Quantitative tomographic imaging of intermolecular FRET in small animals

Vivek Venugopal; Jin Chen; Margarida Barroso; Xavier Intes

doi:10.1364/BOE.3.003161

Quantitative tomographic imaging of intermolecular FRET in small animals

Vivek Venugopal, Jin Chen, Margarida Barroso, and Xavier Intes

Biomedical Optics Express
Vol. 3,
Issue 12,
pp. 3161-3175
(2012)
•doi: 10.1364/BOE.3.003161

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Vivek Venugopal, Jin Chen, Margarida Barroso, and Xavier Intes, "Quantitative tomographic imaging of intermolecular FRET in small animals," Biomed. Opt. Express 3, 3161-3175 (2012)

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Abstract

Forster resonance energy transfer (FRET) is a nonradiative transfer of energy between two fluorescent molecules (a donor and an acceptor) in nanometer range proximity. FRET imaging methods have been applied to proteomic studies and drug discovery applications based on intermolecular FRET efficiency measurements and stoichiometric measurements of FRET interaction as quantitative parameters of interest. Importantly, FRET provides information about biomolecular interactions at a molecular level, well beyond the diffraction limits of standard microscopy techniques. The application of FRET to small animal imaging will allow biomedical researchers to investigate physiological processes occurring at nanometer range in vivo as well as in situ. In this work a new method for the quantitative reconstruction of FRET measurements in small animals, incorporating a full-field tomographic acquisition system with a Monte Carlo based hierarchical reconstruction scheme, is described and validated in murine models. Our main objective is to estimate the relative concentration of two forms of donor species, i.e., a donor molecule involved in FRETing to an acceptor close by and a nonFRETing donor molecule.

