Abstract

A depth resolved hyperspectral imaging spectrometer can provide depth resolved imaging both in the spatial and the spectral domain. Images acquired through a standard imaging Fourier transform spectrometer do not have the depth-resolution. By post processing the spectral cubes (x, y, λ) obtained through a Sagnac interferometer under uniform illumination and structured illumination, spectrally resolved images with depth resolution can be recovered using structured light illumination algorithms such as the HiLo method. The proposed scheme is validated with in vitro specimens including fluorescent solution and fluorescent beads with known spectra. The system is further demonstrated in quantifying spectra from 3D resolved features in biological specimens. The system has demonstrated depth resolution of 1.8 μm and spectral resolution of 7 nm respectively.

© 2014 Optical Society of America

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2013 (2)

2012 (4)

J. Michaelson, H. J. Choi, P. So, and H. D. Huang, “Depth-resolved cellular microrheology using HiLo microscopy,” Biomed. Opt. Express 3(6), 1241–1255 (2012).
[Crossref] [PubMed]

D. Bhattacharya, V. R. Singh, C. Zhi, P. T. C. So, P. Matsudaira, and G. Barbastathis, “Three dimensional HiLo-based structured illumination for a digital scanned laser sheet microscopy (DSLM) in thick tissue imaging,” Opt. Express 20(25), 27337–27347 (2012).
[Crossref] [PubMed]

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. U.S.A. 109(26), E1679–E1687 (2012).
[Crossref] [PubMed]

H. Akbari, L. V. Halig, D. M. Schuster, A. Osunkoya, V. Master, P. T. Nieh, G. Z. Chen, and B. W. Fei, “Hyperspectral imaging and quantitative analysis for prostate cancer detection,” J. Biomed. Opt. 17(7), 076005 (2012).
[Crossref] [PubMed]

2011 (2)

L. E. Grosberg, A. J. Radosevich, S. Asfaha, T. C. Wang, and E. M. C. Hillman, “Spectral Characterization and Unmixing of Intrinsic Contrast in Intact Normal and Diseased Gastric Tissues Using Hyperspectral Two-Photon Microscopy,” PLoS ONE 6(5), e19925 (2011).
[Crossref] [PubMed]

L. Gao, N. Bedard, N. Hagen, R. T. Kester, and T. S. Tkaczyk, “Depth-resolved image mapping spectrometer (IMS) with structured illumination,” Opt. Express 19(18), 17439–17452 (2011).
[Crossref] [PubMed]

2010 (1)

J. Mertz and 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 (1)

2008 (1)

2007 (2)

E. J. Botcherby, R. Juskaitis, M. J. Booth, and T. Wilson, “Aberration-free optical refocusing in high numerical aperture microscopy,” Opt. Lett. 32(14), 2007–2009 (2007).
[Crossref] [PubMed]

T. D. Wang, G. Triadafilopoulos, J. M. Crawford, L. R. Dixon, T. Bhandari, P. Sahbaie, S. Friedland, R. Soetikno, and C. H. Contag, “Detection of endogenous biomolecules in Barrett’s esophagus by Fourier transform infrared spectroscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(40), 15864–15869 (2007).
[Crossref] [PubMed]

2006 (1)

S. Pelet, M. J. R. Previte, and P. T. C. So, “Comparing the quantification of Forster resonance energy transfer measurement accuracies based on intensity, spectral, and lifetime imaging,” J. Biomed. Opt. 11(3), 034017 (2006).
[Crossref] [PubMed]

2005 (5)

L. H. Laiho, S. Pelet, T. M. Hancewicz, P. D. Kaplan, and P. T. C. So, “Two-photon 3-D mapping of ex vivo human skin endogenous fluorescence species based on fluorescence emission spectra,” J. Biomed. Opt. 10(2), 024016 (2005).
[Crossref] [PubMed]

C. Buehler, K. H. Kim, U. Greuter, N. Schlumpf, and P. T. C. So, “Single-photon counting multicolor multiphoton fluorescence microscope,” J. Fluoresc. 15(1), 41–51 (2005).
[Crossref] [PubMed]

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(4), 2736–2749 (2005).
[Crossref] [PubMed]

D. Oron, E. Tal, and Y. Silberberg, “Scanningless depth-resolved microscopy,” Opt. Express 13(5), 1468–1476 (2005).
[Crossref] [PubMed]

G. H. Zhu, J. Van Howe, M. Durst, W. Zipfel, and C. Xu, “Simultaneous spatial and temporal focusing of femtosecond pulses,” Opt. Express 13(6), 2153–2159 (2005).
[Crossref] [PubMed]

2004 (3)

2001 (1)

M. Elangovan and A. Periasamy, “Spectral bleed through and photo bleaching correction in FRET microscopy,” Biophys. J. 80, 161a (2001).

