014).
[Crossref]

D. W. Staudt, J. Liu, K. S. Thorn, N. Stuurman, M. Liebling, and D. Y. R. Stainier, “High-resolution imaging of cardiomyocyte behavior reveals two distinct steps in ventricular trabeculation,” Development 141(3), 585–593 (2014).
[Crossref]

A. Edelstein, N. Amodaj, K. Hoover, R. Vale, and N. Stuurman, “Computer control of microscopes using $\mu$μManager,” Curr. Protoc. Mol. Biol. 92(1), 1–17 (2010).
[Crossref]

Stuyvenberg, L.

P. G. Pitrone, J. Schindelin, L. Stuyvenberg, S. Preibisch, M. Weber, K. W. Eliceiri, J. Huisken, and P. Tomancak, “OpenSPIM: an open-access light-sheet microscopy platform,” Nat. Methods 10(7), 598–599 (2013).
[Crossref]

Tanneti, N. S.

J. B. Bosse, N. S. Tanneti, I. B. Hogue, and L. W. Enquist, “Open led illuminator: A simple and inexpensive LED illuminator for fast multicolor particle tracking in neurons,” PLoS One 10(11), e0143547 (2015).
[Crossref]

Tecza, M.

G. Bub, M. Tecza, M. Helmes, P. Lee, and P. Kohl, “Temporal pixel multiplexing for simultaneous high-speed, high-resolution imaging,” Nat. Methods 7(3), 209–211 (2010).
[Crossref]

Teng, Q.

T. Li, X. He, Q. Teng, Z. Wang, and C. Ren, “Space-time super-resolution with patch group cuts prior,” Signal Process. 30, 147–165 (2015).
[Crossref]

Thorn, K. S.

D. W. Staudt, J. Liu, K. S. Thorn, N. Stuurman, M. Liebling, and D. Y. R. Stainier, “High-resolution imaging of cardiomyocyte behavior reveals two distinct steps in ventricular trabeculation,” Development 141(3), 585–593 (2014).
[Crossref]

Tomancak, P.

P. G. Pitrone, J. Schindelin, L. Stuyvenberg, S. Preibisch, M. Weber, K. W. Eliceiri, J. Huisken, and P. Tomancak, “OpenSPIM: an open-access light-sheet microscopy platform,” Nat. Methods 10(7), 598–599 (2013).
[Crossref]

Trinh, L. A.

K. G. Chan, S. J. Streichan, L. A. Trinh, and M. Liebling, “Simultaneous temporal superresolution and denoising for cardiac fluorescence microscopy,” IEEE Trans. Comput. Imaging 2(3), 348–358 (2016).
[Crossref]

Tsai, T.-H.

Tsuchida, M.

A. Edelstein, M. Tsuchida, N. Amodaj, H. Pinkard, R. Vale, and N. Stuurman, “Advanced methods of microscope control using $\mu$μManager software,” J. Biol. Methods 1(2), 10 (2014).
[Crossref]

Tumblin, J.

R. Raskar, A. Agrawal, and J. Tumblin, “Coded exposure photography: Motion deblurring using fluttered shutter,” ACM Trans. Graph. 25(3), 795–804 (2006).
[Crossref]

Vale, R.

A. Edelstein, M. Tsuchida, N. Amodaj, H. Pinkard, R. Vale, and N. Stuurman, “Advanced methods of microscope control using $\mu$μManager software,” J. Biol. Methods 1(2), 10 (2014).
[Crossref]

A. Edelstein, N. Amodaj, K. Hoover, R. Vale, and N. Stuurman, “Computer control of microscopes using $\mu$μManager,” Curr. Protoc. Mol. Biol. 92(1), 1–17 (2010).
[Crossref]

Vale, T.

E. J. Gualda, T. Vale, P. Almada, J. A. Feijó, G. G. Martins, and N. Moreno, “OpenSpin Microscopy: an open-source integrated microscopy platform,” Nat. Methods 10(7), 599–600 (2013).
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G. H. Golub and C. F. Van Loan, Matrix Computations (The John Hopkins University Press, 1996), 3rd ed.