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B. Huang, M. Bates, and X. Zhuang, “Super-resolution fluorescence microscopy,” Annu. Rev. Biochem. 78(1), 993–1016 (2009).
[Crossref] [PubMed]
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[Crossref] [PubMed]
E. A. Jares-Erijman and T. M. Jovin, “Imaging molecular interactions in living cells by FRET microscopy,” Curr. Opin. Chem. Biol. 10(5), 409–416 (2006).
[Crossref] [PubMed]
A. Miyawaki, J. Llopis, R. Heim, J. M. McCaffery, J. A. Adams, M. Ikura, and R. Y. Tsien, “Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin,” Nature 388(6645), 882–887 (1997).
[Crossref] [PubMed]
M. Mank, D. F. Reiff, N. Heim, M. W. Friedrich, A. Borst, and O. Griesbeck, “A FRET-based calcium biosensor with fast signal kinetics and high fluorescence change,” Biophys. J. 90(5), 1790–1796 (2006).
[Crossref] [PubMed]
H. Ueyama, M. Takagi, and S. Takenaka, “A novel potassium sensing in aqueous media with a synthetic oligonucleotide derivative. Fluorescence resonance energy transfer associated with Guanine quartet-potassium ion complex formation,” J. Am. Chem. Soc. 124(48), 14286–14287 (2002).
[Crossref] [PubMed]
T. Kuner and G. J. Augustine, “A genetically encoded ratiometric indicator for chloride: capturing chloride transients in cultured hippocampal neurons,” Neuron 27(3), 447–459 (2000).
[Crossref] [PubMed]
N. Mochizuki, S. Yamashita, K. Kurokawa, Y. Ohba, T. Nagai, A. Miyawaki, and M. Matsuda, “Spatio-temporal images of growth-factor-induced activation of Ras and Rap1,” Nature 411(6841), 1065–1068 (2001).
[Crossref] [PubMed]
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[Crossref] [PubMed]
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[Crossref] [PubMed]
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[Crossref] [PubMed]
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[Crossref]
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[Crossref] [PubMed]
J. McGinty, H. B. Taylor, L. Chen, L. Bugeon, J. R. Lamb, M. J. Dallman, and P. M. W. French, “In vivo fluorescence lifetime optical projection tomography,” Biomed. Opt. Express 2(5), 1340–1350 (2011).
[Crossref] [PubMed]
C. Vinegoni, C. Pitsouli, D. Razansky, N. Perrimon, and V. Ntziachristos, “In vivo imaging of Drosophila melanogaster pupae with mesoscopic fluorescence tomography,” Nat. Methods 5(1), 45–47 (2008).
[Crossref] [PubMed]
V. Ntziachristos, J. Ripoll, L. V. Wang, and R. Weissleder, “Looking and listening to light: the evolution of whole-body photonic imaging,” Nat. Biotechnol. 23(3), 313–320 (2005).
[Crossref] [PubMed]
V. Gaind, K. J. Webb, S. Kularatne, and C. A. Bouman, “Towards in vivo imaging of intramolecular fluorescence resonance energy transfer parameters,” J. Opt. Soc. Am. A 26(8), 1805–1813 (2009).
[Crossref] [PubMed]
V. Gaind, S. Kularatne, P. S. Low, and K. J. Webb, “Deep-tissue imaging of intramolecular fluorescence resonance energy-transfer parameters,” Opt. Lett. 35(9), 1314–1316 (2010).
[Crossref] [PubMed]
J. McGinty, D. W. Stuckey, V. Y. Soloviev, R. Laine, M. Wylezinska-Arridge, D. J. Wells, S. R. Arridge, P. M. W. French, J. V. Hajnal, and A. Sardini, “In vivo fluorescence lifetime tomography of a FRET probe expressed in mouse,” Biomed. Opt. Express 2(7), 1907–1917 (2011).
[Crossref] [PubMed]
A. K. Kenworthy and M. Edidin, “Distribution of a glycosylphosphatidylinositol-anchored protein at the apical surface of MDCK cells examined at a resolution of <100 A using imaging fluorescence resonance energy transfer,” J. Cell Biol. 142(1), 69–84 (1998).
[Crossref] [PubMed]
H. Wallrabe, Y. Chen, A. Periasamy, and M. Barroso, “Issues in confocal microscopy for quantitative FRET analysis,” Microsc. Res. Tech. 69(3), 196–206 (2006).
[Crossref] [PubMed]
S. Padilla-Parra, N. Audugé, M. Coppey-Moisan, and M. Tramier, “Quantitative FRET analysis by fast acquisition time domain FLIM at high spatial resolution in living cells,” Biophys. J. 95(6), 2976–2988 (2008).
[Crossref] [PubMed]