1997 (2)

M. A. A. Neil, R. Juskaitis, and T. Wilson, “Method of obtaining optical sectioning by using structured light in a conventional microscope,” Opt. Lett. 22(24), 1905–1907 (1997).
[Crossref] [PubMed]

M. J. Korenberg, C. J. H. Brenan, and I. W. Hunter, “Raman spectral estimation via fast orthogonal search,” Analyst (Lond.) 122(9), 879–882 (1997).
[Crossref]

1996 (3)

Z. Malik, D. Cabib, R. A. Buckwald, A. Talmi, Y. Garini, and S. G. Lipson, “Fourier transform multipixel spectroscopy for quantitative cytology,” J. Microsc. (Oxford) 182(2), 133–140 (1996).
[Crossref]

Z. Malik, M. Dishi, and Y. Garini, “Fourier transform multipixel spectroscopy and spectral imaging of protoporphyrin in single melanoma cells,” Photochem. Photobiol. 63(5), 608–614 (1996).
[Crossref] [PubMed]

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. A. Ferguson-Smith, Y. Ning, D. H. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273(5274), 494–497 (1996).
[Crossref] [PubMed]

1995 (2)

C. J. H. Brenan and I. W. Hunter, “Design and characterization of a visible-light Fourier-transform raman spectrometer,” Appl. Spectrosc. 49(8), 1086–1093 (1995).
[Crossref]

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).
[Crossref]

1981 (1)

1968 (1)

1967 (1)

L. Mertz, “Auxiliary Computation for Fourier Spectrometry,” Infrared Phys. 7(1), 17–23 (1967).
[Crossref]

1966 (1)

Akbari, H.

H. Akbari, L. V. Halig, D. M. Schuster, A. Osunkoya, V. Master, P. T. Nieh, G. Z. Chen, and B. W. Fei, “Hyperspectral imaging and quantitative analysis for prostate cancer detection,” J. Biomed. Opt. 17(7), 076005 (2012).
[Crossref] [PubMed]

Asfaha, S.

L. E. Grosberg, A. J. Radosevich, S. Asfaha, T. C. Wang, and E. M. C. Hillman, “Spectral Characterization and Unmixing of Intrinsic Contrast in Intact Normal and Diseased Gastric Tissues Using Hyperspectral Two-Photon Microscopy,” PLoS ONE 6(5), e19925 (2011).
[Crossref] [PubMed]

Bar-Am, I.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. A. Ferguson-Smith, Y. Ning, D. H. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273(5274), 494–497 (1996).
[Crossref] [PubMed]

Barbastathis, G.

Bedard, N.

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).
[Crossref]

Bhandari, T.

T. D. Wang, G. Triadafilopoulos, J. M. Crawford, L. R. Dixon, T. Bhandari, P. Sahbaie, S. Friedland, R. Soetikno, and C. H. Contag, “Detection of endogenous biomolecules in Barrett’s esophagus by Fourier transform infrared spectroscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(40), 15864–15869 (2007).
[Crossref] [PubMed]

Bhattacharya, D.

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(4), 2736–2749 (2005).
[Crossref] [PubMed]

Bobin, J.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. U.S.A. 109(26), E1679–E1687 (2012).
[Crossref] [PubMed]

Booth, M. J.

Botcherby, E. J.

Brenan, C. J. H.

M. J. Korenberg, C. J. H. Brenan, and I. W. Hunter, “Raman spectral estimation via fast orthogonal search,” Analyst (Lond.) 122(9), 879–882 (1997).
[Crossref]

C. J. H. Brenan and I. W. Hunter, “Design and characterization of a visible-light Fourier-transform raman spectrometer,” Appl. Spectrosc. 49(8), 1086–1093 (1995).
[Crossref]

Buckwald, R. A.

Z. Malik, D. Cabib, R. A. Buckwald, A. Talmi, Y. Garini, and S. G. Lipson, “Fourier transform multipixel spectroscopy for quantitative cytology,” J. Microsc. (Oxford) 182(2), 133–140 (1996).
[Crossref]

Buehler, C.

C. Buehler, K. H. Kim, U. Greuter, N. Schlumpf, and P. T. C. So, “Single-photon counting multicolor multiphoton fluorescence microscope,” J. Fluoresc. 15(1), 41–51 (2005).
[Crossref] [PubMed]

Cabib, D.

Z. Malik, D. Cabib, R. A. Buckwald, A. Talmi, Y. Garini, and S. G. Lipson, “Fourier transform multipixel spectroscopy for quantitative cytology,” J. Microsc. (Oxford) 182(2), 133–140 (1996).
[Crossref]

Cameron, D. G.

Candes, E.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. U.S.A. 109(26), E1679–E1687 (2012).
[Crossref] [PubMed]

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).
[Crossref]

Chahid, M.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. U.S.A. 109(26), E1679–E1687 (2012).
[Crossref] [PubMed]

Chen, G. Z.

