Abstract

Spectral imaging is a powerful technique used to simultaneously study multiple fluorophore labels with overlapping emissions. Here, we present a computational spectral imaging method, which uses sample spatial fluorescence information as a reconstruction constraint. Our method addresses both the under-sampling issue of compressive spectral imaging and the low throughput issue of scanning spectral imaging. With simulated and experimental data, we have demonstrated the reconstruction precision of our method in two and three-color imaging. We have experimentally validated this method for differentiating cellular structures labeled with two red-colored fluorescent proteins, tdTomato and mCherry, which have highly overlapping emission spectra. Our method has the advantage of totally free wavelength choice and can also be combined with conventional filter-based sequential multi-color imaging to further improve multiplexing capability.

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

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  1. A. M. Valm, S. Cohen, W. R. Legant, J. Melunis, U. Hershberg, E. Wait, A. R. Cohen, M. W. Davidson, E. Betzig, and J. Lippincott-Schwartz, “Applying systems-level spectral imaging and analysis to reveal the organelle interactome,” Nature 546(7656), 162–167 (2017).
    [Crossref] [PubMed]
  2. Y. Garini, I. T. Young, and G. McNamara, “Spectral imaging: principles and applications,” Cytometry A 69(8), 735–747 (2006).
    [Crossref] [PubMed]
  3. F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
    [Crossref] [PubMed]
  4. L. Gao and R. T. Smith, “Optical hyperspectral imaging in microscopy and spectroscopy - a review of data acquisition,” J. Biophotonics 8(6), 441–456 (2015).
    [Crossref] [PubMed]
  5. W. Jahr, B. Schmid, C. Schmied, F. O. Fahrbach, and J. Huisken, “Hyperspectral light sheet microscopy,” Nat. Commun. 6(1), 7990 (2015).
    [Crossref] [PubMed]
  6. B. Ford, M. Descour, and R. Lynch, “Large-image-format computed tomography imaging spectrometer for fluorescence microscopy,” Opt. Express 9(9), 444–453 (2001).
    [Crossref] [PubMed]
  7. J. Wu, B. Xiong, X. Lin, J. He, J. Suo, and Q. Dai, “Snapshot hyperspectral volumetric microscopy,” Sci. Rep. 6(1), 24624 (2016).
    [Crossref] [PubMed]
  8. M. E. Gehm, R. John, D. J. Brady, R. M. Willett, and T. J. Schulz, “Single-shot compressive spectral imaging with a dual-disperser architecture,” Opt. Express 15(21), 14013–14027 (2007).
    [Crossref] [PubMed]
  9. C. F. Cull, K. Choi, D. J. Brady, and T. Oliver, “Identification of fluorescent beads using a coded aperture snapshot spectral imager,” Appl. Opt. 49(10), B59–B70 (2010).
    [Crossref] [PubMed]
  10. 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]
  11. X. Yuan, T. Tsai, R. Zhu, P. Llull, D. Brady, and L. Carin, “Compressive hyperspectral imaging with side information,” IEEE J. of Selected Topics in Sig. Process. 9(6), 964–976 (2015).
  12. L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516(7529), 74–77 (2014).
    [Crossref] [PubMed]
  13. L. Zhu, Y. Chen, J. Liang, Q. Xu, L. Gao, C. Ma, and L. V. Wang, “Space- and intensity-constrained reconstruction for compressed ultrafast photography,” Optica 3(7), 694–697 (2016).
    [Crossref] [PubMed]
  14. B. Dong, L. Almassalha, B. E. Urban, T.-Q. Nguyen, S. Khuon, T.-L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7(1), 12290 (2016).
    [Crossref] [PubMed]
  15. M. J. Mlodzianoski, N. M. Curthoys, M. S. Gunewardene, S. Carter, and S. T. Hess, “Super-resolution imaging of molecular emission spectra and single molecule spectral fluctuations,” PLoS One 11(3), e0147506 (2016).
    [Crossref] [PubMed]
  16. Z. Zhang, S. J. Kenny, M. Hauser, W. Li, and K. Xu, “Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy,” Nat. Methods 12(10), 935–938 (2015).
    [Crossref] [PubMed]
  17. T. Huang, C. Phelps, J. Wang, L.-J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114(2), 301–310 (2018).
    [Crossref] [PubMed]
  18. J. M. Bioucas-Dias and M. A. T. Figueiredo, “A new TwIST: two-step iterative shrinkage/thresholding algorithms for image restoration,” IEEE Trans. Image Process. 16(12), 2992–3004 (2007).
    [Crossref] [PubMed]
  19. N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J.-C. Olivo-Marin, and J. Zerubia, “Richardson-Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution,” Microsc. Res. Tech. 69(4), 260–266 (2006).
    [Crossref] [PubMed]
  20. K. Chu, P. J. McMillan, Z. J. Smith, J. Yin, J. Atkins, P. Goodwin, S. Wachsmann-Hogiu, and S. Lane, “Image reconstruction for structured-illumination microscopy with low signal level,” Opt. Express 22(7), 8687–8702 (2014).
    [Crossref] [PubMed]
  21. N. Antipa, G. Kuo, R. Heckel, B. Mildenhall, E. Bostan, R. Ng, and L. Waller, “DiffuserCam: lensless single-exposure 3D imaging,” Optica 5(1), 1–9 (2018).
    [Crossref]
  22. B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
    [Crossref] [PubMed]
  23. B. Zitová and J. Flusser, “Image registration methods: a survey,” Image Vis. Comput. 21(11), 977–1000 (2003).
    [Crossref]
  24. F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
    [Crossref] [PubMed]
  25. B. Yang, Y. Wang, S. Feng, V. Pessino, N. Stuurman, and B. Huang, “High numerical aperture epi-illumination selective plane illumination microscopy,” bioRxiv 1, 273359 (2018).