M. J. Niedre, R. H. de Kleine, E. Aikawa, D. G. Kirsch, R. Weissleder, and V. Ntziachristos, “Early photon tomography allows fluorescence detection of lung carcinomas and disease progression in mice in vivo,” Proc. Natl. Acad. Sci. U.S.A. 105(49), 19126–19131 (2008).
[Crossref] [PubMed]
J. Chen, V. Venugopal, and X. Intes, “Monte Carlo based method for fluorescence tomographic imaging with lifetime multiplexing using time gates,” Biomed. Opt. Express 2(4), 871–886 (2011).
[Crossref] [PubMed]
V. Venugopal, J. Chen, and X. Intes, “Development of an optical imaging platform for functional imaging of small animals using wide-field excitation,” Biomed. Opt. Express 1(1), 143–156 (2010).
[Crossref] [PubMed]
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[Crossref] [PubMed]
J. Chen, V. Venugopal, F. Lesage, and X. Intes, “Time-resolved diffuse optical tomography with patterned-light illumination and detection,” Opt. Lett. 35(13), 2121–2123 (2010).
[Crossref] [PubMed]
J. Chen and X. Intes, “Time-gated perturbation Monte Carlo for whole body functional imaging in small animals,” Opt. Express 17(22), 19566–19579 (2009).
[Crossref] [PubMed]
N. Valim, J. Brock, and M. Niedre, “Experimental measurement of time-dependent photon scatter for diffuse optical tomography,” J. Biomed. Opt. 15(6), 065006 (2010).
[Crossref] [PubMed]
A. H. Hielscher, R. E. Alcouffe, and R. L. Barbour, “Comparison of finite-difference transport and diffusion calculations for photon migration in homogeneous and heterogeneous tissues,” Phys. Med. Biol. 43(5), 1285–1302 (1998).
[Crossref] [PubMed]
K. M. Yoo, F. Liu, and R. R. Alfano, “When does the diffusion approximation fail to describe photon transport in random media?” Phys. Rev. Lett. 64(22), 2647–2650 (1990).
[Crossref] [PubMed]
J. Chen and X. Intes, “Mesh-based Monte Carlo method in time-domain widefield fluorescence molecular tomography,” J. Biomed. Opt. 17(10), 106009 (2012).
[Crossref]
S. R. Arridge and W. R. B. Lionheart, “Nonuniqueness in diffusion-based optical tomography,” Opt. Lett. 23(11), 882–884 (1998).
[Crossref] [PubMed]
A. Soubret, J. Ripoll, and V. Ntziachristos, “Accuracy of fluorescent tomography in the presence of heterogeneities: study of the normalized Born ratio,” IEEE Trans. Med. Imaging 24(10), 1377–1386 (2005).
[Crossref] [PubMed]
V. Ntziachristos and R. Weissleder, “Experimental three-dimensional fluorescence reconstruction of diffuse media by use of a normalized Born approximation,” Opt. Lett. 26(12), 893–895 (2001).
[Crossref] [PubMed]
P. J. Verveer, A. Squire, and P. I. Bastiaens, “Global analysis of fluorescence lifetime imaging microscopy data,” Biophys. J. 78(4), 2127–2137 (2000).
[Crossref] [PubMed]
N. A. Rahim, S. Pelet, R. D. Kamm, and P. T. C. So, “Methodological considerations for global analysis of cellular FLIM/FRET measurements,” J. Biomed. Opt. 17(2), 026013 (2012).
[Crossref] [PubMed]
R. Cubeddu, A. Pifferi, P. Taroni, A. Torricelli, and G. Valentini, “Time-resolved imaging on a realistic tissue phantom: μ(s)’ and μ(a) images versus time-integrated images,” Appl. Opt. 35(22), 4533–4540 (1996).
[Crossref] [PubMed]
J. Chen and X. Intes, “Comparison of Monte Carlo methods for fluorescence molecular tomography-computational efficiency,” Med. Phys. 38(10), 5788–5798 (2011).
[Crossref] [PubMed]
S. B. Raymond, D. A. Boas, B. J. Bacskai, and A. T. N. Kumar, “Lifetime-based tomographic multiplexing,” J. Biomed. Opt. 15(4), 046011 (2010).
[Crossref] [PubMed]
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[Crossref] [PubMed]
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A. Periasamy, H. Wallrabe, Y. Chen, and M. Barroso, “Quantitation of protein–protein interactions: confocal FRET microscopy,” in Biophysical Tools for Biologists, Volume Two, Vol. 89 of Methods in Cell Biology (Academic, 2008), pp. 569–598.
H. Li and Z. M. Qian, “Transferrin/transferrin receptor-mediated drug delivery,” Med. Res. Rev. 22(3), 225–250 (2002).
[Crossref] [PubMed]

