Abstract

We introduce a fast, simple, adaptive and experimentally robust method for reconstructing background-rejected optically-sectioned images using two-shot structured illumination microscopy. Our innovative data demodulation method needs two grid-illumination images mutually phase shifted by π (half a grid period) but precise phase displacement between two frames is not required. Upon frames subtraction the input pattern with increased grid modulation is obtained. The first demodulation stage comprises two-dimensional data processing based on the empirical mode decomposition for the object spatial frequency selection (noise reduction and bias term removal). The second stage consists in calculating high contrast image using the two-dimensional spiral Hilbert transform. Our algorithm effectiveness is compared with the results calculated for the same input data using structured-illumination (SIM) and HiLo microscopy methods. The input data were collected for studying highly scattering tissue samples in reflectance mode. Results of our approach compare very favorably with SIM and HiLo techniques.

© 2014 Optical Society of America

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2014

M. Trusiak, M. Wielgus, K. Patorski, “Advanced processing of optical fringe patterns by automated selective reconstruction and enhanced fast empirical mode decomposition,” Opt. Lasers Eng. 52(1), 230–240 (2014).
[CrossRef]

2013

2012

2011

2010

K. Wicker, R. Heintzmann, “Single-shot optical sectioning using polarization-coded structured illumination,” J. Opt. 12(8), 084010 (2010).
[CrossRef]

J. Mertz, J. Kim, “Scanning light-sheet microscopy in the whole mouse brain with HiLo background rejection,” J. Biomed. Opt. 15(1), 016027 (2010).
[CrossRef] [PubMed]

2009

S. Santos, K. K. Chu, D. Lim, N. Bozinovic, T. N. Ford, C. Hourtoule, A. C. Bartoo, S. K. Singh, J. Mertz, “Optically sectioned fluorescence endomicroscopy with hybrid-illumination imaging through a flexible fiber bundle,” J. Biomed. Opt. 14(3), 030502 (2009).
[CrossRef] [PubMed]

2008

2007

2006

K. Patorski, A. Styk, “Interferogram intensity modulation calculations using temporal phase shifting: error analysis,” Opt. Eng. 45(8), 085602 (2006).
[CrossRef]

2005

J.-A. Conchello, J. W. Lichtman, “Optical sectioning microscopy,” Nat. Methods 2(12), 920–931 (2005).
[CrossRef] [PubMed]

C. Damerval, S. Meignen, V. Perrier, “A fast algorithm for bidimensional EMD,” IEEE Signal Process. Lett. 12(10), 701–704 (2005).
[CrossRef]

K. B. Im, S. Han, H. Park, D. Kim, B.-M. Kim, “Simple high-speed confocal line-scanning microscope,” Opt. Express 13(13), 5151–5156 (2005).
[CrossRef] [PubMed]

2004

2003

J. C. Nunes, Y. Bouaoune, E. Delechelle, O. Niang, Ph. Bunel, “Image analysis by bidimensional empirical mode decomposition,” Image Vis. Comput. 21(12), 1019–1026 (2003).
[CrossRef]

K. Sokolov, M. Follen, J. Aaron, I. Pavlova, A. Malpica, R. Lotan, R. Richards-Kortum, “Real time vital imaging of pre-cancer using anti-EGFR antibodies conjugated to gold nanoparticles,” Cancer Res. 63(9), 1999–2004 (2003).
[PubMed]

2001

1998

N. E. Huang, Z. Sheng, S. R. Long, M. C. Wu, W. H. Shih, Q. Zeng, N. C. Yen, C. C. Tung, H. H. Liu, “The empirical mode decomposition and the Hilbert spectrum for non-linear and non-stationary time series analysis,” Proc. R. Soc. Lond. A 454(1971), 903–995 (1998).
[CrossRef]

1997

1996

C. Barber, D. Dobkins, H. Huhdanpaa, “The quickhull algorithm for convex hulls,” ACM Trans. Math. Softw. 22(4), 469–483 (1996).
[CrossRef]

Aaron, J.

K. Sokolov, M. Follen, J. Aaron, I. Pavlova, A. Malpica, R. Lotan, R. Richards-Kortum, “Real time vital imaging of pre-cancer using anti-EGFR antibodies conjugated to gold nanoparticles,” Cancer Res. 63(9), 1999–2004 (2003).
[PubMed]

Barber, C.

