Abstract

We have developed a spectral inversion method for three-dimensional tomography of far-red and near-infrared fluorescent proteins in animals. The method was developed in particular to address the steep light absorption transition of hemoglobin from the visible to the far-red occurring around 600 nm. Using an orthotopic mouse model of brain tumors expressing the red-shifted fluorescent protein mCherry, we demonstrate significant improvements in imaging accuracy over single-wavelength whole body reconstructions. Furthermore, we show an improvement in sensitivity of at least an order of magnitude over green fluorescent protein (GFP) for whole body imaging. We discuss how additional sensitivity gains are expected with the use of further red-shifted fluorescent proteins and we explain the differences and potential advantages of this approach over two-dimensional planar imaging methods.

© 2011 OSA

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  1. B. N. G. Giepmans, S. R. Adams, M. H. Ellisman, and R. Y. Tsien, “The fluorescent toolbox for assessing protein location and function,” Science 312(5771), 217–224 (2006).
    [CrossRef] [PubMed]
  2. R. Weissleder and M. J. Pittet, “Imaging in the era of molecular oncology,” Nature 452(7187), 580–589 (2008).
    [CrossRef] [PubMed]
  3. R. K. Jain, L. L. Munn, and D. Fukumura, “Dissecting tumour pathophysiology using intravital microscopy,” Nat. Rev. Cancer 2(4), 266–276 (2002).
    [CrossRef] [PubMed]
  4. F. Helmchen and W. Denk, “Deep tissue two-photon microscopy,” Nat. Methods 2(12), 932–940 (2005).
    [CrossRef] [PubMed]
  5. M. Yang, E. Baranov, P. Jiang, F. X. Sun, X. M. Li, L. N. Li, S. Hasegawa, M. Bouvet, M. Al-Tuwaijri, T. Chishima, H. Shimada, A. R. Moossa, S. Penman, and R. M. Hoffman, “Whole-body optical imaging of green fluorescent protein-expressing tumors and metastases,” Proc. Natl. Acad. Sci. U.S.A. 97(3), 1206–1211 (2000).
    [CrossRef] [PubMed]
  6. H. Kishimoto, T. Kojima, Y. Watanabe, S. Kagawa, T. Fujiwara, F. Uno, F. Teraishi, S. Kyo, H. Mizuguchi, Y. Hashimoto, Y. Urata, N. Tanaka, and T. Fujiwara, “In vivo imaging of lymph node metastasis with telomerase-specific replication-selective adenovirus,” Nat. Med. 12(10), 1213–1219 (2006).
    [CrossRef] [PubMed]
  7. 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]
  8. N. C. Deliolanis, T. Lasser, D. Hyde, A. Soubret, J. Ripoll, and V. Ntziachristos, “Free-space fluorescence molecular tomography utilizing 360° geometry projections,” Opt. Lett. 32(4), 382–384 (2007).
    [CrossRef] [PubMed]
  9. C. Q. Li, G. S. Mitchell, J. Dutta, S. Ahn, R. M. Leahy, and S. R. Cherry, “A three-dimensional multispectral fluorescence optical tomography imaging system for small animals based on a conical mirror design,” Opt. Express 17(9), 7571–7585 (2009).
    [CrossRef] [PubMed]
  10. G. Zacharakis, H. Kambara, H. Shih, J. Ripoll, J. Grimm, Y. Saeki, R. Weissleder, and V. Ntziachristos, “Volumetric tomography of fluorescent proteins through small animals in vivo,” Proc. Natl. Acad. Sci. U.S.A. 102(51), 18252–18257 (2005).
    [CrossRef] [PubMed]
  11. I. V. Turchin, V. I. Plehanov, A. G. Orlova, V. A. Kamenskiy, M. S. Kleshnin, M. V. Shirmanova, N. M. Shakhova, I. V. Balalaeva, and A. P. Savitskiy, “Fluorescence diffuse tomography of small animals with DsRed2 fluorescent protein,” Laser Phys. 16(5), 741–746 (2006).
    [CrossRef]
  12. I. V. Turchin, V. A. Kamensky, V. I. Plehanov, A. G. Orlova, M. S. Kleshnin, I. I. Fiks, M. V. Shirmanova, I. G. Meerovich, L. R. Arslanbaeva, V. V. Jerdeva, and A. P. Savitsky, “Fluorescence diffuse tomography for detection of red fluorescent protein expressed tumors in small animals,” J. Biomed. Opt. 13(4), 041310 (2008).
    [CrossRef] [PubMed]
  13. R. E. Campbell, O. Tour, A. E. Palmer, P. A. Steinbach, G. S. Baird, D. A. Zacharias, and R. Y. Tsien, “A monomeric red fluorescent protein,” Proc. Natl. Acad. Sci. U.S.A. 99(12), 7877–7882 (2002).
    [CrossRef] [PubMed]
  14. N. C. Shaner, R. E. Campbell, P. A. Steinbach, B. N. G. Giepmans, A. E. Palmer, and R. Y. Tsien, “Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein,” Nat. Biotechnol. 22(12), 1567–1572 (2004).
    [CrossRef] [PubMed]
  15. L. Wang, W. C. Jackson, P. A. Steinbach, and R. Y. Tsien, “Evolution of new nonantibody proteins via iterative somatic hypermutation,” Proc. Natl. Acad. Sci. U.S.A. 101(48), 16745–16749 (2004).
    [CrossRef] [PubMed]
  16. D. Shcherbo, E. M. Merzlyak, T. V. Chepurnykh, A. F. Fradkov, G. V. Ermakova, E. A. Solovieva, K. A. Lukyanov, E. A. Bogdanova, A. G. Zaraisky, S. Lukyanov, and D. M. Chudakov, “Bright far-red fluorescent protein for whole-body imaging,” Nat. Methods 4(9), 741–746 (2007).