H. Akbari, L. V. Halig, D. M. Schuster, A. Osunkoya, V. Master, P. T. Nieh, G. Z. Chen, and B. W. Fei, “Hyperspectral imaging and quantitative analysis for prostate cancer detection,” J. Biomed. Opt. 17(7), 076005 (2012).
[Crossref] [PubMed]

Choi, H.

Choi, H. J.

Chu, K. K.

Contag, C. H.

T. D. Wang, G. Triadafilopoulos, J. M. Crawford, L. R. Dixon, T. Bhandari, P. Sahbaie, S. Friedland, R. Soetikno, and C. H. Contag, “Detection of endogenous biomolecules in Barrett’s esophagus by Fourier transform infrared spectroscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(40), 15864–15869 (2007).
[Crossref] [PubMed]

Crawford, J. M.

T. D. Wang, G. Triadafilopoulos, J. M. Crawford, L. R. Dixon, T. Bhandari, P. Sahbaie, S. Friedland, R. Soetikno, and C. H. Contag, “Detection of endogenous biomolecules in Barrett’s esophagus by Fourier transform infrared spectroscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(40), 15864–15869 (2007).
[Crossref] [PubMed]

Dahan, M.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. U.S.A. 109(26), E1679–E1687 (2012).
[Crossref] [PubMed]

Del Bene, F.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Dishi, M.

Z. Malik, M. Dishi, and Y. Garini, “Fourier transform multipixel spectroscopy and spectral imaging of protoporphyrin in single melanoma cells,” Photochem. Photobiol. 63(5), 608–614 (1996).
[Crossref] [PubMed]

Dixon, L. R.

T. D. Wang, G. Triadafilopoulos, J. M. Crawford, L. R. Dixon, T. Bhandari, P. Sahbaie, S. Friedland, R. Soetikno, and C. H. Contag, “Detection of endogenous biomolecules in Barrett’s esophagus by Fourier transform infrared spectroscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(40), 15864–15869 (2007).
[Crossref] [PubMed]

Du Manoir, S.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. A. Ferguson-Smith, Y. Ning, D. H. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273(5274), 494–497 (1996).
[Crossref] [PubMed]

Durst, M.

Elangovan, M.

M. Elangovan and A. Periasamy, “Spectral bleed through and photo bleaching correction in FRET microscopy,” Biophys. J. 80, 161a (2001).

Fantini, S.

Favreau, P. F.

P. F. Favreau, T. C. Rich, P. Prabhat, and S. J. Leavesley, “Tunable thin-film optical filters for hyperspectral microscopy,” Proc. SPIE 8589, 85890R (2013).
[Crossref]

Fei, B. W.

H. Akbari, L. V. Halig, D. M. Schuster, A. Osunkoya, V. Master, P. T. Nieh, G. Z. Chen, and B. W. Fei, “Hyperspectral imaging and quantitative analysis for prostate cancer detection,” J. Biomed. Opt. 17(7), 076005 (2012).
[Crossref] [PubMed]

Ferguson-Smith, M. A.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. A. Ferguson-Smith, Y. Ning, D. H. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273(5274), 494–497 (1996).
[Crossref] [PubMed]

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).
[Crossref]

Fletcher-Holmes, D. W.

Forman, M. L.

Friedland, S.

T. D. Wang, G. Triadafilopoulos, J. M. Crawford, L. R. Dixon, T. Bhandari, P. Sahbaie, S. Friedland, R. Soetikno, and C. H. Contag, “Detection of endogenous biomolecules in Barrett’s esophagus by Fourier transform infrared spectroscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(40), 15864–15869 (2007).
[Crossref] [PubMed]

Gao, L.

Garini, Y.

Z. Malik, M. Dishi, and Y. Garini, “Fourier transform multipixel spectroscopy and spectral imaging of protoporphyrin in single melanoma cells,” Photochem. Photobiol. 63(5), 608–614 (1996).
[Crossref] [PubMed]

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. A. Ferguson-Smith, Y. Ning, D. H. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273(5274), 494–497 (1996).
[Crossref] [PubMed]

Z. Malik, D. Cabib, R. A. Buckwald, A. Talmi, Y. Garini, and S. G. Lipson, “Fourier transform multipixel spectroscopy for quantitative cytology,” J. Microsc. (Oxford) 182(2), 133–140 (1996).
[Crossref]

Greuter, U.

C. Buehler, K. H. Kim, U. Greuter, N. Schlumpf, and P. T. C. So, “Single-photon counting multicolor multiphoton fluorescence microscope,” J. Fluoresc. 15(1), 41–51 (2005).
[Crossref] [PubMed]

Grosberg, L. E.

L. E. Grosberg, A. J. Radosevich, S. Asfaha, T. C. Wang, and E. M. C. Hillman, “Spectral Characterization and Unmixing of Intrinsic Contrast in Intact Normal and Diseased Gastric Tissues Using Hyperspectral Two-Photon Microscopy,” PLoS ONE 6(5), e19925 (2011).
[Crossref] [PubMed]

Hagen, N.