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[Crossref]

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A. Veeraraghavan, D. Reddy, and R. Raskar, “Coded strobing photography: Compressive sensing of high speed periodic videos,” IEEE Trans. Pattern Anal. Mach. Intell. 33(4), 671–686 (2011).
[Crossref]

A. Agrawal, M. Gupta, A. Veeraraghavan, and S. G. Narasimhan, “Optimal coded sampling for temporal super-resolution,” in CVPR, (2010), pp. 599–606.

Verbeek, P. W.

P. J. Verveer, Q. S. Hanley, P. W. Verbeek, L. J. Van Vliet, and T. M. Jovin, “Theory of confocal fluorescence imaging in the programmable array microscope (pam),” J. Microsc. 189(3), 192–198 (1998).
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Vermot, J.

J. Vermot, S. E. Fraser, and M. Liebling, “Fast fluorescence microscopy for imaging the dynamics of embryonic development,” HFSP J. 2(3), 143–155 (2008).
[Crossref]

Verveer, P. J.

P. J. Verveer, Q. S. Hanley, P. W. Verbeek, L. J. Van Vliet, and T. M. Jovin, “Theory of confocal fluorescence imaging in the programmable array microscope (pam),” J. Microsc. 189(3), 192–198 (1998).
[Crossref]

Wang, Z.

T. Li, X. He, Q. Teng, Z. Wang, and C. Ren, “Space-time super-resolution with patch group cuts prior,” Signal Process. 30, 147–165 (2015).
[Crossref]

Weber, M.

P. G. Pitrone, J. Schindelin, L. Stuyvenberg, S. Preibisch, M. Weber, K. W. Eliceiri, J. Huisken, and P. Tomancak, “OpenSPIM: an open-access light-sheet microscopy platform,” Nat. Methods 10(7), 598–599 (2013).
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R. E. Welsch, “Robust regression using iteratively reweighted least-squares,” Commun. Stat. Theory. 6(9), 813–827 (1977).
[Crossref]

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R. Pournaghi and X. Wu, “Coded Acquisition of High Frame Rate Video,” IEEE Trans. Image Process. 23(12), 5670–5682 (2014).
[Crossref]

Yang, J.

Yin, W. R. U.

R. L. Chartrand and W. R. U. Yin, “Iterativery reweighted algorithms for compressive sensing,” in ICASSP, (2008), pp. 3869–3872.

Yuan, X.

Zimmermann, T.

T. Zimmermann, J. Rietdorf, and R. Pepperkok, “Spectral imaging and its applications in live cell microscopy,” FEBS Lett. 546(1), 87–92 (2003).
[Crossref]

ACM Trans. Graph. (1)

R. Raskar, A. Agrawal, and J. Tumblin, “Coded exposure photography: Motion deblurring using fluttered shutter,” ACM Trans. Graph. 25(3), 795–804 (2006).
[Crossref]

Appl. Opt. (1)

Comm. Pure Appl. Math. (1)

I. Daubechies, R. Devore, M. Fornasier, and C. S. Gunturk, “Iteratively reweighted least squares minimization for sparse recovery,” Comm. Pure Appl. Math. 63(1), 1–38 (2010).
[Crossref]

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R. E. Welsch, “Robust regression using iteratively reweighted least-squares,” Commun. Stat. Theory. 6(9), 813–827 (1977).
[Crossref]

Curr. Protoc. Mol. Biol. (1)

A. Edelstein, N. Amodaj, K. Hoover, R. Vale, and N. Stuurman, “Computer control of microscopes using $\mu$μManager,” Curr. Protoc. Mol. Biol. 92(1), 1–17 (2010).
[Crossref]

Development (1)

D. W. Staudt, J. Liu, K. S. Thorn, N. Stuurman, M. Liebling, and D. Y. R. Stainier, “High-resolution imaging of cardiomyocyte behavior reveals two distinct steps in ventricular trabeculation,” Development 141(3), 585–593 (2014).
[Crossref]

FEBS Lett. (1)

T. Zimmermann, J. Rietdorf, and R. Pepperkok, “Spectral imaging and its applications in live cell microscopy,” FEBS Lett. 546(1), 87–92 (2003).
[Crossref]