2018 (3)

T. Huang, C. Phelps, J. Wang, L.-J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114(2), 301–310 (2018).
[Crossref] [PubMed]

N. Antipa, G. Kuo, R. Heckel, B. Mildenhall, E. Bostan, R. Ng, and L. Waller, “DiffuserCam: lensless single-exposure 3D imaging,” Optica 5(1), 1–9 (2018).
[Crossref]

B. Yang, Y. Wang, S. Feng, V. Pessino, N. Stuurman, and B. Huang, “High numerical aperture epi-illumination selective plane illumination microscopy,” bioRxiv 1, 273359 (2018).

2017 (2)

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[Crossref] [PubMed]

A. M. Valm, S. Cohen, W. R. Legant, J. Melunis, U. Hershberg, E. Wait, A. R. Cohen, M. W. Davidson, E. Betzig, and J. Lippincott-Schwartz, “Applying systems-level spectral imaging and analysis to reveal the organelle interactome,” Nature 546(7656), 162–167 (2017).
[Crossref] [PubMed]

2016 (4)

J. Wu, B. Xiong, X. Lin, J. He, J. Suo, and Q. Dai, “Snapshot hyperspectral volumetric microscopy,” Sci. Rep. 6(1), 24624 (2016).
[Crossref] [PubMed]

L. Zhu, Y. Chen, J. Liang, Q. Xu, L. Gao, C. Ma, and L. V. Wang, “Space- and intensity-constrained reconstruction for compressed ultrafast photography,” Optica 3(7), 694–697 (2016).
[Crossref] [PubMed]

B. Dong, L. Almassalha, B. E. Urban, T.-Q. Nguyen, S. Khuon, T.-L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7(1), 12290 (2016).
[Crossref] [PubMed]

M. J. Mlodzianoski, N. M. Curthoys, M. S. Gunewardene, S. Carter, and S. T. Hess, “Super-resolution imaging of molecular emission spectra and single molecule spectral fluctuations,” PLoS One 11(3), e0147506 (2016).
[Crossref] [PubMed]

2015 (4)

Z. Zhang, S. J. Kenny, M. Hauser, W. Li, and K. Xu, “Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy,” Nat. Methods 12(10), 935–938 (2015).
[Crossref] [PubMed]

X. Yuan, T. Tsai, R. Zhu, P. Llull, D. Brady, and L. Carin, “Compressive hyperspectral imaging with side information,” IEEE J. of Selected Topics in Sig. Process. 9(6), 964–976 (2015).

L. Gao and R. T. Smith, “Optical hyperspectral imaging in microscopy and spectroscopy - a review of data acquisition,” J. Biophotonics 8(6), 441–456 (2015).
[Crossref] [PubMed]

W. Jahr, B. Schmid, C. Schmied, F. O. Fahrbach, and J. Huisken, “Hyperspectral light sheet microscopy,” Nat. Commun. 6(1), 7990 (2015).
[Crossref] [PubMed]

2014 (2)

2013 (1)

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
[Crossref] [PubMed]

2012 (1)

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]

2010 (1)

2008 (1)

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

2007 (2)

J. M. Bioucas-Dias and M. A. T. Figueiredo, “A new TwIST: two-step iterative shrinkage/thresholding algorithms for image restoration,” IEEE Trans. Image Process. 16(12), 2992–3004 (2007).
[Crossref] [PubMed]

M. E. Gehm, R. John, D. J. Brady, R. M. Willett, and T. J. Schulz, “Single-shot compressive spectral imaging with a dual-disperser architecture,” Opt. Express 15(21), 14013–14027 (2007).
[Crossref] [PubMed]

2006 (2)

Y. Garini, I. T. Young, and G. McNamara, “Spectral imaging: principles and applications,” Cytometry A 69(8), 735–747 (2006).
[Crossref] [PubMed]

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J.-C. Olivo-Marin, and J. Zerubia, “Richardson-Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution,” Microsc. Res. Tech. 69(4), 260–266 (2006).
[Crossref] [PubMed]

2003 (1)

B. Zitová and J. Flusser, “Image registration methods: a survey,” Image Vis. Comput. 21(11), 977–1000 (2003).
[Crossref]

2001 (1)

Almassalha, L.