Halig, L. V.

H. Akbari, L. V. Halig, D. M. Schuster, A. Osunkoya, V. Master, P. T. Nieh, G. Z. Chen, and B. W. Fei, “Hyperspectral imaging and quantitative analysis for prostate cancer detection,” J. Biomed. Opt. 17(7), 076005 (2012).
[Crossref] [PubMed]

Hallacoglu, B.

Hancewicz, T. M.

L. H. Laiho, S. Pelet, T. M. Hancewicz, P. D. Kaplan, and P. T. C. So, “Two-photon 3-D mapping of ex vivo human skin endogenous fluorescence species based on fluorescence emission spectra,” J. Biomed. Opt. 10(2), 024016 (2005).
[Crossref] [PubMed]

Harvey, A. R.

Heintzmann, R.

Hillman, E. M. C.

L. E. Grosberg, A. J. Radosevich, S. Asfaha, T. C. Wang, and E. M. C. Hillman, “Spectral Characterization and Unmixing of Intrinsic Contrast in Intact Normal and Diseased Gastric Tissues Using Hyperspectral Two-Photon Microscopy,” PLoS ONE 6(5), e19925 (2011).
[Crossref] [PubMed]

Huang, H. D.

Huisken, J.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Hunter, I. W.

M. J. Korenberg, C. J. H. Brenan, and I. W. Hunter, “Raman spectral estimation via fast orthogonal search,” Analyst (Lond.) 122(9), 879–882 (1997).
[Crossref]

C. J. H. Brenan and I. W. Hunter, “Design and characterization of a visible-light Fourier-transform raman spectrometer,” Appl. Spectrosc. 49(8), 1086–1093 (1995).
[Crossref]

Jovin, T. M.

Juskaitis, R.

Kaplan, P. D.

L. H. Laiho, S. Pelet, T. M. Hancewicz, P. D. Kaplan, and P. T. C. So, “Two-photon 3-D mapping of ex vivo human skin endogenous fluorescence species based on fluorescence emission spectra,” J. Biomed. Opt. 10(2), 024016 (2005).
[Crossref] [PubMed]

Kauppinen, J. K.

Kester, R. T.

Kim, J.

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

Kim, K. H.

C. Buehler, K. H. Kim, U. Greuter, N. Schlumpf, and P. T. C. So, “Single-photon counting multicolor multiphoton fluorescence microscope,” J. Fluoresc. 15(1), 41–51 (2005).
[Crossref] [PubMed]

Korenberg, M. J.

M. J. Korenberg, C. J. H. Brenan, and I. W. Hunter, “Raman spectral estimation via fast orthogonal search,” Analyst (Lond.) 122(9), 879–882 (1997).
[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(4), 2736–2749 (2005).
[Crossref] [PubMed]

Laiho, L. H.

L. H. Laiho, S. Pelet, T. M. Hancewicz, P. D. Kaplan, and P. T. C. So, “Two-photon 3-D mapping of ex vivo human skin endogenous fluorescence species based on fluorescence emission spectra,” J. Biomed. Opt. 10(2), 024016 (2005).
[Crossref] [PubMed]

Leavesley, S. J.

P. F. Favreau, T. C. Rich, P. Prabhat, and S. J. Leavesley, “Tunable thin-film optical filters for hyperspectral microscopy,” Proc. SPIE 8589, 85890R (2013).
[Crossref]

Ledbetter, D. H.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. A. Ferguson-Smith, Y. Ning, D. H. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273(5274), 494–497 (1996).
[Crossref] [PubMed]

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).
[Crossref]

Lidke, K. A.

Lim, D.

Lipson, S. G.

Z. Malik, D. Cabib, R. A. Buckwald, A. Talmi, Y. Garini, and S. G. Lipson, “Fourier transform multipixel spectroscopy for quantitative cytology,” J. Microsc. (Oxford) 182(2), 133–140 (1996).
[Crossref]

Malik, Z.

Z. Malik, D. Cabib, R. A. Buckwald, A. Talmi, Y. Garini, and S. G. Lipson, “Fourier transform multipixel spectroscopy for quantitative cytology,” J. Microsc. (Oxford) 182(2), 133–140 (1996).
[Crossref]

Z. Malik, M. Dishi, and Y. Garini, “Fourier transform multipixel spectroscopy and spectral imaging of protoporphyrin in single melanoma cells,” Photochem. Photobiol. 63(5), 608–614 (1996).
[Crossref] [PubMed]

Mantsch, H. H.

Master, V.

H. Akbari, L. V. Halig, D. M. Schuster, A. Osunkoya, V. Master, P. T. Nieh, G. Z. Chen, and B. W. Fei, “Hyperspectral imaging and quantitative analysis for prostate cancer detection,” J. Biomed. Opt. 17(7), 076005 (2012).
[Crossref] [PubMed]

Matsudaira, P.