HFSP J. (1)

J. Vermot, S. E. Fraser, and M. Liebling, “Fast fluorescence microscopy for imaging the dynamics of embryonic development,” HFSP J. 2(3), 143–155 (2008).
[Crossref]

IEEE Trans. Comput. Imaging (1)

K. G. Chan, S. J. Streichan, L. A. Trinh, and M. Liebling, “Simultaneous temporal superresolution and denoising for cardiac fluorescence microscopy,” IEEE Trans. Comput. Imaging 2(3), 348–358 (2016).
[Crossref]

IEEE Trans. Image Process. (2)

R. Pournaghi and X. Wu, “Coded Acquisition of High Frame Rate Video,” IEEE Trans. Image Process. 23(12), 5670–5682 (2014).
[Crossref]

F. Orieux, E. Sepulveda, V. Loriette, B. Dubertret, and J. Olivo-Marin, “Bayesian estimation for optimized structured illumination microscopy,” IEEE Trans. Image Process. 21(2), 601–614 (2012).
[Crossref]

IEEE Trans. Pattern Anal. Mach. Intell. (2)

A. Veeraraghavan, D. Reddy, and R. Raskar, “Coded strobing photography: Compressive sensing of high speed periodic videos,” IEEE Trans. Pattern Anal. Mach. Intell. 33(4), 671–686 (2011).
[Crossref]

E. Shechtman, Y. Caspi, and M. Irani, “Space-time super-resolution,” IEEE Trans. Pattern Anal. Mach. Intell. 27(4), 531–545 (2005).
[Crossref]

J. Biol. Methods (1)

A. Edelstein, M. Tsuchida, N. Amodaj, H. Pinkard, R. Vale, and N. Stuurman, “Advanced methods of microscope control using $\mu$μManager software,” J. Biol. Methods 1(2), 10 (2014).
[Crossref]

J. Microsc. (3)

L. H. Schaefer, D. Schuster, and J. Schaffer, “Structured illumination microscopy: artefact analysis and reduction utilizing a parameter optimization approach,” J. Microsc. 216(2), 165–174 (2004).
[Crossref]

P. J. Verveer, Q. S. Hanley, P. W. Verbeek, L. J. Van Vliet, and T. M. Jovin, “Theory of confocal fluorescence imaging in the programmable array microscope (pam),” J. Microsc. 189(3), 192–198 (1998).
[Crossref]

M. G. L. Gustafsson, “Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy,” J. Microsc. 198(2), 82–87 (2000).
[Crossref]

J. Opt. Soc. Am. (2)

J. Opt. Soc. Am. A (1)

Nat. Methods (3)

P. G. Pitrone, J. Schindelin, L. Stuyvenberg, S. Preibisch, M. Weber, K. W. Eliceiri, J. Huisken, and P. Tomancak, “OpenSPIM: an open-access light-sheet microscopy platform,” Nat. Methods 10(7), 598–599 (2013).
[Crossref]

E. J. Gualda, T. Vale, P. Almada, J. A. Feijó, G. G. Martins, and N. Moreno, “OpenSpin Microscopy: an open-source integrated microscopy platform,” Nat. Methods 10(7), 599–600 (2013).
[Crossref]

G. Bub, M. Tecza, M. Helmes, P. Lee, and P. Kohl, “Temporal pixel multiplexing for simultaneous high-speed, high-resolution imaging,” Nat. Methods 7(3), 209–211 (2010).
[Crossref]

Nat. Photonics (1)

E. Mudry, K. Belkebir, J. Girard, J. Savatier, E. Le Moal, C. Nicoletti, M. Allain, and A. Sentenac, “Structured illumination microscopy using unknown speckle patterns,” Nat. Photonics 6(5), 312–315 (2012).
[Crossref]

Opt. Express (3)

Opt. Lett. (1)

PLoS One (1)

J. B. Bosse, N. S. Tanneti, I. B. Hogue, and L. W. Enquist, “Open led illuminator: A simple and inexpensive LED illuminator for fast multicolor particle tracking in neurons,” PLoS One 10(11), e0143547 (2015).
[Crossref]

Signal Process. (1)

T. Li, X. He, Q. Teng, Z. Wang, and C. Ren, “Space-time super-resolution with patch group cuts prior,” Signal Process. 30, 147–165 (2015).
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A. Koehler, “Ein neues Beleuchtungsverfahren fur mikrophotographische Zwecke,” Zeitschrift für wissenschaftliche Mikroskopie und für Mikroskopische Technik 10, 433–440 (1893).

