Abstract

Imaging Fourier-transform spectroscopy (IFTS) is a powerful method for biological hyperspectral analysis based on various imaging modalities, such as fluorescence or Raman. Since the measurements are taken in the Fourier space of the spectrum, it can also take advantage of compressed sensing strategies. IFTS has been readily implemented in high-throughput, high-content microscope systems based on wide-field imaging modalities. However, there are limitations in existing wide-field IFTS designs. Non-common-path approaches are less phase-stable. Alternatively, designs based on the common-path Sagnac interferometer are stable, but incompatible with high-throughput imaging. They require exhaustive sequential scanning over large interferometric path delays, making compressive strategic data acquisition impossible. In this paper, we present a novel phase-stable, near-common-path interferometer enabling high-throughput hyperspectral imaging based on strategic data acquisition. Our results suggest that this approach can improve throughput over those of many other wide-field spectral techniques by more than an order of magnitude without compromising phase stability.

© 2017 Optical Society of America

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References

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2016 (1)

2013 (6)

T. Blumensath, “Compressed sensing with nonlinear observations and related nonlinear optimization problems,” IEEE Trans. Inf. Theory 59, 3466–3474 (2013).
[Crossref]

A. Beck and Y. C. Eldar, “Sparsity constrained nonlinear optimization: optimality conditions and algorithms,” SIAM J. Optim. 23, 1480–1509 (2013).
[Crossref]

M. S. Islam, M. Honma, T. Nakabayashi, M. Kinjo, and N. Ohta, “pH dependence of the fluorescence lifetime of FAD in solution and in cells,” Int. J. Mol. Sci. 14, 1952–1963 (2013).
[Crossref]

K. D. Piatkevich, V. N. Malashkevich, K. S. Morozova, N. A. Nemkovich, S. C. Almo, and V. V. Verkhusha, “Extended stokes shift in fluorescent proteins: chromophore–protein interactions in a near-infrared tagrfp675 variant,” Sci. Rep. 3, 1847 (2013).
[Crossref]

Q. Li, X. He, Y. Wang, H. Liu, D. Xu, and F. Guo, “Review of spectral imaging technology in biomedical engineering: achievements and challenges,” J. Biomed. Opt. 18, 100901 (2013).
[Crossref]

J. Maillard, L. Drissen, F. Grandmont, and S. Thibault, “Integral wide-field spectroscopy in astronomy: the imaging FTS solution,” Exp. Astron. 35, 527–559 (2013).
[Crossref]

2012 (1)

T. R. Hillman, N. Lue, Y. Sung, R. R. Dasari, and Z. Yaqoob, “Near-common-path self-reference quantitative phase microscopy,” IEEE Photon. Technol. Lett. 24, 1812–1814 (2012).
[Crossref]

2010 (1)

2009 (2)

D. Needell and J. A. Tropp, “CoSaMP: iterative signal recovery from incomplete and inaccurate samples,” Appl. Comput. Harmon. Anal. 26, 301–321 (2009).
[Crossref]

W. Dai and O. Milenkovic, “Subspace pursuit for compressive sensing signal reconstruction,” IEEE Trans. Inf. Theory 55, 2230–2249 (2009).
[Crossref]

2007 (5)

J. M. Bioucas-Dias and M. A. Figueiredo, “A new twist: two-step iterative shrinkage/thresholding algorithms for image restoration,” IEEE Trans. Image Process. 16, 2992–3004 (2007).
[Crossref]

E. Candes and J. Romberg, “Sparsity and incoherence in compressive sampling,” Inverse Probl. 23, 969–985 (2007).
[Crossref]

R. G. Baraniuk, “Compressive sensing,” IEEE Signal Process. Mag. 24, 118–121 (2007).
[Crossref]

C. Bakal, J. Aach, G. Church, and N. Perrimon, “Quantitative morphological signatures define local signaling networks regulating cell morphology,” Science 316, 1753–1756 (2007).
[Crossref]

S. T. Thurman and J. R. Fienup, “Signal-to-noise ratio trade-offs associated with coarsely sampled Fourier transform spectroscopy,” J. Opt. Soc. Am. A 24, 2817–2821 (2007).
[Crossref]

2006 (2)

G. Popescu, T. Ikeda, R. R. Dasari, and M. S. Feld, “Diffraction phase microscopy for quantifying cell structure and dynamics,” Opt. Lett. 31, 775–777 (2006).
[Crossref]

Y. Ferrec, J. Taboury, H. Sauer, and P. Chavel, “Optimal geometry for Sagnac and Michelson interferometers used as spectral imagers,” Opt. Eng. 45, 115601 (2006).
[Crossref]

2005 (2)

C. Thaler, S. V. Koushik, P. S. Blank, and S. S. Vogel, “Quantitative multiphoton spectral imaging and its use for measuring resonance energy transfer,” Biophys. J. 89, 2736–2749 (2005).
[Crossref]

C. Buehler, K. H. Kim, U. Greuter, N. Schlumpf, and P. T. So, “Single-photon counting multicolor multiphoton fluorescence microscope,” J. Fluoresc. 15, 41–51 (2005).
[Crossref]

2004 (1)

Z. E. Perlman, M. D. Slack, Y. Feng, T. J. Mitchison, L. F. Wu, and S. J. Altschuler, “Multidimensional drug profiling by automated microscopy,” Science 306, 1194–1198 (2004).
[Crossref]

2003 (2)

R. G. Sellar and G. D. Boreman, “Limiting aspect ratios of Sagnac interferometers,” Opt. Eng. 42, 3320–3325 (2003).
[Crossref]

C. A. Lieber and A. Mahadevan-Jansen, “Automated method for subtraction of fluorescence from biological Raman spectra,” Appl. Spectrosc. 57, 1363–1367 (2003).
[Crossref]