Mertz, J.

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

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

Mertz, L.

L. Mertz, “Auxiliary Computation for Fourier Spectrometry,” Infrared Phys. 7(1), 17–23 (1967).
[Crossref]

Michaelson, J.

Moffatt, D. J.

Mousavi, H. S.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. U.S.A. 109(26), E1679–E1687 (2012).
[Crossref] [PubMed]

Neil, M. A. A.

Nieh, P. T.

H. Akbari, L. V. Halig, D. M. Schuster, A. Osunkoya, V. Master, P. T. Nieh, G. Z. Chen, and B. W. Fei, “Hyperspectral imaging and quantitative analysis for prostate cancer detection,” J. Biomed. Opt. 17(7), 076005 (2012).
[Crossref] [PubMed]

Ning, Y.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. A. Ferguson-Smith, Y. Ning, D. H. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273(5274), 494–497 (1996).
[Crossref] [PubMed]

Oron, D.

Osunkoya, A.

H. Akbari, L. V. Halig, D. M. Schuster, A. Osunkoya, V. Master, P. T. Nieh, G. Z. Chen, and B. W. Fei, “Hyperspectral imaging and quantitative analysis for prostate cancer detection,” J. Biomed. Opt. 17(7), 076005 (2012).
[Crossref] [PubMed]

Pelet, S.

S. Pelet, M. J. R. Previte, and P. T. C. So, “Comparing the quantification of Forster resonance energy transfer measurement accuracies based on intensity, spectral, and lifetime imaging,” J. Biomed. Opt. 11(3), 034017 (2006).
[Crossref] [PubMed]

L. H. Laiho, S. Pelet, T. M. Hancewicz, P. D. Kaplan, and P. T. C. So, “Two-photon 3-D mapping of ex vivo human skin endogenous fluorescence species based on fluorescence emission spectra,” J. Biomed. Opt. 10(2), 024016 (2005).
[Crossref] [PubMed]

Periasamy, A.

M. Elangovan and A. Periasamy, “Spectral bleed through and photo bleaching correction in FRET microscopy,” Biophys. J. 80, 161a (2001).

Prabhat, P.

P. F. Favreau, T. C. Rich, P. Prabhat, and S. J. Leavesley, “Tunable thin-film optical filters for hyperspectral microscopy,” Proc. SPIE 8589, 85890R (2013).
[Crossref]

Previte, M. J. R.

S. Pelet, M. J. R. Previte, and P. T. C. So, “Comparing the quantification of Forster resonance energy transfer measurement accuracies based on intensity, spectral, and lifetime imaging,” J. Biomed. Opt. 11(3), 034017 (2006).
[Crossref] [PubMed]

Radosevich, A. J.

L. E. Grosberg, A. J. Radosevich, S. Asfaha, T. C. Wang, and E. M. C. Hillman, “Spectral Characterization and Unmixing of Intrinsic Contrast in Intact Normal and Diseased Gastric Tissues Using Hyperspectral Two-Photon Microscopy,” PLoS ONE 6(5), e19925 (2011).
[Crossref] [PubMed]

Rich, T. C.

P. F. Favreau, T. C. Rich, P. Prabhat, and S. J. Leavesley, “Tunable thin-film optical filters for hyperspectral microscopy,” Proc. SPIE 8589, 85890R (2013).
[Crossref]

Ried, T.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. A. Ferguson-Smith, Y. Ning, D. H. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273(5274), 494–497 (1996).
[Crossref] [PubMed]

Sahbaie, P.

T. D. Wang, G. Triadafilopoulos, J. M. Crawford, L. R. Dixon, T. Bhandari, P. Sahbaie, S. Friedland, R. Soetikno, and C. H. Contag, “Detection of endogenous biomolecules in Barrett’s esophagus by Fourier transform infrared spectroscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(40), 15864–15869 (2007).
[Crossref] [PubMed]

Sakai, H.

Schlumpf, N.

C. Buehler, K. H. Kim, U. Greuter, N. Schlumpf, and P. T. C. So, “Single-photon counting multicolor multiphoton fluorescence microscope,” J. Fluoresc. 15(1), 41–51 (2005).
[Crossref] [PubMed]

Schoell, B.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. A. Ferguson-Smith, Y. Ning, D. H. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273(5274), 494–497 (1996).
[Crossref] [PubMed]

Schröck, E.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. A. Ferguson-Smith, Y. Ning, D. H. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273(5274), 494–497 (1996).
[Crossref] [PubMed]

Schuster, D. M.

H. Akbari, L. V. Halig, D. M. Schuster, A. Osunkoya, V. Master, P. T. Nieh, G. Z. Chen, and B. W. Fei, “Hyperspectral imaging and quantitative analysis for prostate cancer detection,” J. Biomed. Opt. 17(7), 076005 (2012).
[Crossref] [PubMed]

Sheppard, C. J. R.

Silberberg, Y.