C. Barber, D. Dobkins, H. Huhdanpaa, “The quickhull algorithm for convex hulls,” ACM Trans. Math. Softw. 22(4), 469–483 (1996).
[CrossRef]

Bartoo, A. C.

S. Santos, K. K. Chu, D. Lim, N. Bozinovic, T. N. Ford, C. Hourtoule, A. C. Bartoo, S. K. Singh, J. Mertz, “Optically sectioned fluorescence endomicroscopy with hybrid-illumination imaging through a flexible fiber bundle,” J. Biomed. Opt. 14(3), 030502 (2009).
[CrossRef] [PubMed]

Boccara, A. C.

Bone, D. J.

Bouaoune, Y.

J. C. Nunes, Y. Bouaoune, E. Delechelle, O. Niang, Ph. Bunel, “Image analysis by bidimensional empirical mode decomposition,” Image Vis. Comput. 21(12), 1019–1026 (2003).
[CrossRef]

Bozinovic, N.

S. Santos, K. K. Chu, D. Lim, N. Bozinovic, T. N. Ford, C. Hourtoule, A. C. Bartoo, S. K. Singh, J. Mertz, “Optically sectioned fluorescence endomicroscopy with hybrid-illumination imaging through a flexible fiber bundle,” J. Biomed. Opt. 14(3), 030502 (2009).
[CrossRef] [PubMed]

N. Bozinovic, C. Ventalon, T. Ford, J. Mertz, “Fluorescence endomicroscopy with structured illumination,” Opt. Express 16(11), 8016–8025 (2008).
[CrossRef] [PubMed]

Bunel, Ph.

J. C. Nunes, Y. Bouaoune, E. Delechelle, O. Niang, Ph. Bunel, “Image analysis by bidimensional empirical mode decomposition,” Image Vis. Comput. 21(12), 1019–1026 (2003).
[CrossRef]

Chasles, F.

Choi, E. S.

Choi, H.

Choi, W. J.

Chu, K. K.

S. Santos, K. K. Chu, D. Lim, N. Bozinovic, T. N. Ford, C. Hourtoule, A. C. Bartoo, S. K. Singh, J. Mertz, “Optically sectioned fluorescence endomicroscopy with hybrid-illumination imaging through a flexible fiber bundle,” J. Biomed. Opt. 14(3), 030502 (2009).
[CrossRef] [PubMed]

D. Lim, K. K. Chu, J. Mertz, “Wide-field fluorescence sectioning with hybrid speckle and uniform-illumination microscopy,” Opt. Lett. 33(16), 1819–1821 (2008).
[CrossRef] [PubMed]

Conchello, J.-A.

J.-A. Conchello, J. W. Lichtman, “Optical sectioning microscopy,” Nat. Methods 2(12), 920–931 (2005).
[CrossRef] [PubMed]

Damerval, C.

C. Damerval, S. Meignen, V. Perrier, “A fast algorithm for bidimensional EMD,” IEEE Signal Process. Lett. 12(10), 701–704 (2005).
[CrossRef]

Delechelle, E.

J. C. Nunes, Y. Bouaoune, E. Delechelle, O. Niang, Ph. Bunel, “Image analysis by bidimensional empirical mode decomposition,” Image Vis. Comput. 21(12), 1019–1026 (2003).
[CrossRef]

Descour, M. R.

Dobkins, D.

C. Barber, D. Dobkins, H. Huhdanpaa, “The quickhull algorithm for convex hulls,” ACM Trans. Math. Softw. 22(4), 469–483 (1996).
[CrossRef]

Dubertret, B.

Fantini, S.

Follen, M.

K. Sokolov, M. Follen, J. Aaron, I. Pavlova, A. Malpica, R. Lotan, R. Richards-Kortum, “Real time vital imaging of pre-cancer using anti-EGFR antibodies conjugated to gold nanoparticles,” Cancer Res. 63(9), 1999–2004 (2003).
[PubMed]

Ford, T.

Ford, T. N.