2000 (1)

M. G. Shim, L.-M. Wong Kee Song, N. E. Marcon, and B. C. Wilson, “In vivo near-infrared Raman spectroscopy: demonstration of feasibility during clinical gastrointestinal endoscopy,” Photochem. Photobiol. 72, 146–150 (2000).
[Crossref]

1998 (1)

P. Caspers, G. Lucassen, R. Wolthuis, H. Bruining, and G. Puppels, “In vitro and in vivo Raman spectroscopy of human skin,” Biospectroscopy 4, S31–S40 (1998).
[Crossref]

1996 (2)

Z. Malik, D. Cabib, R. Buckwald, A. Talmi, Y. Garini, and S. Lipson, “Fourier transform multipixel spectroscopy for quantitative cytology,” J. Microsc. 182, 133–140 (1996).
[Crossref]

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. Ferguson-Smith, Y. Ning, D. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273, 494–497 (1996).
[Crossref]

1995 (2)

M. R. Carter, C. L. Bennett, D. J. Fields, and F. D. Lee, “Livermore imaging Fourier transform infrared spectrometer (LIFTIRS),” Proc. SPIE 2480, 380–386 (1995).

C. J. Brenan and I. W. Hunter, “Design and characterization of a visible-light Fourier transform Raman spectrometer,” Appl. Spectrosc. 49, 1086–1093 (1995).
[Crossref]

1973 (1)

1972 (1)

Aach, J.

C. Bakal, J. Aach, G. Church, and N. Perrimon, “Quantitative morphological signatures define local signaling networks regulating cell morphology,” Science 316, 1753–1756 (2007).
[Crossref]

Almo, S. C.

K. D. Piatkevich, V. N. Malashkevich, K. S. Morozova, N. A. Nemkovich, S. C. Almo, and V. V. Verkhusha, “Extended stokes shift in fluorescent proteins: chromophore–protein interactions in a near-infrared tagrfp675 variant,” Sci. Rep. 3, 1847 (2013).
[Crossref]

Altschuler, S. J.

Z. E. Perlman, M. D. Slack, Y. Feng, T. J. Mitchison, L. F. Wu, and S. J. Altschuler, “Multidimensional drug profiling by automated microscopy,” Science 306, 1194–1198 (2004).
[Crossref]

Anderson, L.

Bakal, C.

C. Bakal, J. Aach, G. Church, and N. Perrimon, “Quantitative morphological signatures define local signaling networks regulating cell morphology,” Science 316, 1753–1756 (2007).
[Crossref]

Bar-Am, I.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. Ferguson-Smith, Y. Ning, D. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273, 494–497 (1996).
[Crossref]

Baraniuk, R. G.

R. G. Baraniuk, “Compressive sensing,” IEEE Signal Process. Mag. 24, 118–121 (2007).
[Crossref]

Barducci, A.

Beck, A.

A. Beck and Y. C. Eldar, “Sparsity constrained nonlinear optimization: optimality conditions and algorithms,” SIAM J. Optim. 23, 1480–1509 (2013).
[Crossref]

Bennett, C. L.

M. R. Carter, C. L. Bennett, D. J. Fields, and F. D. Lee, “Livermore imaging Fourier transform infrared spectrometer (LIFTIRS),” Proc. SPIE 2480, 380–386 (1995).

Bioucas-Dias, J. M.

J. M. Bioucas-Dias and M. A. Figueiredo, “A new twist: two-step iterative shrinkage/thresholding algorithms for image restoration,” IEEE Trans. Image Process. 16, 2992–3004 (2007).
[Crossref]

Blank, P. S.

C. Thaler, S. V. Koushik, P. S. Blank, and S. S. Vogel, “Quantitative multiphoton spectral imaging and its use for measuring resonance energy transfer,” Biophys. J. 89, 2736–2749 (2005).
[Crossref]

Blumensath, T.

T. Blumensath, “Compressed sensing with nonlinear observations and related nonlinear optimization problems,” IEEE Trans. Inf. Theory 59, 3466–3474 (2013).
[Crossref]

Boreman, G. D.

R. G. Sellar and G. D. Boreman, “Limiting aspect ratios of Sagnac interferometers,” Opt. Eng. 42, 3320–3325 (2003).
[Crossref]

Brenan, C. J.

Bruining, H.

P. Caspers, G. Lucassen, R. Wolthuis, H. Bruining, and G. Puppels, “In vitro and in vivo Raman spectroscopy of human skin,” Biospectroscopy 4, S31–S40 (1998).
[Crossref]

Buckwald, R.

Z. Malik, D. Cabib, R. Buckwald, A. Talmi, Y. Garini, and S. Lipson, “Fourier transform multipixel spectroscopy for quantitative cytology,” J. Microsc. 182, 133–140 (1996).
[Crossref]

Buehler, C.

C. Buehler, K. H. Kim, U. Greuter, N. Schlumpf, and P. T. So, “Single-photon counting multicolor multiphoton fluorescence microscope,” J. Fluoresc. 15, 41–51 (2005).
[Crossref]

Cabib, D.

Z. Malik, D. Cabib, R. Buckwald, A. Talmi, Y. Garini, and S. Lipson, “Fourier transform multipixel spectroscopy for quantitative cytology,” J. Microsc. 182, 133–140 (1996).
[Crossref]

Candes, E.

E. Candes and J. Romberg, “Sparsity and incoherence in compressive sampling,” Inverse Probl. 23, 969–985 (2007).
[Crossref]

Carter, M. R.

M. R. Carter, C. L. Bennett, D. J. Fields, and F. D. Lee, “Livermore imaging Fourier transform infrared spectrometer (LIFTIRS),” Proc. SPIE 2480, 380–386 (1995).