Other (7)

A. Agrawal, M. Gupta, A. Veeraraghavan, and S. G. Narasimhan, “Optimal coded sampling for temporal super-resolution,” in CVPR, (2010), pp. 599–606.

Y. Shiba, S. Ono, R. Furukawa, S. Hiura, and H. Kawasaki, “Temporal shape super-resolution by intra-frame motion encoding using high-fps structured light,” ICCV (2017).

R. L. Chartrand and W. R. U. Yin, “Iterativery reweighted algorithms for compressive sensing,” in ICASSP, (2008), pp. 3869–3872.

G. H. Golub and C. F. Van Loan, Matrix Computations (The John Hopkins University Press, 1996), 3rd ed.

ILOG-CPLEX, “High-performance software for mathematical programming and optimization,” http://www.ilog.com/products/cplex, (2005).

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Supplementary Material (5)

NameDescription
» Visualization 1       This video shows the experiment shown in Figure 2, where we characterise the temporal resolution improvement achieved with our method
» Visualization 2       This video shows the experiment presented in Section 4.3, where the same sample is imaged with various LEDs combinations. The video shows reconstructions with each one of the LEDs combinations. The conditioning number of the system's matrix is given
» Visualization 3       This video shows the experiment presented in Section 4.4, where the same sample is imaged with various illumination temporal sequences (and the same LEDs each time). For each reconstruction, the conditioning number of the system's matrix is given.
» Visualization 4       This video shows the experiment presented in Section 5.1 and Figure 3. Our method allows to recover which model is correct and to retrieve the base hue of the sample, that was calibrated previously.
» Visualization 5       This video present an application of our method to the beating heart of a live zebrafish larva. It highlights the possibilities offered by our method, making it very easy to switch between standard color imaging to fast grayscale imaging.

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Figures (4)

Fig. 1.
Fig. 1. (a) Acquisition setup. The moving sample is imaged with three active light sources $s_i(t)$. The projection of the scene to the camera is shown with $x(t)$. The color (Bayer) filter makes each pixel sensitive to a specific spectrum that is independent of the light sources. Each light source has its own time function, capturing the sample at different times and encoding this information in different spectra which is then captured by the color sensor in the hue domain. (b) Example of possible temporal functions for the three light sources. (c) Real example of acquired data with the depicted system of (a). (d)-(e) Close-ups to the real acquired data, the Bayer filter is visible. (f) Reconstruction of three grayscale frames from the acquisition shown in (c).
Fig. 2.
Fig. 2. Imaging a moving sample with (a, f) a constant white light, (b, g) a 20ms white pulse and (c, d, e, h, i, j) our proposed method (see Visualization 1). The zoom on the element 1 of the group −2 of the USAF-grid (close-up in a, b, c) shows that all three methods can resolve it. It is the limit for the constant illumination. This element is 0.625 mm wide. The detailed views on the whole group −1 (f, g, h) show that the stroboscopic illumination and our method (g, h) are able to resolve up to element 4. This corresponds to a resolution improvement factor of 2.8. Moreover, with our method operating at the same frame-rate, we have six reconstructed frames (c, d, e, h, i, j) while with the two other methods we have two acquired frames (a, b, f, g), thus we improved the frame-rate by a factor of 3.
Fig. 3.
Fig. 3. When any of several objects with different, but known, hues enters the field of view, the system matrix adapted to the object can be automatically selected. (a) Color image of a static scene, with two kind of papers illuminated by a white light. The gray areas show the calibration ROIs. (b) Each sample has a corresponding calibrated set of parameters $\mathbf{\Gamma }$ and $\boldsymbol{D}$ as well as the sample hue. (c) Data acquisition of a dynamic scene with the active illumination. (d) Reconstruction with model selection as explained in Section 3.3. (e, f) Two reconstructions with our method after model selection, using RGB LEDs and reconstructing the hue of the samples from the raw data acquired with our method (see Visualization 4). Scalebar: 5 cm.
Fig. 4.
Fig. 4. Flexible color and fast grayscale imaging of the beating heart in a 4 days post fertilization zebrafish larva. (a) Single frame of an RGB color movie, with (b) ROI with reconstructed grayscale (no hue was measured beforehand, gray reconstruction) movie at threefold increased frame-rate. See Visualization 5 for the full movie. Anatomical features visible include the ventricle (v), the atrium (at), the bulbus arteriosis (BA) and the pericardium (p). Orientation is indicated as V: ventral, D: dorsal, A: anterior, P: posterior. Scalebar: $100 \mu$m.