2012 (2)

J. Chen and X. Intes, “Mesh-based Monte Carlo method in time-domain widefield fluorescence molecular tomography,” J. Biomed. Opt. 17(10), 106009 (2012).
[Crossref]

N. A. Rahim, S. Pelet, R. D. Kamm, and P. T. C. So, “Methodological considerations for global analysis of cellular FLIM/FRET measurements,” J. Biomed. Opt. 17(2), 026013 (2012).
[Crossref] [PubMed]

2011 (7)

J. Chen and X. Intes, “Comparison of Monte Carlo methods for fluorescence molecular tomography-computational efficiency,” Med. Phys. 38(10), 5788–5798 (2011).
[Crossref] [PubMed]

M. Y. Berezin, K. Guo, W. Akers, R. E. Northdurft, J. P. Culver, B. Teng, O. Vasalatiy, K. Barbacow, A. Gandjbakhche, G. L. Griffiths, and S. Achilefu, “Near-infrared fluorescence lifetime pH-sensitive probes,” Biophys. J. 100(8), 2063–2072 (2011).
[Crossref] [PubMed]

N. Gaborit, C. Larbouret, J. Vallaghe, F. Peyrusson, C. Bascoul-Mollevi, E. Crapez, D. Azria, T. Chardès, M.-A. Poul, G. Mathis, H. Bazin, and A. Pèlegrin, “Time-resolved fluorescence resonance energy transfer (TR-FRET) to analyze the disruption of EGFR/HER2 dimers: a new method to evaluate the efficiency of targeted therapy using monoclonal antibodies,” J. Biol. Chem. 286(13), 11337–11345 (2011).
[Crossref] [PubMed]

S. Kumar, D. Alibhai, A. Margineanu, R. Laine, G. Kennedy, J. McGinty, S. Warren, D. Kelly, Y. Alexandrov, I. Munro, C. Talbot, D. W. Stuckey, C. Kimberly, B. Viellerobe, F. Lacombe, E. W.-F. Lam, H. Taylor, M. J. Dallman, G. Stamp, E. J. Murray, F. Stuhmeier, A. Sardini, M. Katan, D. S. Elson, M. A. A. Neil, C. Dunsby, and P. M. W. French, “FLIM FRET technology for drug discovery: automated multiwell-plate high-content analysis, multiplexed readouts and application in situ,” ChemPhysChem 12(3), 609–626 (2011).
[Crossref] [PubMed]

J. Chen, V. Venugopal, and X. Intes, “Monte Carlo based method for fluorescence tomographic imaging with lifetime multiplexing using time gates,” Biomed. Opt. Express 2(4), 871–886 (2011).
[Crossref] [PubMed]

J. McGinty, H. B. Taylor, L. Chen, L. Bugeon, J. R. Lamb, M. J. Dallman, and P. M. W. French, “In vivo fluorescence lifetime optical projection tomography,” Biomed. Opt. Express 2(5), 1340–1350 (2011).
[Crossref] [PubMed]

J. McGinty, D. W. Stuckey, V. Y. Soloviev, R. Laine, M. Wylezinska-Arridge, D. J. Wells, S. R. Arridge, P. M. W. French, J. V. Hajnal, and A. Sardini, “In vivo fluorescence lifetime tomography of a FRET probe expressed in mouse,” Biomed. Opt. Express 2(7), 1907–1917 (2011).
[Crossref] [PubMed]

2010 (6)

V. Gaind, S. Kularatne, P. S. Low, and K. J. Webb, “Deep-tissue imaging of intramolecular fluorescence resonance energy-transfer parameters,” Opt. Lett. 35(9), 1314–1316 (2010).
[Crossref] [PubMed]

J. Chen, V. Venugopal, F. Lesage, and X. Intes, “Time-resolved diffuse optical tomography with patterned-light illumination and detection,” Opt. Lett. 35(13), 2121–2123 (2010).
[Crossref] [PubMed]

V. Venugopal, J. Chen, and X. Intes, “Development of an optical imaging platform for functional imaging of small animals using wide-field excitation,” Biomed. Opt. Express 1(1), 143–156 (2010).
[Crossref] [PubMed]

S. B. Raymond, D. A. Boas, B. J. Bacskai, and A. T. N. Kumar, “Lifetime-based tomographic multiplexing,” J. Biomed. Opt. 15(4), 046011 (2010).
[Crossref] [PubMed]

S. Bélanger, M. Abran, X. Intes, C. Casanova, and F. Lesage, “Real-time diffuse optical tomography based on structured illumination,” J. Biomed. Opt. 15(1), 016006 (2010).
[Crossref] [PubMed]

N. Valim, J. Brock, and M. Niedre, “Experimental measurement of time-dependent photon scatter for diffuse optical tomography,” J. Biomed. Opt. 15(6), 065006 (2010).
[Crossref] [PubMed]

2009 (3)

B. Huang, M. Bates, and X. Zhuang, “Super-resolution fluorescence microscopy,” Annu. Rev. Biochem. 78(1), 993–1016 (2009).
[Crossref] [PubMed]