Caspers, P.

P. Caspers, G. Lucassen, R. Wolthuis, H. Bruining, and G. Puppels, “In vitro and in vivo Raman spectroscopy of human skin,” Biospectroscopy 4, S31–S40 (1998).
[Crossref]

Chartrand, R.

R. Chartrand and W. Yin, “Iteratively reweighted algorithms for compressive sensing,” in 2008 IEEE International Conference on Acoustics, Speech and Signal Processing (IEEE, 2008), pp. 3869–3872.

Chavel, P.

Y. Ferrec, J. Taboury, H. Sauer, and P. Chavel, “Optimal geometry for Sagnac and Michelson interferometers used as spectral imagers,” Opt. Eng. 45, 115601 (2006).
[Crossref]

Chen, Y.

Y. Chen and I. W. Hunter, “Design of a miniature hyperspectral imaging Fourier transform spectrometer for endoscopy,” in Imaging Systems and Applications (Optical Society of America, 2016), paper IW1E.2.

Church, G.

C. Bakal, J. Aach, G. Church, and N. Perrimon, “Quantitative morphological signatures define local signaling networks regulating cell morphology,” Science 316, 1753–1756 (2007).
[Crossref]

Dai, W.

W. Dai and O. Milenkovic, “Subspace pursuit for compressive sensing signal reconstruction,” IEEE Trans. Inf. Theory 55, 2230–2249 (2009).
[Crossref]

Dasari, R. R.

T. R. Hillman, N. Lue, Y. Sung, R. R. Dasari, and Z. Yaqoob, “Near-common-path self-reference quantitative phase microscopy,” IEEE Photon. Technol. Lett. 24, 1812–1814 (2012).
[Crossref]

G. Popescu, T. Ikeda, R. R. Dasari, and M. S. Feld, “Diffraction phase microscopy for quantifying cell structure and dynamics,” Opt. Lett. 31, 775–777 (2006).
[Crossref]

De Haseth, J. A.

P. R. Griffiths and J. A. De Haseth, Fourier Transform Infrared Spectrometry (Wiley, 2007), Vol. 171.

Drissen, L.

J. Maillard, L. Drissen, F. Grandmont, and S. Thibault, “Integral wide-field spectroscopy in astronomy: the imaging FTS solution,” Exp. Astron. 35, 527–559 (2013).
[Crossref]

Du Manoir, S.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. Ferguson-Smith, Y. Ning, D. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273, 494–497 (1996).
[Crossref]

Eldar, Y. C.

A. Beck and Y. C. Eldar, “Sparsity constrained nonlinear optimization: optimality conditions and algorithms,” SIAM J. Optim. 23, 1480–1509 (2013).
[Crossref]

Feld, M. S.

Feng, Y.

Z. E. Perlman, M. D. Slack, Y. Feng, T. J. Mitchison, L. F. Wu, and S. J. Altschuler, “Multidimensional drug profiling by automated microscopy,” Science 306, 1194–1198 (2004).
[Crossref]

Ferguson-Smith, M.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. Ferguson-Smith, Y. Ning, D. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273, 494–497 (1996).
[Crossref]

Ferrec, Y.

Y. Ferrec, J. Taboury, H. Sauer, and P. Chavel, “Optimal geometry for Sagnac and Michelson interferometers used as spectral imagers,” Opt. Eng. 45, 115601 (2006).
[Crossref]

Fields, D. J.

M. R. Carter, C. L. Bennett, D. J. Fields, and F. D. Lee, “Livermore imaging Fourier transform infrared spectrometer (LIFTIRS),” Proc. SPIE 2480, 380–386 (1995).

Fienup, J. R.

Figueiredo, M. A.

J. M. Bioucas-Dias and M. A. Figueiredo, “A new twist: two-step iterative shrinkage/thresholding algorithms for image restoration,” IEEE Trans. Image Process. 16, 2992–3004 (2007).
[Crossref]

Garini, Y.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. Ferguson-Smith, Y. Ning, D. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273, 494–497 (1996).
[Crossref]

Z. Malik, D. Cabib, R. Buckwald, A. Talmi, Y. Garini, and S. Lipson, “Fourier transform multipixel spectroscopy for quantitative cytology,” J. Microsc. 182, 133–140 (1996).
[Crossref]

Grandmont, F.

J. Maillard, L. Drissen, F. Grandmont, and S. Thibault, “Integral wide-field spectroscopy in astronomy: the imaging FTS solution,” Exp. Astron. 35, 527–559 (2013).
[Crossref]

Greuter, U.

C. Buehler, K. H. Kim, U. Greuter, N. Schlumpf, and P. T. So, “Single-photon counting multicolor multiphoton fluorescence microscope,” J. Fluoresc. 15, 41–51 (2005).
[Crossref]

Griffiths, P. R.

P. R. Griffiths and J. A. De Haseth, Fourier Transform Infrared Spectrometry (Wiley, 2007), Vol. 171.

Guo, F.

Q. Li, X. He, Y. Wang, H. Liu, D. Xu, and F. Guo, “Review of spectral imaging technology in biomedical engineering: achievements and challenges,” J. Biomed. Opt. 18, 100901 (2013).
[Crossref]

Guzzi, D.

He, X.

Q. Li, X. He, Y. Wang, H. Liu, D. Xu, and F. Guo, “Review of spectral imaging technology in biomedical engineering: achievements and challenges,” J. Biomed. Opt. 18, 100901 (2013).
[Crossref]

Heintzmann, R.

Hillman, T. R.

T. R. Hillman, N. Lue, Y. Sung, R. R. Dasari, and Z. Yaqoob, “Near-common-path self-reference quantitative phase microscopy,” IEEE Photon. Technol. Lett. 24, 1812–1814 (2012).
[Crossref]

Honma, M.