Singh, V. R.

So, P.

So, P. T. C.

H. Choi, E. Y. S. Yew, B. Hallacoglu, S. Fantini, C. J. R. Sheppard, and P. T. C. So, “Improvement of axial resolution and contrast in temporally focused widefield two-photon microscopy with structured light illumination,” Biomed. Opt. Express 4(7), 995–1005 (2013).
[Crossref] [PubMed]

D. Bhattacharya, V. R. Singh, C. Zhi, P. T. C. So, P. Matsudaira, and G. Barbastathis, “Three dimensional HiLo-based structured illumination for a digital scanned laser sheet microscopy (DSLM) in thick tissue imaging,” Opt. Express 20(25), 27337–27347 (2012).
[Crossref] [PubMed]

S. Pelet, M. J. R. Previte, and P. T. C. So, “Comparing the quantification of Forster resonance energy transfer measurement accuracies based on intensity, spectral, and lifetime imaging,” J. Biomed. Opt. 11(3), 034017 (2006).
[Crossref] [PubMed]

L. H. Laiho, S. Pelet, T. M. Hancewicz, P. D. Kaplan, and P. T. C. So, “Two-photon 3-D mapping of ex vivo human skin endogenous fluorescence species based on fluorescence emission spectra,” J. Biomed. Opt. 10(2), 024016 (2005).
[Crossref] [PubMed]

C. Buehler, K. H. Kim, U. Greuter, N. Schlumpf, and P. T. C. So, “Single-photon counting multicolor multiphoton fluorescence microscope,” J. Fluoresc. 15(1), 41–51 (2005).
[Crossref] [PubMed]

Soenksen, D.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. A. Ferguson-Smith, Y. Ning, D. H. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273(5274), 494–497 (1996).
[Crossref] [PubMed]

Soetikno, R.

T. D. Wang, G. Triadafilopoulos, J. M. Crawford, L. R. Dixon, T. Bhandari, P. Sahbaie, S. Friedland, R. Soetikno, and C. H. Contag, “Detection of endogenous biomolecules in Barrett’s esophagus by Fourier transform infrared spectroscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(40), 15864–15869 (2007).
[Crossref] [PubMed]

Steel, W. H.

Stelzer, E. H. K.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Studer, V.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. U.S.A. 109(26), E1679–E1687 (2012).
[Crossref] [PubMed]

Swoger, J.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Tal, E.

Talmi, A.

Z. Malik, D. Cabib, R. A. Buckwald, A. Talmi, Y. Garini, and S. G. Lipson, “Fourier transform multipixel spectroscopy for quantitative cytology,” J. Microsc. (Oxford) 182(2), 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(4), 2736–2749 (2005).
[Crossref] [PubMed]

Tkaczyk, T. S.

Triadafilopoulos, G.

T. D. Wang, G. Triadafilopoulos, J. M. Crawford, L. R. Dixon, T. Bhandari, P. Sahbaie, S. Friedland, R. Soetikno, and C. H. Contag, “Detection of endogenous biomolecules in Barrett’s esophagus by Fourier transform infrared spectroscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(40), 15864–15869 (2007).
[Crossref] [PubMed]

Van Howe, J.

Vanasse, G. A.

Veldman, T.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. A. Ferguson-Smith, Y. Ning, D. H. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273(5274), 494–497 (1996).
[Crossref] [PubMed]

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(4), 2736–2749 (2005).
[Crossref] [PubMed]

Wang, T. C.

L. E. Grosberg, A. J. Radosevich, S. Asfaha, T. C. Wang, and E. M. C. Hillman, “Spectral Characterization and Unmixing of Intrinsic Contrast in Intact Normal and Diseased Gastric Tissues Using Hyperspectral Two-Photon Microscopy,” PLoS ONE 6(5), e19925 (2011).
[Crossref] [PubMed]

Wang, T. D.

T. D. Wang, G. Triadafilopoulos, J. M. Crawford, L. R. Dixon, T. Bhandari, P. Sahbaie, S. Friedland, R. Soetikno, and C. H. Contag, “Detection of endogenous biomolecules in Barrett’s esophagus by Fourier transform infrared spectroscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(40), 15864–15869 (2007).
[Crossref] [PubMed]

Wienberg, J.

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. A. Ferguson-Smith, Y. Ning, D. H. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273(5274), 494–497 (1996).
[Crossref] [PubMed]

Wilson, T.

Wittbrodt, J.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Xu, C.

Yew, E. Y. S.

Zhi, C.

Zhu, G. H.

Zipfel, W.

Analyst (Lond.) (1)

M. J. Korenberg, C. J. H. Brenan, and I. W. Hunter, “Raman spectral estimation via fast orthogonal search,” Analyst (Lond.) 122(9), 879–882 (1997).
[Crossref]

Appl. Opt. (1)

Appl. Spectrosc. (1)

Biomed. Opt. Express (2)

Biophys. J. (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(4), 2736–2749 (2005).
[Crossref] [PubMed]

M. Elangovan and A. Periasamy, “Spectral bleed through and photo bleaching correction in FRET microscopy,” Biophys. J. 80, 161a (2001).