V. Gaind, K. J. Webb, S. Kularatne, and C. A. Bouman, “Towards in vivo imaging of intramolecular fluorescence resonance energy transfer parameters,” J. Opt. Soc. Am. A 26(8), 1805–1813 (2009).
[Crossref] [PubMed]

J. Chen and X. Intes, “Time-gated perturbation Monte Carlo for whole body functional imaging in small animals,” Opt. Express 17(22), 19566–19579 (2009).
[Crossref] [PubMed]

2008 (6)

J. R. Lakowicz and B. R. Masters, “Principles of fluorescence spectroscopy, third edition,” J. Biomed. Opt. 13(2), 029901 (2008).
[Crossref]

T. Nishioka, K. Aoki, K. Hikake, H. Yoshizaki, E. Kiyokawa, and M. Matsuda, “Rapid turnover rate of phosphoinositides at the front of migrating MDCK cells,” Mol. Biol. Cell 19(10), 4213–4223 (2008).
[Crossref] [PubMed]

B. Breart, F. Lemaître, S. Celli, and P. Bousso, “Two-photon imaging of intratumoral CD8+ T cell cytotoxic activity during adoptive T cell therapy in mice,” J. Clin. Invest. 118(4), 1390–1397 (2008).
[Crossref] [PubMed]

C. Vinegoni, C. Pitsouli, D. Razansky, N. Perrimon, and V. Ntziachristos, “In vivo imaging of Drosophila melanogaster pupae with mesoscopic fluorescence tomography,” Nat. Methods 5(1), 45–47 (2008).
[Crossref] [PubMed]

S. Padilla-Parra, N. Audugé, M. Coppey-Moisan, and M. Tramier, “Quantitative FRET analysis by fast acquisition time domain FLIM at high spatial resolution in living cells,” Biophys. J. 95(6), 2976–2988 (2008).
[Crossref] [PubMed]

M. J. Niedre, R. H. de Kleine, E. Aikawa, D. G. Kirsch, R. Weissleder, and V. Ntziachristos, “Early photon tomography allows fluorescence detection of lung carcinomas and disease progression in mice in vivo,” Proc. Natl. Acad. Sci. U.S.A. 105(49), 19126–19131 (2008).
[Crossref] [PubMed]

2006 (5)

H. Wallrabe, Y. Chen, A. Periasamy, and M. Barroso, “Issues in confocal microscopy for quantitative FRET analysis,” Microsc. Res. Tech. 69(3), 196–206 (2006).
[Crossref] [PubMed]

I. T. Li, E. Pham, and K. Truong, “Protein biosensors based on the principle of fluorescence resonance energy transfer for monitoring cellular dynamics,” Biotechnol. Lett. 28(24), 1971–1982 (2006).
[Crossref] [PubMed]

E. A. Jares-Erijman and T. M. Jovin, “Imaging molecular interactions in living cells by FRET microscopy,” Curr. Opin. Chem. Biol. 10(5), 409–416 (2006).
[Crossref] [PubMed]

M. Mank, D. F. Reiff, N. Heim, M. W. Friedrich, A. Borst, and O. Griesbeck, “A FRET-based calcium biosensor with fast signal kinetics and high fluorescence change,” Biophys. J. 90(5), 1790–1796 (2006).
[Crossref] [PubMed]

A. Nezu, A. Tanimura, T. Morita, A. Shitara, and Y. Tojyo, “A novel fluorescent method employing the FRET-based biosensor “LIBRA” for the identification of ligands of the inositol 1,4,5-trisphosphate receptors,” Biochim. Biophys. Acta 1760(8), 1274–1280 (2006).
[Crossref] [PubMed]

2005 (3)

H. Wallrabe and A. Periasamy, “Imaging protein molecules using FRET and FLIM microscopy,” Curr. Opin. Biotechnol. 16(1), 19–27 (2005).
[Crossref] [PubMed]

V. Ntziachristos, J. Ripoll, L. V. Wang, and R. Weissleder, “Looking and listening to light: the evolution of whole-body photonic imaging,” Nat. Biotechnol. 23(3), 313–320 (2005).
[Crossref] [PubMed]