S. Santos, K. K. Chu, D. Lim, N. Bozinovic, T. N. Ford, C. Hourtoule, A. C. Bartoo, S. K. Singh, J. Mertz, “Optically sectioned fluorescence endomicroscopy with hybrid-illumination imaging through a flexible fiber bundle,” J. Biomed. Opt. 14(3), 030502 (2009).
[CrossRef] [PubMed]

Gao, L.

Hagen, G. M.

P. Krizek, G. M. Hagen, “Current optical sectioning systems in fluorescence microscopy,” Formatex Microscopy Book Series No 5(2), 826–8832 (2012).

Hagen, N.

Hallacoglu, B.

Han, S.

Heintzmann, R.

K. Wicker, R. Heintzmann, “Single-shot optical sectioning using polarization-coded structured illumination,” J. Opt. 12(8), 084010 (2010).
[CrossRef]

Hourtoule, C.

S. Santos, K. K. Chu, D. Lim, N. Bozinovic, T. N. Ford, C. Hourtoule, A. C. Bartoo, S. K. Singh, J. Mertz, “Optically sectioned fluorescence endomicroscopy with hybrid-illumination imaging through a flexible fiber bundle,” J. Biomed. Opt. 14(3), 030502 (2009).
[CrossRef] [PubMed]

Hrebesh, M. S.

M. S. Hrebesh, “Full-field and single shot full-field optical coherence tomography: a novel technique for biomedical imaging applications,” Adv. Opt. Technol. 2012, 435408 (2012).

Huang, H.

Huang, N. E.

N. E. Huang, Z. Sheng, S. R. Long, M. C. Wu, W. H. Shih, Q. Zeng, N. C. Yen, C. C. Tung, H. H. Liu, “The empirical mode decomposition and the Hilbert spectrum for non-linear and non-stationary time series analysis,” Proc. R. Soc. Lond. A 454(1971), 903–995 (1998).
[CrossRef]

Huhdanpaa, H.

C. Barber, D. Dobkins, H. Huhdanpaa, “The quickhull algorithm for convex hulls,” ACM Trans. Math. Softw. 22(4), 469–483 (1996).
[CrossRef]

Im, K. B.

Juskaitis, R.

Karadaglic, D.

D. Karadaglić, T. Wilson, “Image formation in structured illumination wide-field fluorescence microscopy,” Micron 39(7), 808–818 (2008).
[CrossRef] [PubMed]

Kim, B.-M.

Kim, D.

E. Y. S. Yew, H. Choi, D. Kim, P. T. C. So, “Wide-field two-photon microscopy with temporal focusing and HiLo background rejection,” Proc. SPIE 7903, 79031O (2011).
[CrossRef]

K. B. Im, S. Han, H. Park, D. Kim, B.-M. Kim, “Simple high-speed confocal line-scanning microscope,” Opt. Express 13(13), 5151–5156 (2005).
[CrossRef] [PubMed]

Kim, J.

J. Mertz, J. Kim, “Scanning light-sheet microscopy in the whole mouse brain with HiLo background rejection,” J. Biomed. Opt. 15(1), 016027 (2010).
[CrossRef] [PubMed]

Kner, P.

B. Thomas, M. Momany, P. Kner, “Optical sectioning structured illumination microscopy with enhanced sensitivity,” J. Opt. 15(9), 094004 (2013).
[CrossRef]

Krizek, P.

P. Krizek, G. M. Hagen, “Current optical sectioning systems in fluorescence microscopy,” Formatex Microscopy Book Series No 5(2), 826–8832 (2012).

Larkin, K. G.

Lee, B. H.

Lichtman, J. W.

J.-A. Conchello, J. W. Lichtman, “Optical sectioning microscopy,” Nat. Methods 2(12), 920–931 (2005).
[CrossRef] [PubMed]

Lim, D.

S. Santos, K. K. Chu, D. Lim, N. Bozinovic, T. N. Ford, C. Hourtoule, A. C. Bartoo, S. K. Singh, J. Mertz, “Optically sectioned fluorescence endomicroscopy with hybrid-illumination imaging through a flexible fiber bundle,” J. Biomed. Opt. 14(3), 030502 (2009).
[CrossRef] [PubMed]

D. Lim, K. K. Chu, J. Mertz, “Wide-field fluorescence sectioning with hybrid speckle and uniform-illumination microscopy,” Opt. Lett. 33(16), 1819–1821 (2008).
[CrossRef] [PubMed]

Liu, H. H.