Infrared Phys. (1)

L. Mertz, “Auxiliary Computation for Fourier Spectrometry,” Infrared Phys. 7(1), 17–23 (1967).
[Crossref]

J. Biomed. Opt. (4)

L. H. Laiho, S. Pelet, T. M. Hancewicz, P. D. Kaplan, and P. T. C. So, “Two-photon 3-D mapping of ex vivo human skin endogenous fluorescence species based on fluorescence emission spectra,” J. Biomed. Opt. 10(2), 024016 (2005).
[Crossref] [PubMed]

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

H. Akbari, L. V. Halig, D. M. Schuster, A. Osunkoya, V. Master, P. T. Nieh, G. Z. Chen, and B. W. Fei, “Hyperspectral imaging and quantitative analysis for prostate cancer detection,” J. Biomed. Opt. 17(7), 076005 (2012).
[Crossref] [PubMed]

S. Pelet, M. J. R. Previte, and P. T. C. So, “Comparing the quantification of Forster resonance energy transfer measurement accuracies based on intensity, spectral, and lifetime imaging,” J. Biomed. Opt. 11(3), 034017 (2006).
[Crossref] [PubMed]

J. Fluoresc. (1)

C. Buehler, K. H. Kim, U. Greuter, N. Schlumpf, and P. T. C. So, “Single-photon counting multicolor multiphoton fluorescence microscope,” J. Fluoresc. 15(1), 41–51 (2005).
[Crossref] [PubMed]

J. Microsc. (Oxford) (1)

Z. Malik, D. Cabib, R. A. Buckwald, A. Talmi, Y. Garini, and S. G. Lipson, “Fourier transform multipixel spectroscopy for quantitative cytology,” J. Microsc. (Oxford) 182(2), 133–140 (1996).
[Crossref]

J. Opt. Soc. Am. (2)

Opt. Express (7)

Opt. Lett. (3)

Photochem. Photobiol. (1)

Z. Malik, M. Dishi, and Y. Garini, “Fourier transform multipixel spectroscopy and spectral imaging of protoporphyrin in single melanoma cells,” Photochem. Photobiol. 63(5), 608–614 (1996).
[Crossref] [PubMed]

PLoS ONE (1)

L. E. Grosberg, A. J. Radosevich, S. Asfaha, T. C. Wang, and E. M. C. Hillman, “Spectral Characterization and Unmixing of Intrinsic Contrast in Intact Normal and Diseased Gastric Tissues Using Hyperspectral Two-Photon Microscopy,” PLoS ONE 6(5), e19925 (2011).
[Crossref] [PubMed]

Proc. Natl. Acad. Sci. U.S.A. (2)

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. U.S.A. 109(26), E1679–E1687 (2012).
[Crossref] [PubMed]

T. D. Wang, G. Triadafilopoulos, J. M. Crawford, L. R. Dixon, T. Bhandari, P. Sahbaie, S. Friedland, R. Soetikno, and C. H. Contag, “Detection of endogenous biomolecules in Barrett’s esophagus by Fourier transform infrared spectroscopy,” Proc. Natl. Acad. Sci. U.S.A. 104(40), 15864–15869 (2007).
[Crossref] [PubMed]

Proc. SPIE (2)

P. F. Favreau, T. C. Rich, P. Prabhat, and S. J. Leavesley, “Tunable thin-film optical filters for hyperspectral microscopy,” Proc. SPIE 8589, 85890R (2013).
[Crossref]

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).
[Crossref]

Science (2)

E. Schröck, S. Du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. A. Ferguson-Smith, Y. Ning, D. H. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, and T. Ried, “Multicolor spectral karyotyping of human chromosomes,” Science 273(5274), 494–497 (1996).
[Crossref] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Other (2)

R. J. Bell, Introductory Fourier Transform Spectroscopy (Academic, 1972).

D. Cabib, Z. Friedman, S. Lipson, and R. Buckwalf, “Method for simultaneously measuring the spectral intensity as a function of wavelength of all the pixels of a two dimensional scene,” US Patent. 5539517 (1996).