M. S. Islam, M. Honma, T. Nakabayashi, M. Kinjo, and N. Ohta, “pH dependence of the fluorescence lifetime of FAD in solution and in cells,” Int. J. Mol. Sci. 14, 1952–1963 (2013).
[Crossref]

Hunter, I. W.

C. J. Brenan and I. W. Hunter, “Design and characterization of a visible-light Fourier transform Raman spectrometer,” Appl. Spectrosc. 49, 1086–1093 (1995).
[Crossref]

Y. Chen and I. W. Hunter, “Design of a miniature hyperspectral imaging Fourier transform spectrometer for endoscopy,” in Imaging Systems and Applications (Optical Society of America, 2016), paper IW1E.2.

Ikeda, T.

Islam, M. S.

M. S. Islam, M. Honma, T. Nakabayashi, M. Kinjo, and N. Ohta, “pH dependence of the fluorescence lifetime of FAD in solution and in cells,” Int. J. Mol. Sci. 14, 1952–1963 (2013).
[Crossref]

Kielhorn, M.

Kim, K. H.

C. Buehler, K. H. Kim, U. Greuter, N. Schlumpf, and P. T. So, “Single-photon counting multicolor multiphoton fluorescence microscope,” J. Fluoresc. 15, 41–51 (2005).
[Crossref]

Kinjo, M.

M. S. Islam, M. Honma, T. Nakabayashi, M. Kinjo, and N. Ohta, “pH dependence of the fluorescence lifetime of FAD in solution and in cells,” Int. J. Mol. Sci. 14, 1952–1963 (2013).
[Crossref]

Koushik, S. V.

C. Thaler, S. V. Koushik, P. S. Blank, and S. S. Vogel, “Quantitative multiphoton spectral imaging and its use for measuring resonance energy transfer,” Biophys. J. 89, 2736–2749 (2005).
[Crossref]

Kruger, R.

Lastri, C.

Ledbetter, D.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. Ferguson-Smith, Y. Ning, D. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273, 494–497 (1996).
[Crossref]

Lee, F. D.

M. R. Carter, C. L. Bennett, D. J. Fields, and F. D. Lee, “Livermore imaging Fourier transform infrared spectrometer (LIFTIRS),” Proc. SPIE 2480, 380–386 (1995).

Li, Q.

Q. Li, X. He, Y. Wang, H. Liu, D. Xu, and F. Guo, “Review of spectral imaging technology in biomedical engineering: achievements and challenges,” J. Biomed. Opt. 18, 100901 (2013).
[Crossref]

Lieber, C. A.

Lipson, S.

Z. Malik, D. Cabib, R. Buckwald, A. Talmi, Y. Garini, and S. Lipson, “Fourier transform multipixel spectroscopy for quantitative cytology,” J. Microsc. 182, 133–140 (1996).
[Crossref]

Liu, H.

Q. Li, X. He, Y. Wang, H. Liu, D. Xu, and F. Guo, “Review of spectral imaging technology in biomedical engineering: achievements and challenges,” J. Biomed. Opt. 18, 100901 (2013).
[Crossref]

Lucassen, G.

P. Caspers, G. Lucassen, R. Wolthuis, H. Bruining, and G. Puppels, “In vitro and in vivo Raman spectroscopy of human skin,” Biospectroscopy 4, S31–S40 (1998).
[Crossref]

Lue, N.

T. R. Hillman, N. Lue, Y. Sung, R. R. Dasari, and Z. Yaqoob, “Near-common-path self-reference quantitative phase microscopy,” IEEE Photon. Technol. Lett. 24, 1812–1814 (2012).
[Crossref]

Mahadevan-Jansen, A.

Maillard, J.

J. Maillard, L. Drissen, F. Grandmont, and S. Thibault, “Integral wide-field spectroscopy in astronomy: the imaging FTS solution,” Exp. Astron. 35, 527–559 (2013).
[Crossref]

Malashkevich, V. N.

K. D. Piatkevich, V. N. Malashkevich, K. S. Morozova, N. A. Nemkovich, S. C. Almo, and V. V. Verkhusha, “Extended stokes shift in fluorescent proteins: chromophore–protein interactions in a near-infrared tagrfp675 variant,” Sci. Rep. 3, 1847 (2013).
[Crossref]

Malik, Z.

Z. Malik, D. Cabib, R. Buckwald, A. Talmi, Y. Garini, and S. Lipson, “Fourier transform multipixel spectroscopy for quantitative cytology,” J. Microsc. 182, 133–140 (1996).
[Crossref]

Marcoionni, P.

Marcon, N. E.

M. G. Shim, L.-M. Wong Kee Song, N. E. Marcon, and B. C. Wilson, “In vivo near-infrared Raman spectroscopy: demonstration of feasibility during clinical gastrointestinal endoscopy,” Photochem. Photobiol. 72, 146–150 (2000).
[Crossref]

Milenkovic, O.

W. Dai and O. Milenkovic, “Subspace pursuit for compressive sensing signal reconstruction,” IEEE Trans. Inf. Theory 55, 2230–2249 (2009).
[Crossref]

Mitchison, T. J.

Z. E. Perlman, M. D. Slack, Y. Feng, T. J. Mitchison, L. F. Wu, and S. J. Altschuler, “Multidimensional drug profiling by automated microscopy,” Science 306, 1194–1198 (2004).
[Crossref]

Morozova, K. S.

K. D. Piatkevich, V. N. Malashkevich, K. S. Morozova, N. A. Nemkovich, S. C. Almo, and V. V. Verkhusha, “Extended stokes shift in fluorescent proteins: chromophore–protein interactions in a near-infrared tagrfp675 variant,” Sci. Rep. 3, 1847 (2013).
[Crossref]

Müller, W.