N. E. Huang, Z. Sheng, S. R. Long, M. C. Wu, W. H. Shih, Q. Zeng, N. C. Yen, C. C. Tung, H. H. Liu, “The empirical mode decomposition and the Hilbert spectrum for non-linear and non-stationary time series analysis,” Proc. R. Soc. Lond. A 454(1971), 903–995 (1998).
[CrossRef]

Long, S. R.

N. E. Huang, Z. Sheng, S. R. Long, M. C. Wu, W. H. Shih, Q. Zeng, N. C. Yen, C. C. Tung, H. H. Liu, “The empirical mode decomposition and the Hilbert spectrum for non-linear and non-stationary time series analysis,” Proc. R. Soc. Lond. A 454(1971), 903–995 (1998).
[CrossRef]

Lotan, R.

K. Sokolov, M. Follen, J. Aaron, I. Pavlova, A. Malpica, R. Lotan, R. Richards-Kortum, “Real time vital imaging of pre-cancer using anti-EGFR antibodies conjugated to gold nanoparticles,” Cancer Res. 63(9), 1999–2004 (2003).
[PubMed]

Mack, V.

Malpica, A.

K. Sokolov, M. Follen, J. Aaron, I. Pavlova, A. Malpica, R. Lotan, R. Richards-Kortum, “Real time vital imaging of pre-cancer using anti-EGFR antibodies conjugated to gold nanoparticles,” Cancer Res. 63(9), 1999–2004 (2003).
[PubMed]

Meignen, S.

C. Damerval, S. Meignen, V. Perrier, “A fast algorithm for bidimensional EMD,” IEEE Signal Process. Lett. 12(10), 701–704 (2005).
[CrossRef]

Mertz, J.

J. Mertz, J. Kim, “Scanning light-sheet microscopy in the whole mouse brain with HiLo background rejection,” J. Biomed. Opt. 15(1), 016027 (2010).
[CrossRef] [PubMed]

S. Santos, K. K. Chu, D. Lim, N. Bozinovic, T. N. Ford, C. Hourtoule, A. C. Bartoo, S. K. Singh, J. Mertz, “Optically sectioned fluorescence endomicroscopy with hybrid-illumination imaging through a flexible fiber bundle,” J. Biomed. Opt. 14(3), 030502 (2009).
[CrossRef] [PubMed]

N. Bozinovic, C. Ventalon, T. Ford, J. Mertz, “Fluorescence endomicroscopy with structured illumination,” Opt. Express 16(11), 8016–8025 (2008).
[CrossRef] [PubMed]

D. Lim, K. K. Chu, J. Mertz, “Wide-field fluorescence sectioning with hybrid speckle and uniform-illumination microscopy,” Opt. Lett. 33(16), 1819–1821 (2008).
[CrossRef] [PubMed]

Michaelson, J.

Momany, M.

B. Thomas, M. Momany, P. Kner, “Optical sectioning structured illumination microscopy with enhanced sensitivity,” J. Opt. 15(9), 094004 (2013).
[CrossRef]

Na, J.

Neil, M. A. A.

Niang, O.

J. C. Nunes, Y. Bouaoune, E. Delechelle, O. Niang, Ph. Bunel, “Image analysis by bidimensional empirical mode decomposition,” Image Vis. Comput. 21(12), 1019–1026 (2003).
[CrossRef]

Nunes, J. C.

J. C. Nunes, Y. Bouaoune, E. Delechelle, O. Niang, Ph. Bunel, “Image analysis by bidimensional empirical mode decomposition,” Image Vis. Comput. 21(12), 1019–1026 (2003).
[CrossRef]

Oldfield, M. A.

Olfield, M. A.

Park, H.

Patorski, K.

Pavlova, I.

K. Sokolov, M. Follen, J. Aaron, I. Pavlova, A. Malpica, R. Lotan, R. Richards-Kortum, “Real time vital imaging of pre-cancer using anti-EGFR antibodies conjugated to gold nanoparticles,” Cancer Res. 63(9), 1999–2004 (2003).
[PubMed]

Perrier, V.