B. Dong, L. Almassalha, B. E. Urban, T.-Q. Nguyen, S. Khuon, T.-L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7(1), 12290 (2016).
[Crossref] [PubMed]

Antipa, N.

Artiga, M. S.

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[Crossref] [PubMed]

Atkins, J.

Backman, V.

B. Dong, L. Almassalha, B. E. Urban, T.-Q. Nguyen, S. Khuon, T.-L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7(1), 12290 (2016).
[Crossref] [PubMed]

Baird, M. A.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
[Crossref] [PubMed]

Bates, M.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

Betzig, E.

A. M. Valm, S. Cohen, W. R. Legant, J. Melunis, U. Hershberg, E. Wait, A. R. Cohen, M. W. Davidson, E. Betzig, and J. Lippincott-Schwartz, “Applying systems-level spectral imaging and analysis to reveal the organelle interactome,” Nature 546(7656), 162–167 (2017).
[Crossref] [PubMed]

Bewersdorf, J.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
[Crossref] [PubMed]

Bioucas-Dias, J. M.

J. M. Bioucas-Dias and M. A. T. Figueiredo, “A new TwIST: two-step iterative shrinkage/thresholding algorithms for image restoration,” IEEE Trans. Image Process. 16(12), 2992–3004 (2007).
[Crossref] [PubMed]

Bittel, A.

T. Huang, C. Phelps, J. Wang, L.-J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114(2), 301–310 (2018).
[Crossref] [PubMed]

Blanc-Feraud, L.

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J.-C. Olivo-Marin, and J. Zerubia, “Richardson-Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution,” Microsc. Res. Tech. 69(4), 260–266 (2006).
[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]

Bostan, E.

Brady, D.

X. Yuan, T. Tsai, R. Zhu, P. Llull, D. Brady, and L. Carin, “Compressive hyperspectral imaging with side information,” IEEE J. of Selected Topics in Sig. Process. 9(6), 964–976 (2015).

Brady, D. J.

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]

Carin, L.

X. Yuan, T. Tsai, R. Zhu, P. Llull, D. Brady, and L. Carin, “Compressive hyperspectral imaging with side information,” IEEE J. of Selected Topics in Sig. Process. 9(6), 964–976 (2015).

Carter, S.

M. J. Mlodzianoski, N. M. Curthoys, M. S. Gunewardene, S. Carter, and S. T. Hess, “Super-resolution imaging of molecular emission spectra and single molecule spectral fluctuations,” PLoS One 11(3), e0147506 (2016).
[Crossref] [PubMed]

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, Y.

Chew, T.-L.

B. Dong, L. Almassalha, B. E. Urban, T.-Q. Nguyen, S. Khuon, T.-L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7(1), 12290 (2016).
[Crossref] [PubMed]

Chiu, C.-L.

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[Crossref] [PubMed]

Choi, J. M.

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[Crossref] [PubMed]

Choi, K.

Chu, K.

Cohen, A. R.

A. M. Valm, S. Cohen, W. R. Legant, J. Melunis, U. Hershberg, E. Wait, A. R. Cohen, M. W. Davidson, E. Betzig, and J. Lippincott-Schwartz, “Applying systems-level spectral imaging and analysis to reveal the organelle interactome,” Nature 546(7656), 162–167 (2017).
[Crossref] [PubMed]

Cohen, S.

A. M. Valm, S. Cohen, W. R. Legant, J. Melunis, U. Hershberg, E. Wait, A. R. Cohen, M. W. Davidson, E. Betzig, and J. Lippincott-Schwartz, “Applying systems-level spectral imaging and analysis to reveal the organelle interactome,” Nature 546(7656), 162–167 (2017).
[Crossref] [PubMed]

Cull, C. F.

Curthoys, N. M.

M. J. Mlodzianoski, N. M. Curthoys, M. S. Gunewardene, S. Carter, and S. T. Hess, “Super-resolution imaging of molecular emission spectra and single molecule spectral fluctuations,” PLoS One 11(3), e0147506 (2016).
[Crossref] [PubMed]

Cutrale, F.

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[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]

Dai, Q.

J. Wu, B. Xiong, X. Lin, J. He, J. Suo, and Q. Dai, “Snapshot hyperspectral volumetric microscopy,” Sci. Rep. 6(1), 24624 (2016).
[Crossref] [PubMed]

Davidson, M. W.

A. M. Valm, S. Cohen, W. R. Legant, J. Melunis, U. Hershberg, E. Wait, A. R. Cohen, M. W. Davidson, E. Betzig, and J. Lippincott-Schwartz, “Applying systems-level spectral imaging and analysis to reveal the organelle interactome,” Nature 546(7656), 162–167 (2017).
[Crossref] [PubMed]

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
[Crossref] [PubMed]

Descour, M.

Dey, N.

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J.-C. Olivo-Marin, and J. Zerubia, “Richardson-Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution,” Microsc. Res. Tech. 69(4), 260–266 (2006).
[Crossref] [PubMed]

Dong, B.