A. Soubret, J. Ripoll, and V. Ntziachristos, “Accuracy of fluorescent tomography in the presence of heterogeneities: study of the normalized Born ratio,” IEEE Trans. Med. Imaging 24(10), 1377–1386 (2005).
[Crossref] [PubMed]

2002 (2)

H. Li and Z. M. Qian, “Transferrin/transferrin receptor-mediated drug delivery,” Med. Res. Rev. 22(3), 225–250 (2002).
[Crossref] [PubMed]

H. Ueyama, M. Takagi, and S. Takenaka, “A novel potassium sensing in aqueous media with a synthetic oligonucleotide derivative. Fluorescence resonance energy transfer associated with Guanine quartet-potassium ion complex formation,” J. Am. Chem. Soc. 124(48), 14286–14287 (2002).
[Crossref] [PubMed]

2001 (2)

N. Mochizuki, S. Yamashita, K. Kurokawa, Y. Ohba, T. Nagai, A. Miyawaki, and M. Matsuda, “Spatio-temporal images of growth-factor-induced activation of Ras and Rap1,” Nature 411(6841), 1065–1068 (2001).
[Crossref] [PubMed]

V. Ntziachristos and R. Weissleder, “Experimental three-dimensional fluorescence reconstruction of diffuse media by use of a normalized Born approximation,” Opt. Lett. 26(12), 893–895 (2001).
[Crossref] [PubMed]

2000 (2)

P. J. Verveer, A. Squire, and P. I. Bastiaens, “Global analysis of fluorescence lifetime imaging microscopy data,” Biophys. J. 78(4), 2127–2137 (2000).
[Crossref] [PubMed]

T. Kuner and G. J. Augustine, “A genetically encoded ratiometric indicator for chloride: capturing chloride transients in cultured hippocampal neurons,” Neuron 27(3), 447–459 (2000).
[Crossref] [PubMed]

1998 (3)

A. K. Kenworthy and M. Edidin, “Distribution of a glycosylphosphatidylinositol-anchored protein at the apical surface of MDCK cells examined at a resolution of <100 A using imaging fluorescence resonance energy transfer,” J. Cell Biol. 142(1), 69–84 (1998).
[Crossref] [PubMed]

A. H. Hielscher, R. E. Alcouffe, and R. L. Barbour, “Comparison of finite-difference transport and diffusion calculations for photon migration in homogeneous and heterogeneous tissues,” Phys. Med. Biol. 43(5), 1285–1302 (1998).
[Crossref] [PubMed]

S. R. Arridge and W. R. B. Lionheart, “Nonuniqueness in diffusion-based optical tomography,” Opt. Lett. 23(11), 882–884 (1998).
[Crossref] [PubMed]

1997 (1)

A. Miyawaki, J. Llopis, R. Heim, J. M. McCaffery, J. A. Adams, M. Ikura, and R. Y. Tsien, “Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin,” Nature 388(6645), 882–887 (1997).
[Crossref] [PubMed]

1996 (1)

R. Cubeddu, A. Pifferi, P. Taroni, A. Torricelli, and G. Valentini, “Time-resolved imaging on a realistic tissue phantom: μ(s)’ and μ(a) images versus time-integrated images,” Appl. Opt. 35(22), 4533–4540 (1996).
[Crossref] [PubMed]

1990 (1)

K. M. Yoo, F. Liu, and R. R. Alfano, “When does the diffusion approximation fail to describe photon transport in random media?” Phys. Rev. Lett. 64(22), 2647–2650 (1990).
[Crossref] [PubMed]

1978 (1)

L. Stryer, “Fluorescence energy transfer as a spectroscopic ruler,” Annu. Rev. Biochem. 47(1), 819–846 (1978).
[Crossref] [PubMed]

Abran, M.

S. Bélanger, M. Abran, X. Intes, C. Casanova, and F. Lesage, “Real-time diffuse optical tomography based on structured illumination,” J. Biomed. Opt. 15(1), 016006 (2010).
[Crossref] [PubMed]

Achilefu, S.

Adams, J. A.

Aikawa, E.

Akers, W.

Alcouffe, R. E.

Alexandrov, Y.

Alfano, R. R.