    [CrossRef] [PubMed]
  17. D. Shcherbo, C. S. Murphy, G. V. Ermakova, E. A. Solovieva, T. V. Chepurnykh, A. S. Shcheglov, V. V. Verkhusha, V. Z. Pletnev, K. L. Hazelwood, P. M. Roche, S. Lukyanov, A. G. Zaraisky, M. W. Davidson, and D. M. Chudakov, “Far-red fluorescent tags for protein imaging in living tissues,” Biochem. J. 418(3), 567–574 (2009).
    [CrossRef] [PubMed]
  18. K. S. Morozova, K. D. Piatkevich, T. J. Gould, J. H. Zhang, J. Bewersdorf, and V. V. Verkhusha, “Far-red fluorescent protein excitable with red lasers for flow cytometry and superresolution STED nanoscopy,” Biophys. J. 99(2), L13–L15 (2010).
    [CrossRef] [PubMed]
  19. D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
    [CrossRef] [PubMed]
  20. X. Shu, A. Royant, M. Z. Lin, T. A. Aguilera, V. Lev-Ram, P. A. Steinbach, and R. Y. Tsien, “Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome,” Science 324(5928), 804–807 (2009).
    [CrossRef] [PubMed]
  21. N. C. Deliolanis, R. Kasmieh, T. Wurdinger, B. A. Tannous, K. Shah, and V. Ntziachristos, “Performance of the red-shifted fluorescent proteins in deep-tissue molecular imaging applications,” J. Biomed. Opt. 13(4), 044008 (2008).
    [CrossRef] [PubMed]
  22. T. Lasser, A. Soubret, J. Ripoll, and V. Ntziachristos, “Surface Reconstruction for free-space 360 degrees fluorescence molecular tomography and the effects of animal motion,” IEEE Trans. Med. Imaging 27(2), 188–194 (2008).
    [CrossRef] [PubMed]
  23. M. Potmesil, “Generating octree models of 3d objects from their silhouettes in a sequence of images,” Comput. Vis. Graph. Image Process. 40(1), 1–29 (1987).
    [CrossRef]
  24. M. Sena-Esteves, J. C. Tebbets, S. Steffens, T. Crombleholme, and A. W. Flake, “Optimized large-scale production of high titer lentivirus vector pseudotypes,” J. Virol. Methods 122(2), 131–139 (2004).
    [CrossRef] [PubMed]
  25. T. Wurdinger, C. Badr, L. Pike, R. de Kleine, R. Weissleder, X. O. Breakefield, and B. A. Tannous, “A secreted luciferase for ex vivo monitoring of in vivo processes,” Nat. Methods 5(2), 171–173 (2008).
    [CrossRef] [PubMed]
  26. H. Du, R. C. A. Fuh, J. Z. Li, L. A. Corkan, and J. S. Lindsey, “PhotochemCAD: A computer-aided design and research tool in photochemistry,” Photochem. Photobiol. 68, 141–142 (1998).
  27. A. Ishimaru, Wave Propagation and Scattering in Random Media (IEEE Press, 1997).
  28. G. Alexandrakis, F. R. Rannou, and A. F. Chatziioannou, “Tomographic bioluminescence imaging by use of a combined optical-PET (OPET) system: a computer simulation feasibility study,” Phys. Med. Biol. 50(17), 4225–4241 (2005).
    [CrossRef] [PubMed]
  29. W. F. Cheong, S. A. Prahl, and A. J. Welch, “A review of the optical properties of biological tissues,” IEEE J. Quantum Electron. 26(12), 2166–2185 (1990).
    [CrossRef]
  30. M. J. Niedre, G. M. Turner, and V. Ntziachristos, “Time-resolved imaging of optical coefficients through murine chest cavities,” J. Biomed. Opt. 11(6), 064017 (2006).
    [CrossRef] [PubMed]
  31. S. A. Prahl, “Optical Properties Spectra,” (2001), retrieved http://omlc.ogi.edu/spectra/ .
  32. L. Lüdemann, B. Hamm, and C. Zimmer, “Pharmacokinetic analysis of glioma compartments with dynamic Gd-DTPA-enhanced magnetic resonance imaging,” Magn. Reson. Imaging 18(10), 1201–1214 (2000).
    [CrossRef] [PubMed]
  33. I. Georgakoudi, M. G. Muller, and M. S. Feld, “Intrinsic fluorescence spectroscopy of biological tissue,” in Fluorescence in Biomedicine, M. A. Mycek and B. Pogue, eds. (Marcel Decker, 2002), pp. 109–142.
  34. R. Weissleder and V. Ntziachristos, “Shedding light onto live molecular targets,” Nat. Med. 9(1), 123–128 (2003).
    [CrossRef] [PubMed]
  35. B. Brooksby, S. Srinivasan, S. D. Jiang, H. Dehghani, B. W. Pogue, K. D. Paulsen, J. Weaver, C. Kogel, and S. P. Poplack, “Spectral priors improve near-infrared diffuse tomography more than spatial priors,” Opt. Lett. 30(15), 1968–1970 (2005).
    [CrossRef] [PubMed]
  36. A. J. Chaudhari, F. Darvas, J. R. Bading, R. A. Moats, P. S. Conti, D. J. Smith, S. R. Cherry, and R. M. Leahy, “Hyperspectral and multispectral bioluminescence optical tomography for small animal imaging,” Phys. Med. Biol. 50(23), 5421–5441 (2005).
    [CrossRef] [PubMed]
  37. A. Corlu, T. Durduran, R. Choe, M. Schweiger, E. M. C. Hillman, S. R. Arridge, and A. G. Yodh, “Uniqueness and wavelength optimization in continuous-wave multispectral diffuse optical tomography,” Opt. Lett. 28(23), 2339–2341 (2003).
    [CrossRef] [PubMed]