Nakabayashi, T.

M. S. Islam, M. Honma, T. Nakabayashi, M. Kinjo, and N. Ohta, “pH dependence of the fluorescence lifetime of FAD in solution and in cells,” Int. J. Mol. Sci. 14, 1952–1963 (2013).
[Crossref]

Nardino, V.

Needell, D.

D. Needell and J. A. Tropp, “CoSaMP: iterative signal recovery from incomplete and inaccurate samples,” Appl. Comput. Harmon. Anal. 26, 301–321 (2009).
[Crossref]

Nemkovich, N. A.

K. D. Piatkevich, V. N. Malashkevich, K. S. Morozova, N. A. Nemkovich, S. C. Almo, and V. V. Verkhusha, “Extended stokes shift in fluorescent proteins: chromophore–protein interactions in a near-infrared tagrfp675 variant,” Sci. Rep. 3, 1847 (2013).
[Crossref]

Ning, Y.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. Ferguson-Smith, Y. Ning, D. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273, 494–497 (1996).
[Crossref]

Ohta, N.

M. S. Islam, M. Honma, T. Nakabayashi, M. Kinjo, and N. Ohta, “pH dependence of the fluorescence lifetime of FAD in solution and in cells,” Int. J. Mol. Sci. 14, 1952–1963 (2013).
[Crossref]

Perlman, Z. E.

Z. E. Perlman, M. D. Slack, Y. Feng, T. J. Mitchison, L. F. Wu, and S. J. Altschuler, “Multidimensional drug profiling by automated microscopy,” Science 306, 1194–1198 (2004).
[Crossref]

Perrimon, N.

C. Bakal, J. Aach, G. Church, and N. Perrimon, “Quantitative morphological signatures define local signaling networks regulating cell morphology,” Science 316, 1753–1756 (2007).
[Crossref]

Piatkevich, K. D.

K. D. Piatkevich, V. N. Malashkevich, K. S. Morozova, N. A. Nemkovich, S. C. Almo, and V. V. Verkhusha, “Extended stokes shift in fluorescent proteins: chromophore–protein interactions in a near-infrared tagrfp675 variant,” Sci. Rep. 3, 1847 (2013).
[Crossref]

Pippi, I.

Popescu, G.

Popp, J.

Puppels, G.

P. Caspers, G. Lucassen, R. Wolthuis, H. Bruining, and G. Puppels, “In vitro and in vivo Raman spectroscopy of human skin,” Biospectroscopy 4, S31–S40 (1998).
[Crossref]

Ried, T.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. Ferguson-Smith, Y. Ning, D. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273, 494–497 (1996).
[Crossref]

Roesler, F.

Romberg, J.

E. Candes and J. Romberg, “Sparsity and incoherence in compressive sampling,” Inverse Probl. 23, 969–985 (2007).
[Crossref]

Sauer, H.

Y. Ferrec, J. Taboury, H. Sauer, and P. Chavel, “Optimal geometry for Sagnac and Michelson interferometers used as spectral imagers,” Opt. Eng. 45, 115601 (2006).
[Crossref]

Schlumpf, N.

C. Buehler, K. H. Kim, U. Greuter, N. Schlumpf, and P. T. So, “Single-photon counting multicolor multiphoton fluorescence microscope,” J. Fluoresc. 15, 41–51 (2005).
[Crossref]

Schmitt, M.

Schoell, B.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. Ferguson-Smith, Y. Ning, D. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273, 494–497 (1996).
[Crossref]

Schröck, E.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. Ferguson-Smith, Y. Ning, D. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273, 494–497 (1996).
[Crossref]

Sellar, R. G.

R. G. Sellar and G. D. Boreman, “Limiting aspect ratios of Sagnac interferometers,” Opt. Eng. 42, 3320–3325 (2003).
[Crossref]

Shim, M. G.

M. G. Shim, L.-M. Wong Kee Song, N. E. Marcon, and B. C. Wilson, “In vivo near-infrared Raman spectroscopy: demonstration of feasibility during clinical gastrointestinal endoscopy,” Photochem. Photobiol. 72, 146–150 (2000).
[Crossref]

Slack, M. D.

Z. E. Perlman, M. D. Slack, Y. Feng, T. J. Mitchison, L. F. Wu, and S. J. Altschuler, “Multidimensional drug profiling by automated microscopy,” Science 306, 1194–1198 (2004).
[Crossref]

So, P. T.

C. Buehler, K. H. Kim, U. Greuter, N. Schlumpf, and P. T. So, “Single-photon counting multicolor multiphoton fluorescence microscope,” J. Fluoresc. 15, 41–51 (2005).
[Crossref]

Soenksen, D.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. Ferguson-Smith, Y. Ning, D. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273, 494–497 (1996).
[Crossref]

Sung, Y.

T. R. Hillman, N. Lue, Y. Sung, R. R. Dasari, and Z. Yaqoob, “Near-common-path self-reference quantitative phase microscopy,” IEEE Photon. Technol. Lett. 24, 1812–1814 (2012).
[Crossref]

Taboury, J.

Y. Ferrec, J. Taboury, H. Sauer, and P. Chavel, “Optimal geometry for Sagnac and Michelson interferometers used as spectral imagers,” Opt. Eng. 45, 115601 (2006).
[Crossref]

Talmi, A.

Z. Malik, D. Cabib, R. Buckwald, A. Talmi, Y. Garini, and S. Lipson, “Fourier transform multipixel spectroscopy for quantitative cytology,” J. Microsc. 182, 133–140 (1996).
[Crossref]

Thaler, C.

C. Thaler, S. V. Koushik, P. S. Blank, and S. S. Vogel, “Quantitative multiphoton spectral imaging and its use for measuring resonance energy transfer,” Biophys. J. 89, 2736–2749 (2005).
[Crossref]

Thibault, S.

