Abstract

Raman microscopy is a powerful method combining non-invasiveness with no special sample preparation. Because of this remarkable simplicity, it has been widely exploited in many fields, ranging from life and materials sciences to engineering. Notoriously, due to the required imaging speeds for bio-imaging, it has remained a challenge how to use this technique for dynamic and large-scale imaging. Recently, a supervised compressive Raman framework has been put forward, allowing for fast imaging, therefore alleviating the issue of speed. Yet, due to the need for strong a priori information of the species forming the hyperspectrum, it has remained elusive how to apply this supervised method for microspectroscopy of (dynamic) biological tissues. Combining an original spectral under-sampling measurement technique with a matrix completion framework for reconstruction, we demonstrate fast and inexpensive label-free molecular imaging of biological specimens (brain tissues and single cells). Using the matrix completion outcome with the supervised method allows for large compressions (64×) and bio-imaging speeds surpassing current technology in spontaneous Raman microspectroscopy. Therefore, our results open interesting perspectives for clinical and cell biology applications using the much faster compressive Raman framework.

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

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References

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2018 (7)

C. Scotté, H. B. de Aguiar, D. Marguet, E. Green, P. Bouzy, S. Vergnole, P. Winlove, N. Stone, and H. Rigneault, “Assessment of compressive Raman versus hyperspectral Raman for microcalcification chemical imaging,” Anal. Chem. 90, 7197–7203 (2018).
[Crossref]

S. H. Donaldson and H. B. de Aguiar, “Molecular imaging of cholesterol and lipid distributions in model membranes,” J. Phys. Chem. Lett. 9, 1528–1533 (2018).
[Crossref]

B. Prats-Mateu, M. Felhofer, A. de Juan, and N. Gierlinger, “Multivariate unmixing approaches on Raman images of plant cell walls: new insights or overinterpretation of results?” Plant Methods 14, 52 (2018).
[Crossref]

D. J. Starling and J. Ranalli, “Compressive sensing for spatial and spectral flame diagnostics,” Sci. Rep. 8, 2556 (2018).
[Crossref]

P. Réfrégier, C. Scotté, H. B. de Aguiar, H. Rigneault, and F. Galland, “Precision of proportion estimation with binary compressed Raman spectrum,” J. Opt. Soc. Am. A 35, 125–134 (2018).
[Crossref]

O. G. Rehrauer, V. C. Dinh, B. R. Mankani, G. T. Buzzard, B. J. Lucier, and D. Ben-Amotz, “Binary complementary filters for compressive Raman spectroscopy,” Appl. Spectrosc. 72, 69–78 (2018).
[Crossref]

T. C. Corcoran, “Compressive detection of highly overlapped spectra using Walsh-Hadamard-based filter functions,” Appl. Spectrosc. 72, 392–403 (2018).
[Crossref]

2017 (5)

2016 (4)

G. Bodelón, V. Montes-García, V. López-Puente, E. H. Hill, C. Hamon, M. N. Sanz-Ortiz, S. Rodal-Cedeira, C. Costas, S. Celiksoy, I. Pérez-Juste, L. Scarabelli, A. La Porta, J. Pérez-Juste, I. Pastoriza-Santos, and L. M. Liz-Marzán, “Detection and imaging of quorum sensing in pseudomonas aeruginosa biofilm communities by surface-enhanced resonance Raman scattering,” Nat. Mater. 15, 1203–1211 (2016).
[Crossref]

W. Müller, M. Kielhorn, M. Schmitt, J. Popp, and R. Heintzmann, “Light sheet Raman micro-spectroscopy,” Optica 3, 452–457 (2016).
[Crossref]

D. Wei, S. Chen, Y. H. Ong, C. Perlaki, and Q. Liu, “Fast wide-field Raman spectroscopic imaging based on simultaneous multi-channel image acquisition and wiener estimation,” Opt. Lett. 41, 2783–2786 (2016).
[Crossref]

N. Pavillon and N. Smith, “Compressed sensing laser scanning microscopy,” Opt. Express 24, 30038–30052 (2016).
[Crossref]

2015 (4)

A. Hashimoto, Y. Yamaguchi, L.-D. Chiu, C. Morimoto, K. Fujita, M. Takedachi, S. Kawata, S. Murakami, and E. Tamiya, “Time-lapse Raman imaging of osteoblast differentiation,” Sci. Rep. 5, 12529 (2015).
[Crossref]

F.-K. Lu, S. Basu, V. Igras, M. P. Hoang, M. Ji, D. Fu, G. R. Holtom, V. A. Neel, C. W. Freudiger, D. E. Fisher, and X. S. Xie, “Label-free DNA imaging in vivo with stimulated Raman scattering microscopy,” Proc. Natl. Acad. Sci. USA 112, 11624–11629 (2015).
[Crossref]

S. Harmsen, R. Huang, M. A. Wall, H. Karabeber, J. M. Samii, M. Spaliviero, J. R. White, S. Monette, R. O’Connor, K. L. Pitter, S. A. Sastra, M. Saborowski, E. C. Holland, S. Singer, K. P. Olive, S. W. Lowe, R. G. Blasberg, and M. F. Kircher, “Surface-enhanced resonance Raman scattering nanostars for high-precision cancer imaging,” Sci. Transl. Med. 7, 271ra7 (2015).
[Crossref]