B. Dong, L. Almassalha, B. E. Urban, T.-Q. Nguyen, S. Khuon, T.-L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7(1), 12290 (2016).
[Crossref] [PubMed]

Duim, W. C.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
[Crossref] [PubMed]

Fahrbach, F. O.

W. Jahr, B. Schmid, C. Schmied, F. O. Fahrbach, and J. Huisken, “Hyperspectral light sheet microscopy,” Nat. Commun. 6(1), 7990 (2015).
[Crossref] [PubMed]

Feng, S.

B. Yang, Y. Wang, S. Feng, V. Pessino, N. Stuurman, and B. Huang, “High numerical aperture epi-illumination selective plane illumination microscopy,” bioRxiv 1, 273359 (2018).

Figueiredo, M. A. T.

J. M. Bioucas-Dias and M. A. T. Figueiredo, “A new TwIST: two-step iterative shrinkage/thresholding algorithms for image restoration,” IEEE Trans. Image Process. 16(12), 2992–3004 (2007).
[Crossref] [PubMed]

Flusser, J.

B. Zitová and J. Flusser, “Image registration methods: a survey,” Image Vis. Comput. 21(11), 977–1000 (2003).
[Crossref]

Ford, B.

Fraser, S. E.

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[Crossref] [PubMed]

Gao, L.

L. Zhu, Y. Chen, J. Liang, Q. Xu, L. Gao, C. Ma, and L. V. Wang, “Space- and intensity-constrained reconstruction for compressed ultrafast photography,” Optica 3(7), 694–697 (2016).
[Crossref] [PubMed]

L. Gao and R. T. Smith, “Optical hyperspectral imaging in microscopy and spectroscopy - a review of data acquisition,” J. Biophotonics 8(6), 441–456 (2015).
[Crossref] [PubMed]

L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516(7529), 74–77 (2014).
[Crossref] [PubMed]

Garini, Y.

Y. Garini, I. T. Young, and G. McNamara, “Spectral imaging: principles and applications,” Cytometry A 69(8), 735–747 (2006).
[Crossref] [PubMed]

Gehm, M. E.

Gibbs, S. L.

T. Huang, C. Phelps, J. Wang, L.-J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114(2), 301–310 (2018).
[Crossref] [PubMed]

Goodwin, P.

Gray, J. W.

T. Huang, C. Phelps, J. Wang, L.-J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114(2), 301–310 (2018).
[Crossref] [PubMed]

Gunewardene, M. S.

M. J. Mlodzianoski, N. M. Curthoys, M. S. Gunewardene, S. Carter, and S. T. Hess, “Super-resolution imaging of molecular emission spectra and single molecule spectral fluctuations,” PLoS One 11(3), e0147506 (2016).
[Crossref] [PubMed]

Hartwich, T. M. P.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
[Crossref] [PubMed]

Hauser, M.

Z. Zhang, S. J. Kenny, M. Hauser, W. Li, and K. Xu, “Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy,” Nat. Methods 12(10), 935–938 (2015).
[Crossref] [PubMed]

He, J.

J. Wu, B. Xiong, X. Lin, J. He, J. Suo, and Q. Dai, “Snapshot hyperspectral volumetric microscopy,” Sci. Rep. 6(1), 24624 (2016).
[Crossref] [PubMed]

Heckel, R.

Hershberg, U.

A. M. Valm, S. Cohen, W. R. Legant, J. Melunis, U. Hershberg, E. Wait, A. R. Cohen, M. W. Davidson, E. Betzig, and J. Lippincott-Schwartz, “Applying systems-level spectral imaging and analysis to reveal the organelle interactome,” Nature 546(7656), 162–167 (2017).
[Crossref] [PubMed]

Hess, S. T.

M. J. Mlodzianoski, N. M. Curthoys, M. S. Gunewardene, S. Carter, and S. T. Hess, “Super-resolution imaging of molecular emission spectra and single molecule spectral fluctuations,” PLoS One 11(3), e0147506 (2016).
[Crossref] [PubMed]

Huang, B.

B. Yang, Y. Wang, S. Feng, V. Pessino, N. Stuurman, and B. Huang, “High numerical aperture epi-illumination selective plane illumination microscopy,” bioRxiv 1, 273359 (2018).

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

Huang, F.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
[Crossref] [PubMed]

Huang, T.

T. Huang, C. Phelps, J. Wang, L.-J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114(2), 301–310 (2018).
[Crossref] [PubMed]

Huisken, J.

W. Jahr, B. Schmid, C. Schmied, F. O. Fahrbach, and J. Huisken, “Hyperspectral light sheet microscopy,” Nat. Commun. 6(1), 7990 (2015).
[Crossref] [PubMed]

Jacques, S.

T. Huang, C. Phelps, J. Wang, L.-J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114(2), 301–310 (2018).
[Crossref] [PubMed]

Jahr, W.

W. Jahr, B. Schmid, C. Schmied, F. O. Fahrbach, and J. Huisken, “Hyperspectral light sheet microscopy,” Nat. Commun. 6(1), 7990 (2015).
[Crossref] [PubMed]

John, R.