J. Maillard, L. Drissen, F. Grandmont, and S. Thibault, “Integral wide-field spectroscopy in astronomy: the imaging FTS solution,” Exp. Astron. 35, 527–559 (2013).
[Crossref]

Thurman, S. T.

Tropp, J. A.

D. Needell and J. A. Tropp, “CoSaMP: iterative signal recovery from incomplete and inaccurate samples,” Appl. Comput. Harmon. Anal. 26, 301–321 (2009).
[Crossref]

Veldman, T.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. Ferguson-Smith, Y. Ning, D. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273, 494–497 (1996).
[Crossref]

Verkhusha, V. V.

K. D. Piatkevich, V. N. Malashkevich, K. S. Morozova, N. A. Nemkovich, S. C. Almo, and V. V. Verkhusha, “Extended stokes shift in fluorescent proteins: chromophore–protein interactions in a near-infrared tagrfp675 variant,” Sci. Rep. 3, 1847 (2013).
[Crossref]

Vogel, S. S.

C. Thaler, S. V. Koushik, P. S. Blank, and S. S. Vogel, “Quantitative multiphoton spectral imaging and its use for measuring resonance energy transfer,” Biophys. J. 89, 2736–2749 (2005).
[Crossref]

Wang, Y.

Q. Li, X. He, Y. Wang, H. Liu, D. Xu, and F. Guo, “Review of spectral imaging technology in biomedical engineering: achievements and challenges,” J. Biomed. Opt. 18, 100901 (2013).
[Crossref]

Wienberg, J.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. Ferguson-Smith, Y. Ning, D. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273, 494–497 (1996).
[Crossref]

Wilson, B. C.

M. G. Shim, L.-M. Wong Kee Song, N. E. Marcon, and B. C. Wilson, “In vivo near-infrared Raman spectroscopy: demonstration of feasibility during clinical gastrointestinal endoscopy,” Photochem. Photobiol. 72, 146–150 (2000).
[Crossref]

Wolthuis, R.

P. Caspers, G. Lucassen, R. Wolthuis, H. Bruining, and G. Puppels, “In vitro and in vivo Raman spectroscopy of human skin,” Biospectroscopy 4, S31–S40 (1998).
[Crossref]

Wong Kee Song, L.-M.

M. G. Shim, L.-M. Wong Kee Song, N. E. Marcon, and B. C. Wilson, “In vivo near-infrared Raman spectroscopy: demonstration of feasibility during clinical gastrointestinal endoscopy,” Photochem. Photobiol. 72, 146–150 (2000).
[Crossref]

Wu, L. F.

Z. E. Perlman, M. D. Slack, Y. Feng, T. J. Mitchison, L. F. Wu, and S. J. Altschuler, “Multidimensional drug profiling by automated microscopy,” Science 306, 1194–1198 (2004).
[Crossref]

Xu, D.

Q. Li, X. He, Y. Wang, H. Liu, D. Xu, and F. Guo, “Review of spectral imaging technology in biomedical engineering: achievements and challenges,” J. Biomed. Opt. 18, 100901 (2013).
[Crossref]

Yaqoob, Z.

T. R. Hillman, N. Lue, Y. Sung, R. R. Dasari, and Z. Yaqoob, “Near-common-path self-reference quantitative phase microscopy,” IEEE Photon. Technol. Lett. 24, 1812–1814 (2012).
[Crossref]

Yin, W.

R. Chartrand and W. Yin, “Iteratively reweighted algorithms for compressive sensing,” in 2008 IEEE International Conference on Acoustics, Speech and Signal Processing (IEEE, 2008), pp. 3869–3872.

Appl. Comput. Harmon. Anal. (1)

D. Needell and J. A. Tropp, “CoSaMP: iterative signal recovery from incomplete and inaccurate samples,” Appl. Comput. Harmon. Anal. 26, 301–321 (2009).
[Crossref]

Appl. Opt. (1)

Appl. Spectrosc. (2)

Biophys. J. (1)

C. Thaler, S. V. Koushik, P. S. Blank, and S. S. Vogel, “Quantitative multiphoton spectral imaging and its use for measuring resonance energy transfer,” Biophys. J. 89, 2736–2749 (2005).
[Crossref]

Biospectroscopy (1)

P. Caspers, G. Lucassen, R. Wolthuis, H. Bruining, and G. Puppels, “In vitro and in vivo Raman spectroscopy of human skin,” Biospectroscopy 4, S31–S40 (1998).
[Crossref]

Exp. Astron. (1)

J. Maillard, L. Drissen, F. Grandmont, and S. Thibault, “Integral wide-field spectroscopy in astronomy: the imaging FTS solution,” Exp. Astron. 35, 527–559 (2013).
[Crossref]

IEEE Photon. Technol. Lett. (1)

T. R. Hillman, N. Lue, Y. Sung, R. R. Dasari, and Z. Yaqoob, “Near-common-path self-reference quantitative phase microscopy,” IEEE Photon. Technol. Lett. 24, 1812–1814 (2012).
[Crossref]

IEEE Signal Process. Mag. (1)

R. G. Baraniuk, “Compressive sensing,” IEEE Signal Process. Mag. 24, 118–121 (2007).
[Crossref]

IEEE Trans. Image Process. (1)

J. M. Bioucas-Dias and M. A. Figueiredo, “A new twist: two-step iterative shrinkage/thresholding algorithms for image restoration,” IEEE Trans. Image Process. 16, 2992–3004 (2007).
[Crossref]

IEEE Trans. Inf. Theory (2)

T. Blumensath, “Compressed sensing with nonlinear observations and related nonlinear optimization problems,” IEEE Trans. Inf. Theory 59, 3466–3474 (2013).
[Crossref]