M. Jermyn, K. Mok, J. Mercier, J. Desroches, J. Pichette, K. Saint-Arnaud, L. Bernstein, M.-C. Guiot, K. Petrecca, and F. Leblond, “Intraoperative brain cancer detection with Raman spectroscopy in humans,” Sci. Transl. Med. 7, 274ra19 (2015).
[Crossref]

2014 (1)

D. F. Galvis-Carreño, Y. H. Mejía-Melgarejo, and H. Arguello-Fuentes, “Efficient reconstruction of Raman spectroscopy imaging based on compressive sensing,” Dyna 81, 116–124 (2014).
[Crossref]

2013 (2)

D. S. Wilcox, G. T. Buzzard, B. J. Lucier, O. G. Rehrauer, P. Wang, and D. Ben-Amotz, “Digital compressive chemical quantitation and hyperspectral imaging,” Analyst 138, 4982–4990 (2013).
[Crossref]

Y. August, C. Vachman, Y. Rivenson, and A. Stern, “Compressive hyperspectral imaging by random separable projections in both the spatial and the spectral domains,” Appl. Opt. 52, D46–D54 (2013).
[Crossref]

2012 (4)

Y. Xu, W. Yin, Z. Wen, and Y. Zhang, “An alternating direction algorithm for matrix completion with nonnegative factors,” Front. Math. China 7, 365–384 (2012).
[Crossref]

D. S. Wilcox, G. T. Buzzard, B. J. Lucier, P. Wang, and D. Ben-Amotz, “Photon level chemical classification using digital compressive detection,” Anal. Chim. Acta 755, 17–27 (2012).
[Crossref]

K. Klein, A. M. Gigler, T. Aschenbrenner, R. Monetti, W. Bunk, F. Jamitzky, G. Morfill, R. W. Stark, and J. Schlegel, “Label-free live-cell imaging with confocal Raman microscopy,” Biophys. J. 102, 360–368 (2012).
[Crossref]

M. Okada, N. I. Smith, A. F. Palonpon, H. Endo, S. Kawata, M. Sodeoka, and K. Fujita, “Label-free Raman observation of cytochrome c dynamics during apoptosis,” Proc. Natl. Acad. Sci. USA 109, 28–32 (2012).
[Crossref]

2011 (1)

B. M. Davis, A. J. Hemphill, D. Cebeci Maltas, M. A. Zipper, P. Wang, and D. Ben-Amotz, “Multivariate hyperspectral Raman imaging using compressive detection,” Anal. Chem. 83, 5086–5092 (2011).
[Crossref]

2010 (1)

J.-F. Cai, E. J. Candès, and Z. Shen, “A singular value thresholding algorithm for matrix completion,” SIAM J. Optim. 20, 1956–1982 (2010).
[Crossref]

2009 (1)

E. J. Candès and B. Recht, “Exact matrix completion via convex optimization,” Found. Comput. Math. 9, 717–772 (2009).
[Crossref]

2007 (1)

C. Matthäus, T. Chernenko, J. A. Newmark, C. M. Warner, and M. Diem, “Label-free detection of mitochondrial distribution in cells by nonresonant Raman microspectroscopy,” Biophys. J. 93, 668–673 (2007).
[Crossref]

2005 (1)

C. Krafft, T. Knetschke, R. H. Funk, and R. Salzer, “Identification of organelles and vesicles in single cells by Raman microspectroscopic mapping,” Vib. Spectrosc. 38, 85–93 (2005).
[Crossref]

2003 (1)

N. Uzunbajakava, A. Lenferink, Y. Kraan, E. Volokhina, G. Vrensen, J. Greve, and C. Otto, “Nonresonant confocal Raman imaging of DNA and protein distribution in apoptotic cells,” Biophys. J. 84, 3968–3981 (2003).
[Crossref]

1998 (1)

Q. Wu, W. Nelson, P. Hargraves, J. Zhang, C. Brown, and J. Seelenbinder, “Differentiation of algae clones on the basis of resonance Raman spectra excited by visible light,” Anal. Chem. 70, 1782–1787 (1998).
[Crossref]

Arguello-Fuentes, H.

D. F. Galvis-Carreño, Y. H. Mejía-Melgarejo, and H. Arguello-Fuentes, “Efficient reconstruction of Raman spectroscopy imaging based on compressive sensing,” Dyna 81, 116–124 (2014).
[Crossref]

Aschenbrenner, T.

K. Klein, A. M. Gigler, T. Aschenbrenner, R. Monetti, W. Bunk, F. Jamitzky, G. Morfill, R. W. Stark, and J. Schlegel, “Label-free live-cell imaging with confocal Raman microscopy,” Biophys. J. 102, 360–368 (2012).
[Crossref]

August, Y.

Basu, S.

F.-K. Lu, S. Basu, V. Igras, M. P. Hoang, M. Ji, D. Fu, G. R. Holtom, V. A. Neel, C. W. Freudiger, D. E. Fisher, and X. S. Xie, “Label-free DNA imaging in vivo with stimulated Raman scattering microscopy,” Proc. Natl. Acad. Sci. USA 112, 11624–11629 (2015).
[Crossref]

Ben-Amotz, D.