Kam, Z.

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J.-C. Olivo-Marin, and J. Zerubia, “Richardson-Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution,” Microsc. Res. Tech. 69(4), 260–266 (2006).
[Crossref] [PubMed]

Kenny, S. J.

Z. Zhang, S. J. Kenny, M. Hauser, W. Li, and K. Xu, “Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy,” Nat. Methods 12(10), 935–938 (2015).
[Crossref] [PubMed]

Khuon, S.

B. Dong, L. Almassalha, B. E. Urban, T.-Q. Nguyen, S. Khuon, T.-L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7(1), 12290 (2016).
[Crossref] [PubMed]

Kuo, G.

Lane, S.

Legant, W. R.

A. M. Valm, S. Cohen, W. R. Legant, J. Melunis, U. Hershberg, E. Wait, A. R. Cohen, M. W. Davidson, E. Betzig, and J. Lippincott-Schwartz, “Applying systems-level spectral imaging and analysis to reveal the organelle interactome,” Nature 546(7656), 162–167 (2017).
[Crossref] [PubMed]

Li, C.

L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516(7529), 74–77 (2014).
[Crossref] [PubMed]

Li, W.

Z. Zhang, S. J. Kenny, M. Hauser, W. Li, and K. Xu, “Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy,” Nat. Methods 12(10), 935–938 (2015).
[Crossref] [PubMed]

Liang, J.

L. Zhu, Y. Chen, J. Liang, Q. Xu, L. Gao, C. Ma, and L. V. Wang, “Space- and intensity-constrained reconstruction for compressed ultrafast photography,” Optica 3(7), 694–697 (2016).
[Crossref] [PubMed]

L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516(7529), 74–77 (2014).
[Crossref] [PubMed]

Lin, L.-J.

T. Huang, C. Phelps, J. Wang, L.-J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114(2), 301–310 (2018).
[Crossref] [PubMed]

Lin, X.

J. Wu, B. Xiong, X. Lin, J. He, J. Suo, and Q. Dai, “Snapshot hyperspectral volumetric microscopy,” Sci. Rep. 6(1), 24624 (2016).
[Crossref] [PubMed]

Lin, Y.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
[Crossref] [PubMed]

Lippincott-Schwartz, J.

A. M. Valm, S. Cohen, W. R. Legant, J. Melunis, U. Hershberg, E. Wait, A. R. Cohen, M. W. Davidson, E. Betzig, and J. Lippincott-Schwartz, “Applying systems-level spectral imaging and analysis to reveal the organelle interactome,” Nature 546(7656), 162–167 (2017).
[Crossref] [PubMed]

Llull, P.

X. Yuan, T. Tsai, R. Zhu, P. Llull, D. Brady, and L. Carin, “Compressive hyperspectral imaging with side information,” IEEE J. of Selected Topics in Sig. Process. 9(6), 964–976 (2015).

Long, J. J.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
[Crossref] [PubMed]

Lynch, R.

Ma, C.

McMillan, P. J.

McNamara, G.

Y. Garini, I. T. Young, and G. McNamara, “Spectral imaging: principles and applications,” Cytometry A 69(8), 735–747 (2006).
[Crossref] [PubMed]

Melunis, J.

A. M. Valm, S. Cohen, W. R. Legant, J. Melunis, U. Hershberg, E. Wait, A. R. Cohen, M. W. Davidson, E. Betzig, and J. Lippincott-Schwartz, “Applying systems-level spectral imaging and analysis to reveal the organelle interactome,” Nature 546(7656), 162–167 (2017).
[Crossref] [PubMed]

Mildenhall, B.

Mlodzianoski, M. J.

M. J. Mlodzianoski, N. M. Curthoys, M. S. Gunewardene, S. Carter, and S. T. Hess, “Super-resolution imaging of molecular emission spectra and single molecule spectral fluctuations,” PLoS One 11(3), e0147506 (2016).
[Crossref] [PubMed]

Mothes, W.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
[Crossref] [PubMed]

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]

Myers, J. R.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
[Crossref] [PubMed]

Nan, X.

T. Huang, C. Phelps, J. Wang, L.-J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114(2), 301–310 (2018).
[Crossref] [PubMed]

Ng, R.

Nguyen, T.-Q.

B. Dong, L. Almassalha, B. E. Urban, T.-Q. Nguyen, S. Khuon, T.-L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7(1), 12290 (2016).
[Crossref] [PubMed]

Oliver, T.

Olivo-Marin, J.-C.

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J.-C. Olivo-Marin, and J. Zerubia, “Richardson-Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution,” Microsc. Res. Tech. 69(4), 260–266 (2006).
[Crossref] [PubMed]

Pessino, V.

B. Yang, Y. Wang, S. Feng, V. Pessino, N. Stuurman, and B. Huang, “High numerical aperture epi-illumination selective plane illumination microscopy,” bioRxiv 1, 273359 (2018).

Phelps, C.