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Figures (8)

Fig. 1
Fig. 1 Schematic diagram of the depth-resolved imaging Fourier transform spectrometer. Enclosed by dotted line is the Sagnac interferometer. M: mirror, DM: dichroic mirror, DOE: diffractive optical element, OS: optical shutter, PBS: polarizing beam cube splitter, BS: 50R/50T plate beam splitter, QWP: quarter-wave plate, EmF: emission filter, PA: piezo actuator, FFP: front focal plane, OBJ: objective lens (Zeiss 20x Water NA1.0), ROBJ: remote focusing objective lens (Nikon 20x Air NA0.75)
Fig. 2
Fig. 2 Imaging Fourier transform spectrometer based on Sagnac interferometer (a) Ray tracing from the intermediate image plane to the detector at central position of the Sagnac interferometer. Color represents the spatial field points. (b) Photograph of the setup installed in the emission beam path of the imaging spectrometer. (c) OPD as a function of the rotational angle of the Sagnac interferometer for the spatial field point on the optical axis (the rays represented in green color in (a) with the following parameters: β = 45°, t = 2.93mm, n = 1.517 (Refractive index of N-BK7)
Fig. 3
Fig. 3 Sampling of the interferogram (a) Fringe pattern of a quad band emission filtered white light LED at θ = 0° sampled by the sCMOS camera. The dotted yellow vertical line represents a zero OPD which shifts to the left as the interferometer rotates. Pixels in each column see the same OPD and each column see a linearly varying OPD (b) Sampled interferogram after removing dc component observed by the yellow pixel at ∆θ = 0.005° (2 pixel or 170nm in OPD space). (c) Recovered spectrum of LED with minimum detectable wavelength of 340nm.
Fig. 4
Fig. 4 Interferogram after removing dc component of 6μm yellow green fluorescent bead (a), Rhodamine 6G solution (b), 4μm red fluorescent bead (c) and its the processed spectrum are (d), (e) and (f). Green curve in spectral graph is the reference value from http://www.lifetechnologies.com/us/en/home/life-science/cell-analysis/labeling-chemistry/fluorescence-spectraviewer.html
Fig. 5
Fig. 5 (a) Two color image of the muntjac skin fibroblast cells (F36925, Invitrogen). The green color represents filamentous actin imaged with the 525nm/35nm bandpass filter (FF01-520/35, Semrock) and the orange color represents mitochondria imaged with 609nm/54nm band pass filter (FF01-609/54, Semrock). (b) λ plane images of the region marked in red box in (a) at selected wavelengths. The area selected is a part of field of view without vignetting effect caused by excessive rotation of the Sagnac interferometer.
Fig. 6
Fig. 6 (a) Spectral images from UI, SI and after HiLo processing at λ = 521nm and λ = 608nm (b) Spectra for UI and after HiLo processing. The spectrum from the out-of-focus Rhodamine solution is rejected after the HiLo processing.
Fig. 7
Fig. 7 λ plane images of the muntjac skin fibroblast cells (F36925, Invitrogen) with Rhodamine background for UI and after HiLo processing.
Fig. 8
Fig. 8 (a) Spectral 3D volume images for a UI (b) Spectral 3D volume images after HiLo processing (c) True color images of mouse kidney (F24630, Invitrogen) for UI and after HiLo processing. Green colored feature represents the elements of the glomeruli and convoluted tubules labeled with Alexa Fluor 488. Orange colored feature represents the filamentous actin and the brush border labeled with Alexa fluor 568.

Equations (13)

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E(x,y,ν)=A(x,y,ν)exp[ i( 2πνt+ϕ(x,y,ν) ) ]
E 1 + E 2 =A(x,y,ν)exp[ i( 2πνt+ϕ(x,y,ν) ) ]( 1+exp[ i( 2πν /c )δ ] )
I(x,y,δ)=2 | A(x,y,ν) | 2 ( 1+cos( ( 2πν /c )δ ) )
I(x,y,δ)=2 | A(x,y,ν) | 2 ( 1+cos( ( 2πν /c )δ ) ) dν
OPD(β,θ,t,n)=t[ ( n 2 sin 2 (β+θ) ) 0.5 ( n 2 sin 2 (βθ) ) 0.5 +2sinβsinθ ]
OPD(β,θ,t,n)2tsinβ[ 1 ( n 2 sin 2 β ) 0.5 cosβ ]θ
λ min ( or 1/ σ max )=2Δ OPD
Δσ 1 OP D max
C F 1 = 473 λ m , C F 2 = 561 λ m , C F 3 = 660 λ m CF= ( C F 1 +C F 2 +C F 3 ) /3 OP D rescaled =CFOP D calculated
I ex ( k ex ,x)=2( 1+cos( k ex x) ) I 0 ( k ex )
I em ( k ex , k em ,x)= m SLI I ex ( k ex ,x) S em ( k em ,x)ρ(x) S ex ( k ex ,x)
I det (δ, k ex ,x)= 0 ( 1+ m bs cos( k em δ) ) I em ( k ex , k em ,x)d k em =[ m SLI I ex ( k ex ,x)ρ(x) S ex ( k ex ,x) ] 0 ( 1+ m bs cos( k em δ) ) S em ( k em ,x)d k em
S SI ( k em ,x)= δ max/2 + δ max/2 I det (δ, k ex ,x) e jδ k em dδ =[ m SLI I ex ( k ex ,x) ][ m bs ρ(x) S ex ( k ex ,x) ] S em ( k em ,x)

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