O. G. Rehrauer, V. C. Dinh, B. R. Mankani, G. T. Buzzard, B. J. Lucier, and D. Ben-Amotz, “Binary complementary filters for compressive Raman spectroscopy,” Appl. Spectrosc. 72, 69–78 (2018).
[Crossref]

D. S. Wilcox, G. T. Buzzard, B. J. Lucier, O. G. Rehrauer, P. Wang, and D. Ben-Amotz, “Digital compressive chemical quantitation and hyperspectral imaging,” Analyst 138, 4982–4990 (2013).
[Crossref]

D. S. Wilcox, G. T. Buzzard, B. J. Lucier, P. Wang, and D. Ben-Amotz, “Photon level chemical classification using digital compressive detection,” Anal. Chim. Acta 755, 17–27 (2012).
[Crossref]

B. M. Davis, A. J. Hemphill, D. Cebeci Maltas, M. A. Zipper, P. Wang, and D. Ben-Amotz, “Multivariate hyperspectral Raman imaging using compressive detection,” Anal. Chem. 83, 5086–5092 (2011).
[Crossref]

Bernstein, L.

M. Jermyn, K. Mok, J. Mercier, J. Desroches, J. Pichette, K. Saint-Arnaud, L. Bernstein, M.-C. Guiot, K. Petrecca, and F. Leblond, “Intraoperative brain cancer detection with Raman spectroscopy in humans,” Sci. Transl. Med. 7, 274ra19 (2015).
[Crossref]

Berto, P.

Bixler, J. N.

Blasberg, R. G.

S. Harmsen, R. Huang, M. A. Wall, H. Karabeber, J. M. Samii, M. Spaliviero, J. R. White, S. Monette, R. O’Connor, K. L. Pitter, S. A. Sastra, M. Saborowski, E. C. Holland, S. Singer, K. P. Olive, S. W. Lowe, R. G. Blasberg, and M. F. Kircher, “Surface-enhanced resonance Raman scattering nanostars for high-precision cancer imaging,” Sci. Transl. Med. 7, 271ra7 (2015).
[Crossref]

Bodelón, G.

G. Bodelón, V. Montes-García, V. López-Puente, E. H. Hill, C. Hamon, M. N. Sanz-Ortiz, S. Rodal-Cedeira, C. Costas, S. Celiksoy, I. Pérez-Juste, L. Scarabelli, A. La Porta, J. Pérez-Juste, I. Pastoriza-Santos, and L. M. Liz-Marzán, “Detection and imaging of quorum sensing in pseudomonas aeruginosa biofilm communities by surface-enhanced resonance Raman scattering,” Nat. Mater. 15, 1203–1211 (2016).
[Crossref]

Bouzy, P.

C. Scotté, H. B. de Aguiar, D. Marguet, E. Green, P. Bouzy, S. Vergnole, P. Winlove, N. Stone, and H. Rigneault, “Assessment of compressive Raman versus hyperspectral Raman for microcalcification chemical imaging,” Anal. Chem. 90, 7197–7203 (2018).
[Crossref]

Brown, C.

Q. Wu, W. Nelson, P. Hargraves, J. Zhang, C. Brown, and J. Seelenbinder, “Differentiation of algae clones on the basis of resonance Raman spectra excited by visible light,” Anal. Chem. 70, 1782–1787 (1998).
[Crossref]

Bunk, W.

K. Klein, A. M. Gigler, T. Aschenbrenner, R. Monetti, W. Bunk, F. Jamitzky, G. Morfill, R. W. Stark, and J. Schlegel, “Label-free live-cell imaging with confocal Raman microscopy,” Biophys. J. 102, 360–368 (2012).
[Crossref]

Buzzard, G. T.

O. G. Rehrauer, V. C. Dinh, B. R. Mankani, G. T. Buzzard, B. J. Lucier, and D. Ben-Amotz, “Binary complementary filters for compressive Raman spectroscopy,” Appl. Spectrosc. 72, 69–78 (2018).
[Crossref]

D. S. Wilcox, G. T. Buzzard, B. J. Lucier, O. G. Rehrauer, P. Wang, and D. Ben-Amotz, “Digital compressive chemical quantitation and hyperspectral imaging,” Analyst 138, 4982–4990 (2013).
[Crossref]

D. S. Wilcox, G. T. Buzzard, B. J. Lucier, P. Wang, and D. Ben-Amotz, “Photon level chemical classification using digital compressive detection,” Anal. Chim. Acta 755, 17–27 (2012).
[Crossref]

Cai, J.-F.

J.-F. Cai, E. J. Candès, and Z. Shen, “A singular value thresholding algorithm for matrix completion,” SIAM J. Optim. 20, 1956–1982 (2010).
[Crossref]

Candès, E. J.

J.-F. Cai, E. J. Candès, and Z. Shen, “A singular value thresholding algorithm for matrix completion,” SIAM J. Optim. 20, 1956–1982 (2010).
[Crossref]

E. J. Candès and B. Recht, “Exact matrix completion via convex optimization,” Found. Comput. Math. 9, 717–772 (2009).
[Crossref]

Cebeci Maltas, D.