T. Huang, C. Phelps, J. Wang, L.-J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114(2), 301–310 (2018).
[Crossref] [PubMed]

Rivera-Molina, F. E.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
[Crossref] [PubMed]

Roux, P.

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J.-C. Olivo-Marin, and J. Zerubia, “Richardson-Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution,” Microsc. Res. Tech. 69(4), 260–266 (2006).
[Crossref] [PubMed]

Schmid, B.

W. Jahr, B. Schmid, C. Schmied, F. O. Fahrbach, and J. Huisken, “Hyperspectral light sheet microscopy,” Nat. Commun. 6(1), 7990 (2015).
[Crossref] [PubMed]

Schmied, C.

W. Jahr, B. Schmid, C. Schmied, F. O. Fahrbach, and J. Huisken, “Hyperspectral light sheet microscopy,” Nat. Commun. 6(1), 7990 (2015).
[Crossref] [PubMed]

Schulz, T. J.

Scott, Z.

T. Huang, C. Phelps, J. Wang, L.-J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114(2), 301–310 (2018).
[Crossref] [PubMed]

Smith, R. T.

L. Gao and R. T. Smith, “Optical hyperspectral imaging in microscopy and spectroscopy - a review of data acquisition,” J. Biophotonics 8(6), 441–456 (2015).
[Crossref] [PubMed]

Smith, Z. J.

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]

Stuurman, N.

B. Yang, Y. Wang, S. Feng, V. Pessino, N. Stuurman, and B. Huang, “High numerical aperture epi-illumination selective plane illumination microscopy,” bioRxiv 1, 273359 (2018).

Sun, C.

B. Dong, L. Almassalha, B. E. Urban, T.-Q. Nguyen, S. Khuon, T.-L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7(1), 12290 (2016).
[Crossref] [PubMed]

Suo, J.

J. Wu, B. Xiong, X. Lin, J. He, J. Suo, and Q. Dai, “Snapshot hyperspectral volumetric microscopy,” Sci. Rep. 6(1), 24624 (2016).
[Crossref] [PubMed]

Toomre, D.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
[Crossref] [PubMed]

Trinh, L. A.

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[Crossref] [PubMed]

Trivedi, V.

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[Crossref] [PubMed]

Tsai, T.

X. Yuan, T. Tsai, R. Zhu, P. Llull, D. Brady, and L. Carin, “Compressive hyperspectral imaging with side information,” IEEE J. of Selected Topics in Sig. Process. 9(6), 964–976 (2015).

Uchil, P. D.

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
[Crossref] [PubMed]

Urban, B. E.

B. Dong, L. Almassalha, B. E. Urban, T.-Q. Nguyen, S. Khuon, T.-L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7(1), 12290 (2016).
[Crossref] [PubMed]

Valm, A. M.

A. M. Valm, S. Cohen, W. R. Legant, J. Melunis, U. Hershberg, E. Wait, A. R. Cohen, M. W. Davidson, E. Betzig, and J. Lippincott-Schwartz, “Applying systems-level spectral imaging and analysis to reveal the organelle interactome,” Nature 546(7656), 162–167 (2017).
[Crossref] [PubMed]

Wachsmann-Hogiu, S.

Wait, E.

A. M. Valm, S. Cohen, W. R. Legant, J. Melunis, U. Hershberg, E. Wait, A. R. Cohen, M. W. Davidson, E. Betzig, and J. Lippincott-Schwartz, “Applying systems-level spectral imaging and analysis to reveal the organelle interactome,” Nature 546(7656), 162–167 (2017).
[Crossref] [PubMed]

Waller, L.

Wang, J.

T. Huang, C. Phelps, J. Wang, L.-J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114(2), 301–310 (2018).
[Crossref] [PubMed]

Wang, L. V.

L. Zhu, Y. Chen, J. Liang, Q. Xu, L. Gao, C. Ma, and L. V. Wang, “Space- and intensity-constrained reconstruction for compressed ultrafast photography,” Optica 3(7), 694–697 (2016).
[Crossref] [PubMed]

L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516(7529), 74–77 (2014).
[Crossref] [PubMed]

Wang, W.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

Wang, Y.

B. Yang, Y. Wang, S. Feng, V. Pessino, N. Stuurman, and B. Huang, “High numerical aperture epi-illumination selective plane illumination microscopy,” bioRxiv 1, 273359 (2018).

Willett, R. M.

Wu, J.

J. Wu, B. Xiong, X. Lin, J. He, J. Suo, and Q. Dai, “Snapshot hyperspectral volumetric microscopy,” Sci. Rep. 6(1), 24624 (2016).
[Crossref] [PubMed]

Xiong, B.

J. Wu, B. Xiong, X. Lin, J. He, J. Suo, and Q. Dai, “Snapshot hyperspectral volumetric microscopy,” Sci. Rep. 6(1), 24624 (2016).
[Crossref] [PubMed]

Xu, K.

Z. Zhang, S. J. Kenny, M. Hauser, W. Li, and K. Xu, “Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy,” Nat. Methods 12(10), 935–938 (2015).
[Crossref] [PubMed]

Xu, Q.