W. Dai and O. Milenkovic, “Subspace pursuit for compressive sensing signal reconstruction,” IEEE Trans. Inf. Theory 55, 2230–2249 (2009).
[Crossref]

Int. J. Mol. Sci. (1)

M. S. Islam, M. Honma, T. Nakabayashi, M. Kinjo, and N. Ohta, “pH dependence of the fluorescence lifetime of FAD in solution and in cells,” Int. J. Mol. Sci. 14, 1952–1963 (2013).
[Crossref]

Inverse Probl. (1)

E. Candes and J. Romberg, “Sparsity and incoherence in compressive sampling,” Inverse Probl. 23, 969–985 (2007).
[Crossref]

J. Biomed. Opt. (1)

Q. Li, X. He, Y. Wang, H. Liu, D. Xu, and F. Guo, “Review of spectral imaging technology in biomedical engineering: achievements and challenges,” J. Biomed. Opt. 18, 100901 (2013).
[Crossref]

J. Fluoresc. (1)

C. Buehler, K. H. Kim, U. Greuter, N. Schlumpf, and P. T. So, “Single-photon counting multicolor multiphoton fluorescence microscope,” J. Fluoresc. 15, 41–51 (2005).
[Crossref]

J. Microsc. (1)

Z. Malik, D. Cabib, R. Buckwald, A. Talmi, Y. Garini, and S. Lipson, “Fourier transform multipixel spectroscopy for quantitative cytology,” J. Microsc. 182, 133–140 (1996).
[Crossref]

J. Opt. Soc. Am. (1)

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

Opt. Eng. (2)

R. G. Sellar and G. D. Boreman, “Limiting aspect ratios of Sagnac interferometers,” Opt. Eng. 42, 3320–3325 (2003).
[Crossref]

Y. Ferrec, J. Taboury, H. Sauer, and P. Chavel, “Optimal geometry for Sagnac and Michelson interferometers used as spectral imagers,” Opt. Eng. 45, 115601 (2006).
[Crossref]

Opt. Express (1)

Opt. Lett. (1)

Optica (1)

Photochem. Photobiol. (1)

M. G. Shim, L.-M. Wong Kee Song, N. E. Marcon, and B. C. Wilson, “In vivo near-infrared Raman spectroscopy: demonstration of feasibility during clinical gastrointestinal endoscopy,” Photochem. Photobiol. 72, 146–150 (2000).
[Crossref]

Proc. SPIE (1)

M. R. Carter, C. L. Bennett, D. J. Fields, and F. D. Lee, “Livermore imaging Fourier transform infrared spectrometer (LIFTIRS),” Proc. SPIE 2480, 380–386 (1995).

Sci. Rep. (1)

K. D. Piatkevich, V. N. Malashkevich, K. S. Morozova, N. A. Nemkovich, S. C. Almo, and V. V. Verkhusha, “Extended stokes shift in fluorescent proteins: chromophore–protein interactions in a near-infrared tagrfp675 variant,” Sci. Rep. 3, 1847 (2013).
[Crossref]

Science (3)

C. Bakal, J. Aach, G. Church, and N. Perrimon, “Quantitative morphological signatures define local signaling networks regulating cell morphology,” Science 316, 1753–1756 (2007).
[Crossref]

Z. E. Perlman, M. D. Slack, Y. Feng, T. J. Mitchison, L. F. Wu, and S. J. Altschuler, “Multidimensional drug profiling by automated microscopy,” Science 306, 1194–1198 (2004).
[Crossref]

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. Ferguson-Smith, Y. Ning, D. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273, 494–497 (1996).
[Crossref]

SIAM J. Optim. (1)

A. Beck and Y. C. Eldar, “Sparsity constrained nonlinear optimization: optimality conditions and algorithms,” SIAM J. Optim. 23, 1480–1509 (2013).
[Crossref]

Other (3)

Y. Chen and I. W. Hunter, “Design of a miniature hyperspectral imaging Fourier transform spectrometer for endoscopy,” in Imaging Systems and Applications (Optical Society of America, 2016), paper IW1E.2.

P. R. Griffiths and J. A. De Haseth, Fourier Transform Infrared Spectrometry (Wiley, 2007), Vol. 171.

R. Chartrand and W. Yin, “Iteratively reweighted algorithms for compressive sensing,” in 2008 IEEE International Conference on Acoustics, Speech and Signal Processing (IEEE, 2008), pp. 3869–3872.

Supplementary Material (1)

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Figures (6)

Fig. 1.
Fig. 1.

(A1) Schematic of the proposed new near-common-path interferometer system. MIC=microscope; IP=image plane of MIC; G1=G2=diffraction gratings; ϕ=Phase delay from OPD scanning; L1=L2=150  mm; L3=100  mm; L4=200  mm; A=aperture to block off-axis orders. (A2) Prism-based OPD scanning mechanism. (A3) Rotating slab-based OPD scanning mechanism. (B) Experimentally measured OPD variation across the FOV. OPD variation is nearly uniform—with less than two wavelengths throughout the FOV. (C) Phase stability for a fixed OPD position. Maximum change in phase angle=50  mrad (4.2 nm in OPD) over 50 s.

Fig. 2.
Fig. 2.

(A1) Interferogram of 488 nm laser light at a representative pixel (inset: a zoomed-in region). (A2) Spectrum of 488 nm laser light recovered from the interferogram shown in “A1”. Spectral power peak was used to calibrate the wavelength axis (first calibration process). (B1). Interferogram of a broadband light source at the same representative pixel as “A1”. (B2). Reference: spectrum of the broadband-light source through a band-pass filter measured using a commercial spectrometer. Uncalibrated: spectrum of the same source recovered from the interferogram shown in “B1”; Calibrated: spectrum of the same source after the second calibration process. (C) Calibration curve from the second step of the calibration process. (D1) Interferogram of a red LED light source at a representative pixel. (D2) Spectrum of the same Red LED light source as in “D1” measured using the calibrated system (measured) and measured using a commercial spectrometer (reference).