B. M. Davis, A. J. Hemphill, D. Cebeci Maltas, M. A. Zipper, P. Wang, and D. Ben-Amotz, “Multivariate hyperspectral Raman imaging using compressive detection,” Anal. Chem. 83, 5086–5092 (2011).
[Crossref]

Celiksoy, S.

G. Bodelón, V. Montes-García, V. López-Puente, E. H. Hill, C. Hamon, M. N. Sanz-Ortiz, S. Rodal-Cedeira, C. Costas, S. Celiksoy, I. Pérez-Juste, L. Scarabelli, A. La Porta, J. Pérez-Juste, I. Pastoriza-Santos, and L. M. Liz-Marzán, “Detection and imaging of quorum sensing in pseudomonas aeruginosa biofilm communities by surface-enhanced resonance Raman scattering,” Nat. Mater. 15, 1203–1211 (2016).
[Crossref]

Chen, S.

Chernenko, T.

C. Matthäus, T. Chernenko, J. A. Newmark, C. M. Warner, and M. Diem, “Label-free detection of mitochondrial distribution in cells by nonresonant Raman microspectroscopy,” Biophys. J. 93, 668–673 (2007).
[Crossref]

Chiu, L.-D.

A. Hashimoto, Y. Yamaguchi, L.-D. Chiu, C. Morimoto, K. Fujita, M. Takedachi, S. Kawata, S. Murakami, and E. Tamiya, “Time-lapse Raman imaging of osteoblast differentiation,” Sci. Rep. 5, 12529 (2015).
[Crossref]

Choi, H.

Corcoran, T. C.

Costas, C.

G. Bodelón, V. Montes-García, V. López-Puente, E. H. Hill, C. Hamon, M. N. Sanz-Ortiz, S. Rodal-Cedeira, C. Costas, S. Celiksoy, I. Pérez-Juste, L. Scarabelli, A. La Porta, J. Pérez-Juste, I. Pastoriza-Santos, and L. M. Liz-Marzán, “Detection and imaging of quorum sensing in pseudomonas aeruginosa biofilm communities by surface-enhanced resonance Raman scattering,” Nat. Mater. 15, 1203–1211 (2016).
[Crossref]

Davis, B. M.

B. M. Davis, A. J. Hemphill, D. Cebeci Maltas, M. A. Zipper, P. Wang, and D. Ben-Amotz, “Multivariate hyperspectral Raman imaging using compressive detection,” Anal. Chem. 83, 5086–5092 (2011).
[Crossref]

de Aguiar, H. B.

S. H. Donaldson and H. B. de Aguiar, “Molecular imaging of cholesterol and lipid distributions in model membranes,” J. Phys. Chem. Lett. 9, 1528–1533 (2018).
[Crossref]

C. Scotté, H. B. de Aguiar, D. Marguet, E. Green, P. Bouzy, S. Vergnole, P. Winlove, N. Stone, and H. Rigneault, “Assessment of compressive Raman versus hyperspectral Raman for microcalcification chemical imaging,” Anal. Chem. 90, 7197–7203 (2018).
[Crossref]

P. Réfrégier, C. Scotté, H. B. de Aguiar, H. Rigneault, and F. Galland, “Precision of proportion estimation with binary compressed Raman spectrum,” J. Opt. Soc. Am. A 35, 125–134 (2018).
[Crossref]

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Kircher, M. F.

S. Harmsen, R. Huang, M. A. Wall, H. Karabeber, J. M. Samii, M. Spaliviero, J. R. White, S. Monette, R. O’Connor, K. L. Pitter, S. A. Sastra, M. Saborowski, E. C. Holland, S. Singer, K. P. Olive, S. W. Lowe, R. G. Blasberg, and M. F. Kircher, “Surface-enhanced resonance Raman scattering nanostars for high-precision cancer imaging,” Sci. Transl. Med. 7, 271ra7 (2015).
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Matthäus, C.

C. Matthäus, T. Chernenko, J. A. Newmark, C. M. Warner, and M. Diem, “Label-free detection of mitochondrial distribution in cells by nonresonant Raman microspectroscopy,” Biophys. J. 93, 668–673 (2007).
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D. F. Galvis-Carreño, Y. H. Mejía-Melgarejo, and H. Arguello-Fuentes, “Efficient reconstruction of Raman spectroscopy imaging based on compressive sensing,” Dyna 81, 116–124 (2014).
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M. Jermyn, K. Mok, J. Mercier, J. Desroches, J. Pichette, K. Saint-Arnaud, L. Bernstein, M.-C. Guiot, K. Petrecca, and F. Leblond, “Intraoperative brain cancer detection with Raman spectroscopy in humans,” Sci. Transl. Med. 7, 274ra19 (2015).
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Murakami, S.

A. Hashimoto, Y. Yamaguchi, L.-D. Chiu, C. Morimoto, K. Fujita, M. Takedachi, S. Kawata, S. Murakami, and E. Tamiya, “Time-lapse Raman imaging of osteoblast differentiation,” Sci. Rep. 5, 12529 (2015).
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Notingher, I.

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Pérez-Juste, I.