Tables (2)

Tables Icon

Table 1. Condition number $\kappa$ depending on the LEDs used (see Visualization 2).

Tables Icon

Table 2. Condition number $\kappa$ with various time functions. $R_1, R_2, R_3$ are the values of the red LED respectively at the first, second and third time-steps of the whole exposure time (see Visualization 3).

Equations (21)

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Y c = 0 E ( = 1 L γ , c x ( t ) s ( t ) ) d t + D c
= D c + = 1 L γ , c 0 E x ( t ) s ( t ) d t ,
x ( t ) = i = 1 Q x [ i ] β 0 ( Q ( t i ) ) ,
β 0 ( t ) = { 1 if  0 t < E Q 0 otherwise,
Y c = D c + = 1 L γ , c 0 E i = 1 Q x [ i ] β 0 ( Q ( t i ) ) s ( t ) d t = D c + = 1 L γ , c i = 1 Q x [ i ] 0 E β 0 ( Q ( t i ) ) s ( t ) d t = D c + = 1 L γ , c i = 1 Q x [ i ] S [ i ] ,
S [ i ] = 0 E β 0 ( Q ( t i ) ) s ( t ) d t = ( i 1 ) E / Q i E / Q s ( t ) d t .
Y = S Q Γ Q x + D ,
S Q = ( S Q 1 S Q S Q L ) C × C Q L ,
S Q = ( ( S [ 1 ] , , S [ Q ] ) 0 1 × Q 0 1 × Q 0 1 × Q 0 1 × Q 0 1 × Q 0 1 × Q ( S [ 1 ] , , S [ Q ] ) ) C × C Q .
Γ Q = [ ( Γ Q 1 Γ Q Γ Q L ) ] C Q L × Q ,
Γ Q = [ ( γ 1 , I Q γ c , I Q γ C , I Q ) ] C Q × Q ,
x = min x Y D S Q Γ Q x 2 2 .
[ Y ] C × 1 = [ S 1 ] C × C L [ Γ 1 ] C L × 1 [ x ] 1 × 1 + [ D ] C × 1 ,
Y = ( x S 1 I C ) ( Γ 1 D ) ,
( Y 1 , 1 Y 1 , 2 Y 1 , P Y 2 , 1 Y M , P ) Y cal = ( x 1 S 1 1 I C x 1 S 1 2 I C x 1 S 1 P I C x 2 S 1 1 I C x M S 1 P I C ) A cal ( Γ 1 D ) ,
e ( Γ 1 , D ) = Y cal A cal ( Γ 1 D ) 1 .
u ( t + 1 ) = argmin u W ( t ) Y cal W ( t ) A cal u ( t ) 2 2 ,
w k ( t + 1 ) = ( ( Y cal , k A cal u k ( t ) ) 2 + ϵ ( t ) ) 1 / 2 .
R ( n ) = i = 1 Q 1 | x ( n ) [ i ] x ( n ) [ i + 1 ] |
S 1 [ i ] = [ 1 , 0 , 0 ] S 2 [ i ] = [ 0 , 1 , 0 ] S 3 [ i ] = [ 0 , 0 , 1 ] ,
κ ( A ) = σ max ( A ) σ min ( A ) ,

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