C. Damerval, S. Meignen, V. Perrier, “A fast algorithm for bidimensional EMD,” IEEE Signal Process. Lett. 12(10), 701–704 (2005).
[CrossRef]

Pokorski, K.

Rahman, M.

Richards-Kortum, R.

T. S. Tkaczyk, M. Rahman, V. Mack, K. Sokolov, J. D. Rogers, R. Richards-Kortum, M. R. Descour, “High resolution, molecular-specific, reflectance imaging in optically dense tissue phantoms with structured-illumination,” Opt. Express 12(16), 3745–3758 (2004).
[CrossRef] [PubMed]

K. Sokolov, M. Follen, J. Aaron, I. Pavlova, A. Malpica, R. Lotan, R. Richards-Kortum, “Real time vital imaging of pre-cancer using anti-EGFR antibodies conjugated to gold nanoparticles,” Cancer Res. 63(9), 1999–2004 (2003).
[PubMed]

Rogers, J. D.

Ryu, S. Y.

Santos, S.

S. Santos, K. K. Chu, D. Lim, N. Bozinovic, T. N. Ford, C. Hourtoule, A. C. Bartoo, S. K. Singh, J. Mertz, “Optically sectioned fluorescence endomicroscopy with hybrid-illumination imaging through a flexible fiber bundle,” J. Biomed. Opt. 14(3), 030502 (2009).
[CrossRef] [PubMed]

Schaefer, L. H.

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

Schaffer, J.

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

Schuster, D.

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

Sheng, Z.

N. E. Huang, Z. Sheng, S. R. Long, M. C. Wu, W. H. Shih, Q. Zeng, N. C. Yen, C. C. Tung, H. H. Liu, “The empirical mode decomposition and the Hilbert spectrum for non-linear and non-stationary time series analysis,” Proc. R. Soc. Lond. A 454(1971), 903–995 (1998).
[CrossRef]

Sheppard, C. J. R.

Shih, W. H.

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Figures (6)

Fig. 1
Fig. 1

Layout of the typical SIM system [5].

Fig. 2
Fig. 2

Images of phantoms containing SiHa cervical cancer cells labeled with anti-EGFR gold conjugates. The field of view is 54 x 54 μm2. The approximate depth of the imaged optical section is 15-20 μm below the phantom surface. Part (a) shows an inverted widefield reflectance microscope image, and part (b) shows a structured illumination raw image [10].

Fig. 3
Fig. 3

Reconstructed optically sectioned images using 3-frame SIM technique (a), HiLo microscopy (b), and our FABEMD-HS algorithm (c), respectively.

Fig. 4
Fig. 4

(a) Input pattern obtained subtracting two mutually π-phase shifted grid patterns, (b) input pattern after FABEMD adaptive band-pass filtering, (c)-(f) the FABEMD-HS results for reconstruction of optically sectioned images using two grid patterns phase-shifted by π/3, 2π/3, 4π/3 and 2π, respectively.

Fig. 5
Fig. 5

First ten BIMFs of the input pattern (two subtracted raw frames phase shifted by 4π/3) obtained employing the FABEMD OSFW2 algorithm (a)-(j), decomposition residue (k) and the low-frequency fringe free residual bias term defined as a sum of BIMF5-BIMF10 and the residue (l).

Fig. 6
Fig. 6

Optically sectioned images reconstructed using input pattern (a), sum of BIMF1-BIMF4 (b), sum of BIMF3 and BIMF4 (c), only BIMF2 (d), input pattern with BIMF1 removed (e) and only BIMF1 (f).

Equations (4)

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

s A (x,y)=s(x,y)+i s H (x,y).
s H =iexp(iβ) F 1 {P( ζ 1 , ζ 2 )F[s(x,y)]},
P( ζ 1 , ζ 2 )= ζ 1 +i ζ 2 ζ 1 2 + ζ 2 2
| A(x,y) |= s 2 (x,y)+ | F 1 {P( ζ 1 , ζ 2 )F[s(x,y)]} | 2 .

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