G. Bodelón, V. Montes-García, V. López-Puente, E. H. Hill, C. Hamon, M. N. Sanz-Ortiz, S. Rodal-Cedeira, C. Costas, S. Celiksoy, I. Pérez-Juste, L. Scarabelli, A. La Porta, J. Pérez-Juste, I. Pastoriza-Santos, and L. M. Liz-Marzán, “Detection and imaging of quorum sensing in pseudomonas aeruginosa biofilm communities by surface-enhanced resonance Raman scattering,” Nat. Mater. 15, 1203–1211 (2016).
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G. Bodelón, V. Montes-García, V. López-Puente, E. H. Hill, C. Hamon, M. N. Sanz-Ortiz, S. Rodal-Cedeira, C. Costas, S. Celiksoy, I. Pérez-Juste, L. Scarabelli, A. La Porta, J. Pérez-Juste, I. Pastoriza-Santos, and L. M. Liz-Marzán, “Detection and imaging of quorum sensing in pseudomonas aeruginosa biofilm communities by surface-enhanced resonance Raman scattering,” Nat. Mater. 15, 1203–1211 (2016).
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M. Jermyn, K. Mok, J. Mercier, J. Desroches, J. Pichette, K. Saint-Arnaud, L. Bernstein, M.-C. Guiot, K. Petrecca, and F. Leblond, “Intraoperative brain cancer detection with Raman spectroscopy in humans,” Sci. Transl. Med. 7, 274ra19 (2015).
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M. Jermyn, K. Mok, J. Mercier, J. Desroches, J. Pichette, K. Saint-Arnaud, L. Bernstein, M.-C. Guiot, K. Petrecca, and F. Leblond, “Intraoperative brain cancer detection with Raman spectroscopy in humans,” Sci. Transl. Med. 7, 274ra19 (2015).
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S. Harmsen, R. Huang, M. A. Wall, H. Karabeber, J. M. Samii, M. Spaliviero, J. R. White, S. Monette, R. O’Connor, K. L. Pitter, S. A. Sastra, M. Saborowski, E. C. Holland, S. Singer, K. P. Olive, S. W. Lowe, R. G. Blasberg, and M. F. Kircher, “Surface-enhanced resonance Raman scattering nanostars for high-precision cancer imaging,” Sci. Transl. Med. 7, 271ra7 (2015).
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B. Lorenz, C. Wichmann, S. Stöckel, P. Rösch, and J. Popp, “Cultivation-free Raman spectroscopic investigations of bacteria,” Trends Microbiol. 25, 413–424 (2017).
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B. Prats-Mateu, M. Felhofer, A. de Juan, and N. Gierlinger, “Multivariate unmixing approaches on Raman images of plant cell walls: new insights or overinterpretation of results?” Plant Methods 14, 52 (2018).
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D. J. Starling and J. Ranalli, “Compressive sensing for spatial and spectral flame diagnostics,” Sci. Rep. 8, 2556 (2018).
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E. J. Candès and B. Recht, “Exact matrix completion via convex optimization,” Found. Comput. Math. 9, 717–772 (2009).
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P. Réfrégier, C. Scotté, H. B. de Aguiar, H. Rigneault, and F. Galland, “Precision of proportion estimation with binary compressed Raman spectrum,” J. Opt. Soc. Am. A 35, 125–134 (2018).
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Rivenson, Y.

Rodal-Cedeira, S.

G. Bodelón, V. Montes-García, V. López-Puente, E. H. Hill, C. Hamon, M. N. Sanz-Ortiz, S. Rodal-Cedeira, C. Costas, S. Celiksoy, I. Pérez-Juste, L. Scarabelli, A. La Porta, J. Pérez-Juste, I. Pastoriza-Santos, and L. M. Liz-Marzán, “Detection and imaging of quorum sensing in pseudomonas aeruginosa biofilm communities by surface-enhanced resonance Raman scattering,” Nat. Mater. 15, 1203–1211 (2016).
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B. Lorenz, C. Wichmann, S. Stöckel, P. Rösch, and J. Popp, “Cultivation-free Raman spectroscopic investigations of bacteria,” Trends Microbiol. 25, 413–424 (2017).
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S. Harmsen, R. Huang, M. A. Wall, H. Karabeber, J. M. Samii, M. Spaliviero, J. R. White, S. Monette, R. O’Connor, K. L. Pitter, S. A. Sastra, M. Saborowski, E. C. Holland, S. Singer, K. P. Olive, S. W. Lowe, R. G. Blasberg, and M. F. Kircher, “Surface-enhanced resonance Raman scattering nanostars for high-precision cancer imaging,” Sci. Transl. Med. 7, 271ra7 (2015).
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M. Jermyn, K. Mok, J. Mercier, J. Desroches, J. Pichette, K. Saint-Arnaud, L. Bernstein, M.-C. Guiot, K. Petrecca, and F. Leblond, “Intraoperative brain cancer detection with Raman spectroscopy in humans,” Sci. Transl. Med. 7, 274ra19 (2015).
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G. Bodelón, V. Montes-García, V. López-Puente, E. H. Hill, C. Hamon, M. N. Sanz-Ortiz, S. Rodal-Cedeira, C. Costas, S. Celiksoy, I. Pérez-Juste, L. Scarabelli, A. La Porta, J. Pérez-Juste, I. Pastoriza-Santos, and L. M. Liz-Marzán, “Detection and imaging of quorum sensing in pseudomonas aeruginosa biofilm communities by surface-enhanced resonance Raman scattering,” Nat. Mater. 15, 1203–1211 (2016).
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G. Bodelón, V. Montes-García, V. López-Puente, E. H. Hill, C. Hamon, M. N. Sanz-Ortiz, S. Rodal-Cedeira, C. Costas, S. Celiksoy, I. Pérez-Juste, L. Scarabelli, A. La Porta, J. Pérez-Juste, I. Pastoriza-Santos, and L. M. Liz-Marzán, “Detection and imaging of quorum sensing in pseudomonas aeruginosa biofilm communities by surface-enhanced resonance Raman scattering,” Nat. Mater. 15, 1203–1211 (2016).
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K. Klein, A. M. Gigler, T. Aschenbrenner, R. Monetti, W. Bunk, F. Jamitzky, G. Morfill, R. W. Stark, and J. Schlegel, “Label-free live-cell imaging with confocal Raman microscopy,” Biophys. J. 102, 360–368 (2012).
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D. J. Starling and J. Ranalli, “Compressive sensing for spatial and spectral flame diagnostics,” Sci. Rep. 8, 2556 (2018).
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B. Lorenz, C. Wichmann, S. Stöckel, P. Rösch, and J. Popp, “Cultivation-free Raman spectroscopic investigations of bacteria,” Trends Microbiol. 25, 413–424 (2017).
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C. Scotté, H. B. de Aguiar, D. Marguet, E. Green, P. Bouzy, S. Vergnole, P. Winlove, N. Stone, and H. Rigneault, “Assessment of compressive Raman versus hyperspectral Raman for microcalcification chemical imaging,” Anal. Chem. 90, 7197–7203 (2018).
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B. Sturm, F. Soldevila, E. Tajahuerce, S. Gigan, H. Rigneault, and H. B. de Aguiar, “High-sensitivity high-speed compressive spectrometer for Raman imaging,” arXiv:1811.06954 (2018).