K. M. Yoo, F. Liu, and R. R. Alfano, “When does the diffusion approximation fail to describe photon transport in random media?” Phys. Rev. Lett. 64(22), 2647–2650 (1990).
[Crossref] [PubMed]

Alibhai, D.

Aoki, K.

Arridge, S. R.

S. R. Arridge and W. R. B. Lionheart, “Nonuniqueness in diffusion-based optical tomography,” Opt. Lett. 23(11), 882–884 (1998).
[Crossref] [PubMed]

Audugé, N.

Augustine, G. J.

Azria, D.

Bacskai, B. J.

S. B. Raymond, D. A. Boas, B. J. Bacskai, and A. T. N. Kumar, “Lifetime-based tomographic multiplexing,” J. Biomed. Opt. 15(4), 046011 (2010).
[Crossref] [PubMed]

Barbacow, K.

Barbour, R. L.

Barroso, M.

H. Wallrabe, Y. Chen, A. Periasamy, and M. Barroso, “Issues in confocal microscopy for quantitative FRET analysis,” Microsc. Res. Tech. 69(3), 196–206 (2006).
[Crossref] [PubMed]

Bascoul-Mollevi, C.

Bastiaens, P. I.

P. J. Verveer, A. Squire, and P. I. Bastiaens, “Global analysis of fluorescence lifetime imaging microscopy data,” Biophys. J. 78(4), 2127–2137 (2000).
[Crossref] [PubMed]

Bates, M.

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J. Chen and X. Intes, “Comparison of Monte Carlo methods for fluorescence molecular tomography-computational efficiency,” Med. Phys. 38(10), 5788–5798 (2011).
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H. Wallrabe, Y. Chen, A. Periasamy, and M. Barroso, “Issues in confocal microscopy for quantitative FRET analysis,” Microsc. Res. Tech. 69(3), 196–206 (2006).
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J. Chen and X. Intes, “Mesh-based Monte Carlo method in time-domain widefield fluorescence molecular tomography,” J. Biomed. Opt. 17(10), 106009 (2012).
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J. Chen and X. Intes, “Comparison of Monte Carlo methods for fluorescence molecular tomography-computational efficiency,” Med. Phys. 38(10), 5788–5798 (2011).
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Annu. Rev. Biochem. (2)

B. Huang, M. Bates, and X. Zhuang, “Super-resolution fluorescence microscopy,” Annu. Rev. Biochem. 78(1), 993–1016 (2009).
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Appl. Opt. (1)

Biochim. Biophys. Acta (1)

Biomed. Opt. Express (4)

Biophys. J. (4)

P. J. Verveer, A. Squire, and P. I. Bastiaens, “Global analysis of fluorescence lifetime imaging microscopy data,” Biophys. J. 78(4), 2127–2137 (2000).
[Crossref] [PubMed]

Biotechnol. Lett. (1)

ChemPhysChem (1)

Curr. Opin. Biotechnol. (1)

H. Wallrabe and A. Periasamy, “Imaging protein molecules using FRET and FLIM microscopy,” Curr. Opin. Biotechnol. 16(1), 19–27 (2005).
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Curr. Opin. Chem. Biol. (1)

E. A. Jares-Erijman and T. M. Jovin, “Imaging molecular interactions in living cells by FRET microscopy,” Curr. Opin. Chem. Biol. 10(5), 409–416 (2006).
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IEEE Trans. Med. Imaging (1)

J. Am. Chem. Soc. (1)

J. Biol. Chem. (1)

J. Biomed. Opt. (6)

S. B. Raymond, D. A. Boas, B. J. Bacskai, and A. T. N. Kumar, “Lifetime-based tomographic multiplexing,” J. Biomed. Opt. 15(4), 046011 (2010).
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J. Clin. Invest. (1)

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J. Chen and X. Intes, “Comparison of Monte Carlo methods for fluorescence molecular tomography-computational efficiency,” Med. Phys. 38(10), 5788–5798 (2011).
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H. Wallrabe, Y. Chen, A. Periasamy, and M. Barroso, “Issues in confocal microscopy for quantitative FRET analysis,” Microsc. Res. Tech. 69(3), 196–206 (2006).
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Mol. Biol. Cell (1)

Nat. Biotechnol. (1)

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Nature (2)

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Supplementary Material (1)

» Media 1: AVI (4636 KB)

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Fig. 1

a, Schematic of the tomographic imaging platform. b, Excerpt from video showing imaging protocol for wide-field time-resolved tomography (Media 1) c, Hierarchical reconstruction scheme flowchart.