Yang, B.

B. Yang, Y. Wang, S. Feng, V. Pessino, N. Stuurman, and B. Huang, “High numerical aperture epi-illumination selective plane illumination microscopy,” bioRxiv 1, 273359 (2018).

Yin, J.

Young, I. T.

Y. Garini, I. T. Young, and G. McNamara, “Spectral imaging: principles and applications,” Cytometry A 69(8), 735–747 (2006).
[Crossref] [PubMed]

Yuan, X.

X. Yuan, T. Tsai, R. Zhu, P. Llull, D. Brady, and L. Carin, “Compressive hyperspectral imaging with side information,” IEEE J. of Selected Topics in Sig. Process. 9(6), 964–976 (2015).

Zerubia, J.

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J.-C. Olivo-Marin, and J. Zerubia, “Richardson-Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution,” Microsc. Res. Tech. 69(4), 260–266 (2006).
[Crossref] [PubMed]

Zhang, H. F.

B. Dong, L. Almassalha, B. E. Urban, T.-Q. Nguyen, S. Khuon, T.-L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7(1), 12290 (2016).
[Crossref] [PubMed]

Zhang, Z.

Z. Zhang, S. J. Kenny, M. Hauser, W. Li, and K. Xu, “Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy,” Nat. Methods 12(10), 935–938 (2015).
[Crossref] [PubMed]

Zhu, L.

Zhu, R.

X. Yuan, T. Tsai, R. Zhu, P. Llull, D. Brady, and L. Carin, “Compressive hyperspectral imaging with side information,” IEEE J. of Selected Topics in Sig. Process. 9(6), 964–976 (2015).

Zhuang, X.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

Zimmer, C.

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J.-C. Olivo-Marin, and J. Zerubia, “Richardson-Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution,” Microsc. Res. Tech. 69(4), 260–266 (2006).
[Crossref] [PubMed]

Zitová, B.

B. Zitová and J. Flusser, “Image registration methods: a survey,” Image Vis. Comput. 21(11), 977–1000 (2003).
[Crossref]

Appl. Opt. (1)

Biophys. J. (1)

T. Huang, C. Phelps, J. Wang, L.-J. Lin, A. Bittel, Z. Scott, S. Jacques, S. L. Gibbs, J. W. Gray, and X. Nan, “Simultaneous multicolor single-molecule tracking with single-laser excitation via spectral imaging,” Biophys. J. 114(2), 301–310 (2018).
[Crossref] [PubMed]

bioRxiv (1)

B. Yang, Y. Wang, S. Feng, V. Pessino, N. Stuurman, and B. Huang, “High numerical aperture epi-illumination selective plane illumination microscopy,” bioRxiv 1, 273359 (2018).

Cytometry A (1)

Y. Garini, I. T. Young, and G. McNamara, “Spectral imaging: principles and applications,” Cytometry A 69(8), 735–747 (2006).
[Crossref] [PubMed]

IEEE J. of Selected Topics in Sig. Process. (1)

X. Yuan, T. Tsai, R. Zhu, P. Llull, D. Brady, and L. Carin, “Compressive hyperspectral imaging with side information,” IEEE J. of Selected Topics in Sig. Process. 9(6), 964–976 (2015).

IEEE Trans. Image Process. (1)

J. M. Bioucas-Dias and M. A. T. Figueiredo, “A new TwIST: two-step iterative shrinkage/thresholding algorithms for image restoration,” IEEE Trans. Image Process. 16(12), 2992–3004 (2007).
[Crossref] [PubMed]

Image Vis. Comput. (1)

B. Zitová and J. Flusser, “Image registration methods: a survey,” Image Vis. Comput. 21(11), 977–1000 (2003).
[Crossref]

J. Biophotonics (1)

L. Gao and R. T. Smith, “Optical hyperspectral imaging in microscopy and spectroscopy - a review of data acquisition,” J. Biophotonics 8(6), 441–456 (2015).
[Crossref] [PubMed]

Microsc. Res. Tech. (1)

N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. Kam, J.-C. Olivo-Marin, and J. Zerubia, “Richardson-Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution,” Microsc. Res. Tech. 69(4), 260–266 (2006).
[Crossref] [PubMed]

Nat. Commun. (2)

W. Jahr, B. Schmid, C. Schmied, F. O. Fahrbach, and J. Huisken, “Hyperspectral light sheet microscopy,” Nat. Commun. 6(1), 7990 (2015).
[Crossref] [PubMed]

B. Dong, L. Almassalha, B. E. Urban, T.-Q. Nguyen, S. Khuon, T.-L. Chew, V. Backman, C. Sun, and H. F. Zhang, “Super-resolution spectroscopic microscopy via photon localization,” Nat. Commun. 7(1), 12290 (2016).
[Crossref] [PubMed]

Nat. Methods (3)