Tajahuerce, E.

B. Sturm, F. Soldevila, E. Tajahuerce, S. Gigan, H. Rigneault, and H. B. de Aguiar, “High-sensitivity high-speed compressive spectrometer for Raman imaging,” arXiv:1811.06954 (2018).

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A. Hashimoto, Y. Yamaguchi, L.-D. Chiu, C. Morimoto, K. Fujita, M. Takedachi, S. Kawata, S. Murakami, and E. Tamiya, “Time-lapse Raman imaging of osteoblast differentiation,” Sci. Rep. 5, 12529 (2015).
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Vergnole, S.

C. Scotté, H. B. de Aguiar, D. Marguet, E. Green, P. Bouzy, S. Vergnole, P. Winlove, N. Stone, and H. Rigneault, “Assessment of compressive Raman versus hyperspectral Raman for microcalcification chemical imaging,” Anal. Chem. 90, 7197–7203 (2018).
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Wadduwage, D. N.

Wall, M. A.

S. Harmsen, R. Huang, M. A. Wall, H. Karabeber, J. M. Samii, M. Spaliviero, J. R. White, S. Monette, R. O’Connor, K. L. Pitter, S. A. Sastra, M. Saborowski, E. C. Holland, S. Singer, K. P. Olive, S. W. Lowe, R. G. Blasberg, and M. F. Kircher, “Surface-enhanced resonance Raman scattering nanostars for high-precision cancer imaging,” Sci. Transl. Med. 7, 271ra7 (2015).
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D. S. Wilcox, G. T. Buzzard, B. J. Lucier, O. G. Rehrauer, P. Wang, and D. Ben-Amotz, “Digital compressive chemical quantitation and hyperspectral imaging,” Analyst 138, 4982–4990 (2013).
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D. S. Wilcox, G. T. Buzzard, B. J. Lucier, P. Wang, and D. Ben-Amotz, “Photon level chemical classification using digital compressive detection,” Anal. Chim. Acta 755, 17–27 (2012).
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B. M. Davis, A. J. Hemphill, D. Cebeci Maltas, M. A. Zipper, P. Wang, and D. Ben-Amotz, “Multivariate hyperspectral Raman imaging using compressive detection,” Anal. Chem. 83, 5086–5092 (2011).
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Y. Xu, W. Yin, Z. Wen, and Y. Zhang, “An alternating direction algorithm for matrix completion with nonnegative factors,” Front. Math. China 7, 365–384 (2012).
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S. Harmsen, R. Huang, M. A. Wall, H. Karabeber, J. M. Samii, M. Spaliviero, J. R. White, S. Monette, R. O’Connor, K. L. Pitter, S. A. Sastra, M. Saborowski, E. C. Holland, S. Singer, K. P. Olive, S. W. Lowe, R. G. Blasberg, and M. F. Kircher, “Surface-enhanced resonance Raman scattering nanostars for high-precision cancer imaging,” Sci. Transl. Med. 7, 271ra7 (2015).
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B. Lorenz, C. Wichmann, S. Stöckel, P. Rösch, and J. Popp, “Cultivation-free Raman spectroscopic investigations of bacteria,” Trends Microbiol. 25, 413–424 (2017).
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D. S. Wilcox, G. T. Buzzard, B. J. Lucier, O. G. Rehrauer, P. Wang, and D. Ben-Amotz, “Digital compressive chemical quantitation and hyperspectral imaging,” Analyst 138, 4982–4990 (2013).
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D. S. Wilcox, G. T. Buzzard, B. J. Lucier, P. Wang, and D. Ben-Amotz, “Photon level chemical classification using digital compressive detection,” Anal. Chim. Acta 755, 17–27 (2012).
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C. Scotté, H. B. de Aguiar, D. Marguet, E. Green, P. Bouzy, S. Vergnole, P. Winlove, N. Stone, and H. Rigneault, “Assessment of compressive Raman versus hyperspectral Raman for microcalcification chemical imaging,” Anal. Chem. 90, 7197–7203 (2018).
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Q. Wu, W. Nelson, P. Hargraves, J. Zhang, C. Brown, and J. Seelenbinder, “Differentiation of algae clones on the basis of resonance Raman spectra excited by visible light,” Anal. Chem. 70, 1782–1787 (1998).
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Yin, W.