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Fig. 2

NIR FRET pair. a, Fluorescence spectra of the Alexa Fluor 700 (donor) and Alexa Fluor 750 (acceptor) dyes. b, Temporal measurements acquired upon direct imaging of multiple mixtures of acceptor and donor fluorophores in varying ratios. c, Fraction of FRETing donor molecules in multiple mixtures with varying Acceptor:Donor (A:D) ratios.

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Fig. 3

a, Design of murine phantom with four inclusions carrying mixtures with different acceptor to donor ratios (Red- 1:4, Green-1:2, Cyan-2:1 and Blue-4:1). The orange boundary indicates the area of full-field excitation. b, An example of the normalized temporal measurements acquired at detectors directly above the four inclusions when excited by a full-field excitation pattern. c, Histogram of the value of shorter lifetime (FRETing donor) component for all detectors above signal threshold for all excitation patterns.

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Fig. 4

a, 50% iso volume of total reconstructed fluorescence yield. b, Reconstructed quantum yield of the shorter component thresholded at 50% of maximum value at the slice at depth of 11 mm. c, Quantitative comparison of tomographic estimates of FRETing donor fraction from above reconstruction.

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Fig. 5

a, 3D rendering of the CT images of the mouse model showing the location of two capillary tubes carrying donor acceptor mixtures with A:D ratio of 1:4 (green) and 4:1 (blue). The black border represents the registered field of view on the optical imaging platform. b, An example of the temporal measurements acquired at detectors directly above the four inclusions when excited by a full-field excitation pattern. c, Histogram of the value of shorter lifetime (FRETing donor) component for all detectors above signal threshold for all excitation patterns.

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Fig. 6

a, 50% iso-volumes of total reconstructed donor quantum yield. b, The relative reconstructed quantum yield of the shorter component thresholded at 50% of maximum value overlaid on the corresponding slice from the CT volume. c, Quantitative comparison of tomographic estimates of FRETing donor fraction from above reconstruction.

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Equations (5)

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η (r) = \frac{μ_{a f}^{x} (r) ϕ}{μ_{a}^{x} (r)}

W^{f l u o} (t) = \int_{0}^{t} d t' W^{a} (t') e^{- (t - t') / τ}

Φ = \frac{M_{i}^{m} (t)}{M_{i}^{x}} = \frac{α}{U_{i}^{x}} [\int d^{3} r W_{i}^{F R E T} (t) η^{F R E T} + \int d^{3} r W_{i}^{n o n F R E T} (t) η^{n o n F R E T}]

[\begin{matrix} Φ_{1} \\ ⋮ \\ Φ_{K} \end{matrix}] = [\begin{matrix} β_{1} W_{1, 1}^{F R E T} & \dots & β_{1} W_{1, J}^{F R E T} & β_{1} W_{1, 1,}^{n o n F R E T} & \dots & β_{1} W_{1, J}^{n o n F R E T} \\ ⋮ & ⋱ & ⋮ & ⋮ & ⋱ & ⋮ \\ β_{K} W_{K, 1}^{F R E T} & \dots & β_{K} W_{K, J}^{F R E T} & β_{K} W_{K, 1}^{n o n F R E T} & \dots & β_{K} W_{K, J}^{n o n F R E T} \end{matrix}] [\begin{matrix} η_{1}^{F R E T} \\ ⋮ \\ η_{J}^{F R E T} \\ η_{1}^{n o n F R E T} \\ ⋮ \\ η_{J}^{n o n F R E T} \end{matrix}]

Γ_{e m} (t) = I R F (t) * (N + A_{F R E T} e^{- t / τ_{F R E T}} + A_{n o n F R E T} e^{- t / τ_{n o n F R E T}})