F. Huang, T. M. P. Hartwich, F. E. Rivera-Molina, Y. Lin, W. C. Duim, J. J. Long, P. D. Uchil, J. R. Myers, M. A. Baird, W. Mothes, M. W. Davidson, D. Toomre, and J. Bewersdorf, “Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms,” Nat. Methods 10(7), 653–658 (2013).
[Crossref] [PubMed]

Z. Zhang, S. J. Kenny, M. Hauser, W. Li, and K. Xu, “Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy,” Nat. Methods 12(10), 935–938 (2015).
[Crossref] [PubMed]

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[Crossref] [PubMed]

Nature (2)

A. M. Valm, S. Cohen, W. R. Legant, J. Melunis, U. Hershberg, E. Wait, A. R. Cohen, M. W. Davidson, E. Betzig, and J. Lippincott-Schwartz, “Applying systems-level spectral imaging and analysis to reveal the organelle interactome,” Nature 546(7656), 162–167 (2017).
[Crossref] [PubMed]

L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516(7529), 74–77 (2014).
[Crossref] [PubMed]

Opt. Express (3)

Optica (2)

PLoS One (1)

M. J. Mlodzianoski, N. M. Curthoys, M. S. Gunewardene, S. Carter, and S. T. Hess, “Super-resolution imaging of molecular emission spectra and single molecule spectral fluctuations,” PLoS One 11(3), e0147506 (2016).
[Crossref] [PubMed]

Proc. Natl. Acad. Sci. U.S.A. (1)

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]

Sci. Rep. (1)

J. Wu, B. Xiong, X. Lin, J. He, J. Suo, and Q. Dai, “Snapshot hyperspectral volumetric microscopy,” Sci. Rep. 6(1), 24624 (2016).
[Crossref] [PubMed]

Science (1)

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

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Figures (4)

Fig. 1
Fig. 1 Space-constrained computational spectral imaging detection system. (a) Schematic of the setup. The emitting light from the sample is split evenly by a beam splitter to generate an undispersed spatial image (Path 1) and a dispersed spectral image (Path 2) respectively on the left and right parts of the same camera. L, lens. (b) Illustration of overall space-constrained computational spectral imaging approach using green and red fluorescent beads. (c) Registered spatial (blue) and spectral (red) images of fluorescent beads at different wavelength. Scale bar: 1 µm. (d) Measured lateral spatial shift and its corresponding polynomial fitting. The measurement is averaged from 5 independent experiments, with a negligible standard deviation.
Fig. 2
Fig. 2 Simulated results of two-color imaging using space-constrained computational spectral imaging. (a, b) “Ground truth” microtubule and mitochondria images. Image size: 128 × 128 pixels. (c) The normalized emission spectrum of EGFP and EYFP, showing the ~20 nm emission peak separation and the filter passing band. (d, e) Simulated spatial (d) and spectral (e) images by assuming that microtubule and mitochondria are label by EGFP and EYFP respectively. (f,g) Representative reconstructed results from (d) and (e) showing clean signal separation. Average signal level and background were 1000 and 300. (h) The dependence of EGFP-EYFP reconstruction root mean square error (RMSE) of our method on average signal level when there is no background. (i) The dependence of EGFP-EYFP reconstruction RMSE on SBR. The signal level was 1000. (j) The normalized emission spectrum of tdTomato and mCherry and the filter passing band. (k,l) The dependence of tdTomato-mCheery reconstruction RMSE on signal level and SBR.
Fig. 3
Fig. 3 Experimental results of snapshot two-color imaging using space-constrained computational spectral imaging. Images shown here are BSC-1 cells expressing mCherry-Vimentin-C-18 and tdTomato-Clathrin-15. (a, b) Experimental images from spatial and spectral image paths. Scale bar: 1 µm. (c) Emission spectrum of mCherry and tdTomato, the orange shaded area shows the region of detection filter used in our system. (d) Calibrated emission from single-color imaging experiments. (e, f) Reconstructed images for tdTomato-clathrin (e) and mCherry-vimentin (f) respectively. (g) The intensity profile along the yellow line in (a,d,e), showing the algorithm successfully separates clathrin and vimentin structures.
Fig. 4
Fig. 4 Multi-color computational spectral imaging scheme. (a) Illustration of excitation scheme, in which a DMD is placed at the conjugate plane of the sample to generate random illumination. Representative simulated spatial (left) and spectral (right) images after adding a random illumination pattern to the ground truth were shown. (b) “Ground truth” microtubule, mitochondria and clathrin images. Image size: 64 x 64 pixels. (c) Representative reconstructed images of the three color channels. Average signal level and background was set to 1000 and 300 respectively. The number of illumination patterns is 5. (d) Dependence of reconstruction RMSE on the number of snapshots and oversampling ratio (calculated by dividing measured number of pixels and reconstructed number of pixels).

Equations (6)

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y spatial = A spatial x=[ I 1 , I 2 ,, I K ]x,
y spectral_m = A spectral x.
y=Ax,
argmin{ 1 2 yAx 2 +βΨ( x ) },
Ψ( x )= k=1 K Δ i [ x( k ) ]+ Δ j [ x( k ) ] 2 ,
y=ADx,

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