Y. Xu, W. Yin, Z. Wen, and Y. Zhang, “An alternating direction algorithm for matrix completion with nonnegative factors,” Front. Math. China 7, 365–384 (2012).
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Q. Wu, W. Nelson, P. Hargraves, J. Zhang, C. Brown, and J. Seelenbinder, “Differentiation of algae clones on the basis of resonance Raman spectra excited by visible light,” Anal. Chem. 70, 1782–1787 (1998).
[Crossref]

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Y. Xu, W. Yin, Z. Wen, and Y. Zhang, “An alternating direction algorithm for matrix completion with nonnegative factors,” Front. Math. China 7, 365–384 (2012).
[Crossref]

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B. M. Davis, A. J. Hemphill, D. Cebeci Maltas, M. A. Zipper, P. Wang, and D. Ben-Amotz, “Multivariate hyperspectral Raman imaging using compressive detection,” Anal. Chem. 83, 5086–5092 (2011).
[Crossref]

Adv. Opt. Photon. (1)

Anal. Chem. (3)

Q. Wu, W. Nelson, P. Hargraves, J. Zhang, C. Brown, and J. Seelenbinder, “Differentiation of algae clones on the basis of resonance Raman spectra excited by visible light,” Anal. Chem. 70, 1782–1787 (1998).
[Crossref]

B. M. Davis, A. J. Hemphill, D. Cebeci Maltas, M. A. Zipper, P. Wang, and D. Ben-Amotz, “Multivariate hyperspectral Raman imaging using compressive detection,” Anal. Chem. 83, 5086–5092 (2011).
[Crossref]

C. Scotté, H. B. de Aguiar, D. Marguet, E. Green, P. Bouzy, S. Vergnole, P. Winlove, N. Stone, and H. Rigneault, “Assessment of compressive Raman versus hyperspectral Raman for microcalcification chemical imaging,” Anal. Chem. 90, 7197–7203 (2018).
[Crossref]

Anal. Chim. Acta (1)

D. S. Wilcox, G. T. Buzzard, B. J. Lucier, P. Wang, and D. Ben-Amotz, “Photon level chemical classification using digital compressive detection,” Anal. Chim. Acta 755, 17–27 (2012).
[Crossref]

Analyst (1)

D. S. Wilcox, G. T. Buzzard, B. J. Lucier, O. G. Rehrauer, P. Wang, and D. Ben-Amotz, “Digital compressive chemical quantitation and hyperspectral imaging,” Analyst 138, 4982–4990 (2013).
[Crossref]

Appl. Opt. (1)

Appl. Spectrosc. (2)

Biophys. J. (3)

C. Matthäus, T. Chernenko, J. A. Newmark, C. M. Warner, and M. Diem, “Label-free detection of mitochondrial distribution in cells by nonresonant Raman microspectroscopy,” Biophys. J. 93, 668–673 (2007).
[Crossref]

K. Klein, A. M. Gigler, T. Aschenbrenner, R. Monetti, W. Bunk, F. Jamitzky, G. Morfill, R. W. Stark, and J. Schlegel, “Label-free live-cell imaging with confocal Raman microscopy,” Biophys. J. 102, 360–368 (2012).
[Crossref]

N. Uzunbajakava, A. Lenferink, Y. Kraan, E. Volokhina, G. Vrensen, J. Greve, and C. Otto, “Nonresonant confocal Raman imaging of DNA and protein distribution in apoptotic cells,” Biophys. J. 84, 3968–3981 (2003).
[Crossref]

Dyna (1)

D. F. Galvis-Carreño, Y. H. Mejía-Melgarejo, and H. Arguello-Fuentes, “Efficient reconstruction of Raman spectroscopy imaging based on compressive sensing,” Dyna 81, 116–124 (2014).
[Crossref]

Found. Comput. Math. (1)

E. J. Candès and B. Recht, “Exact matrix completion via convex optimization,” Found. Comput. Math. 9, 717–772 (2009).
[Crossref]

Front. Math. China (1)

Y. Xu, W. Yin, Z. Wen, and Y. Zhang, “An alternating direction algorithm for matrix completion with nonnegative factors,” Front. Math. China 7, 365–384 (2012).
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J. Opt. Soc. Am. A (1)