Fig. 3.
Fig. 3.

Simulated demonstration for measurement of peak wavelength for a QD (peak wavelength range 450–850 nm) using an IFTS system and the greedy single wavenumber search. (A) Full interferogram for the emission spectrum of a representative QD with a peak wavelength of 660 nm. M measurements were taken to find the most dominant wavelength. (B) The spectrum of the QD in “A”. The recovered peak emission wavelength, λM, from “M” random measurements is indicated by a red arrow. The ground truth peak emission wavelength is denoted by λGT. “Err” is the measurement error (exaggerated here). (C) Measurement error versus M (i.e., number of measurements) when the measurements’ OPD positions were chosen randomly. The worst case, average case and best case are shown in the graph. The broad difference versus the best and average case suggests that there are optimized OPD position sets that lead to better results. (D) Measurement error versus M in the presence of Poisson noise for the optimum OPD position set. Number of photons per measurement: Blue, 100; Red, 1000; Black, 10,000.

Fig. 4.
Fig. 4.

(A1) Test sample with two types of 6 μm fluorescent beads: one with ex/em=503/511  nm (beads 1, 3 and 5) and the other with ex/em=511/524  nm (beads 2 and 4). (A2). Recovered spectra for the beads in “A1”. The system recovered the expected spectral peaks to a few nanometer accuracy in wavelength highlighting the capability to distinguish two close fluorescence spectra. (B1) A HeLa cell sample labelled with AlexaFluor488. (B2). Recovered spectra of three cells marked in “B1”. (C1) A mouse muscle tissue sample with some regenerated cells expressing mYFP (ex/em=508/524  nm) and some with nuclei expressing hrGFPII (ex/em=500/506  nm). (C2) Recovered spectra for two pixels marked in “C1”. (F) Recovered hyperspectral images of sample in “C1” at representative spectral bands.

Fig. 5.
Fig. 5.

(A) Measured Raman spectrum of a 4-acetamidophenol sample at a representative pixel location (marked in “C” and “D”). Shown in blue is the spectrum recovered using a conventional Fourier-transform-based algorithm (FT) at Nyquist sampling (number of samples=2951). The spectrum recovered using TwIST with band-limited sampling (number of samples=295) is shown in brown. Two spectra are nearly the same, with an exception of higher noise of the latter. (B) The same Raman spectrum as in “A” recovered using TwIST with additional sparsity priors for denoising (shown in yellow). (C) Images at five dominant wavelength bands of spectrum in “A” recovered using FT (corresponds to the blue spectrum in A and B). The scale bars are 20 μm in length. (D) Images at dominant wavelength bands of spectrum in “A” recovered using TwIST using no sparsity priors (corresponds to the brown spectrum in A). (E) Images at dominant wavelength bands of spectrum in “B” recovered using TwIST using sparsity priors (corresponds to the yellow spectrum in B).

Fig. 6.
Fig. 6.

(A) Peak wavelengths recovered using a greedy single wavenumber search for 6 μm fluorescent beads (ex/em=503/511  nm) using a complete Nyquist sampled interferogram (A1 and A4), an optimized compressive sampled interferogram with 20% samples (A2 and A5) and an optimized compressive sampled interferogram with 5% samples (A3 and A6). Here A1–A3 are intensity-weighted true-color images and A4–A6 are their respective non-weighted counterparts. It should be noted that the random colors of the background in A4–A6 are due to no signal from the background regions and the yellow ring-like feature is due to leaked room light, which is very weak. (B) Peak wavelengths recovered using a greedy single wavenumber search for a mouse muscle tissue sample with regenerated cells. (C) Average measurement error (in nm) with random sampling (black curves in C2) and optimized sampling (blue) for the specimen in “B” for varying compression ratios. Here n=number of compressive measurements and N=number of Nyquist measurements. C1 shows the pixels over which the peak wavelength measurements were averaged.

Equations (24)

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

τ=[2sin(θ)cos(β)(ngcos(βθ)na)]u[t0(ngna)].
τ=t1(ngna)(1cos(θ0)1cos(θ)).
E0(x,y,z,t)=kE(x,y,z,t)eik(zct).
E1(x,y,z,t)=E0(x,y,z,t)2(eik0x+eik0x).
E2(x,y,z,t)=E0(x,y,z,t)2(eik0x+eik0xϕ).
ϕ=kT(ngna)=kTΔn,
E3(x,y,z,t)=E2(x,y,z,t)2(eik0x+eik0x)=E0(x,y,z,t)4(ei2k0x+ei2k0xϕ+1+eiϕ).
E2(x,y,z,t)=14kE(x,y,t)eik(zct)iϕ/2(eiϕ/2+eiϕ/2).
I(x,y,T)=14kE2(x,y,k)cos2(ϕ/2)=18kE2(x,y,k)(1+cos(kTΔn)).
J(x,y,T)=k18E2(x,y,k)cos(kTΔn).
J(x1,y1,T)=k18E2(x1,y1,k)cos(kTΔn).
J(t)=kS(k)cos(kτ).
J=AS,
Jn=AS+η,
S=A1Jn.
S^=argminS{12(JnAS)22+γR(S)}.
R(S)=S1,
S^=argminS{12(JnAS)22+γS1}.
S^=argminS{12(JnAS)22},
S0=1.
Error=|λMλGT|.
N=2λ2δλλmin.
ΔOPDΔX=0.0145  [AU].
Error=|λGTλn/N|.

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