J. Phys. Chem. Lett. (1)

S. H. Donaldson and H. B. de Aguiar, “Molecular imaging of cholesterol and lipid distributions in model membranes,” J. Phys. Chem. Lett. 9, 1528–1533 (2018).
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Nat. Mater. (1)

G. Bodelón, V. Montes-García, V. López-Puente, E. H. Hill, C. Hamon, M. N. Sanz-Ortiz, S. Rodal-Cedeira, C. Costas, S. Celiksoy, I. Pérez-Juste, L. Scarabelli, A. La Porta, J. Pérez-Juste, I. Pastoriza-Santos, and L. M. Liz-Marzán, “Detection and imaging of quorum sensing in pseudomonas aeruginosa biofilm communities by surface-enhanced resonance Raman scattering,” Nat. Mater. 15, 1203–1211 (2016).
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Opt. Express (1)

Opt. Lett. (3)

Optica (2)

Plant Methods (1)

B. Prats-Mateu, M. Felhofer, A. de Juan, and N. Gierlinger, “Multivariate unmixing approaches on Raman images of plant cell walls: new insights or overinterpretation of results?” Plant Methods 14, 52 (2018).
[Crossref]

Proc. Natl. Acad. Sci. USA (2)

F.-K. Lu, S. Basu, V. Igras, M. P. Hoang, M. Ji, D. Fu, G. R. Holtom, V. A. Neel, C. W. Freudiger, D. E. Fisher, and X. S. Xie, “Label-free DNA imaging in vivo with stimulated Raman scattering microscopy,” Proc. Natl. Acad. Sci. USA 112, 11624–11629 (2015).
[Crossref]

M. Okada, N. I. Smith, A. F. Palonpon, H. Endo, S. Kawata, M. Sodeoka, and K. Fujita, “Label-free Raman observation of cytochrome c dynamics during apoptosis,” Proc. Natl. Acad. Sci. USA 109, 28–32 (2012).
[Crossref]

Sci. Rep. (2)

A. Hashimoto, Y. Yamaguchi, L.-D. Chiu, C. Morimoto, K. Fujita, M. Takedachi, S. Kawata, S. Murakami, and E. Tamiya, “Time-lapse Raman imaging of osteoblast differentiation,” Sci. Rep. 5, 12529 (2015).
[Crossref]

D. J. Starling and J. Ranalli, “Compressive sensing for spatial and spectral flame diagnostics,” Sci. Rep. 8, 2556 (2018).
[Crossref]

Sci. Transl. Med. (2)

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Supplementary Material (1)

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Figures (3)

Fig. 1.
Fig. 1. Concept proposed. In Raman microspectroscopy, the hyperspectrum tensor (A) has a matrix representation H (B, leftmost panel). H can be factorized into matrices U, S, V, which have considerably lower sizes than H, i.e., H is low rank. Therefore, one can undersample H (C) and use recent signal processing algorithms’ so-called matrix completion for computational reconstruction. In our development (D), instead of using a spectrometer with costly cameras (left panel), H is undersampled at high speed using a programmable spectrometer (right panel) that selects spectral bins (in the canonical representation), or a combination of spectral bins (in the multiplex approach), at random, but ensures uniform spatial sampling for high-sensitivity imaging. The lower panels illustrate the image plane spatial scanning and upper panels spectrometer wavelength sampling.
Fig. 2.
Fig. 2. Proof-of-principle experiments. (A) Experimental hyperspectrum, before reconstruction, of polymer beads spread over a glass coverslip and embedded in water. In this particular example, only about 12% of experimental samples have been acquired, as clearly seen in the zoomed-in region (bottom left panel). After computational reconstruction a high-fidelity hyperspectrum is achieved (bottom right panel). (B) Average spectra of regions containing beads (red) and water plus glass (green). (C) Chemically selective images merged, following the colorcode of (B), for different levels of compression (indicated on top of each panel). Effective pixel dwell time (left to right): 10.2 ms, 5.1 ms, 5 ms. Scale bars: 20 μm. (D) Fidelity of the reconstruction for the two species at various compression ratios. The analysis is performed separately for the spectral (continuous line) and spatial (dashed lines) domains.
Fig. 3.
Fig. 3. High-sensitivity bio-imaging of opaque and optically clear specimens. (A) High-sensitivity image of a cheek cell from integrated C-H stretch spectral region (28003000cm1). (lower panel) The averaged background-corrected spectra in three regions of the cell, namely, nucleus, membrane, and round organelles. Effective pixel dwell time: 18.8 ms. Compression: 2.4. (B) Compressed Raman microspectroscopy of opaque brain tissue. (left panels) Lipid-rich (red) and protein-rich (blue) images, merged from their eigenimages (lower panels). The respective averaged spectra based on the eigenimages (upper right panel), highlighting the lipid-rich and protein-rich C-H stretch spectra differences (inset). Effective pixel dwell time: 19.6 ms. Compression: 2.4. (C) Supervised compressive Raman microspectroscopy images, using optimized filters based on the eigenspectra in (B). Note that samples in (B) and (C) are different; however, both are from cerebellum tissues. Effective pixel dwell time: 0.4 ms. Compression: 64. Scale bars: 20 μm.