2010

K. S. Morozova, K. D. Piatkevich, T. J. Gould, J. H. Zhang, J. Bewersdorf, and V. V. Verkhusha, “Far-red fluorescent protein excitable with red lasers for flow cytometry and superresolution STED nanoscopy,” Biophys. J. 99(2), L13–L15 (2010).
[CrossRef] [PubMed]

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

2009

X. Shu, A. Royant, M. Z. Lin, T. A. Aguilera, V. Lev-Ram, P. A. Steinbach, and R. Y. Tsien, “Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome,” Science 324(5928), 804–807 (2009).
[CrossRef] [PubMed]

D. Shcherbo, C. S. Murphy, G. V. Ermakova, E. A. Solovieva, T. V. Chepurnykh, A. S. Shcheglov, V. V. Verkhusha, V. Z. Pletnev, K. L. Hazelwood, P. M. Roche, S. Lukyanov, A. G. Zaraisky, M. W. Davidson, and D. M. Chudakov, “Far-red fluorescent tags for protein imaging in living tissues,” Biochem. J. 418(3), 567–574 (2009).
[CrossRef] [PubMed]

C. Q. Li, G. S. Mitchell, J. Dutta, S. Ahn, R. M. Leahy, and S. R. Cherry, “A three-dimensional multispectral fluorescence optical tomography imaging system for small animals based on a conical mirror design,” Opt. Express 17(9), 7571–7585 (2009).
[CrossRef] [PubMed]

2008

I. V. Turchin, V. A. Kamensky, V. I. Plehanov, A. G. Orlova, M. S. Kleshnin, I. I. Fiks, M. V. Shirmanova, I. G. Meerovich, L. R. Arslanbaeva, V. V. Jerdeva, and A. P. Savitsky, “Fluorescence diffuse tomography for detection of red fluorescent protein expressed tumors in small animals,” J. Biomed. Opt. 13(4), 041310 (2008).
[CrossRef] [PubMed]

R. Weissleder and M. J. Pittet, “Imaging in the era of molecular oncology,” Nature 452(7187), 580–589 (2008).
[CrossRef] [PubMed]

T. Wurdinger, C. Badr, L. Pike, R. de Kleine, R. Weissleder, X. O. Breakefield, and B. A. Tannous, “A secreted luciferase for ex vivo monitoring of in vivo processes,” Nat. Methods 5(2), 171–173 (2008).
[CrossRef] [PubMed]

N. C. Deliolanis, R. Kasmieh, T. Wurdinger, B. A. Tannous, K. Shah, and V. Ntziachristos, “Performance of the red-shifted fluorescent proteins in deep-tissue molecular imaging applications,” J. Biomed. Opt. 13(4), 044008 (2008).
[CrossRef] [PubMed]

T. Lasser, A. Soubret, J. Ripoll, and V. Ntziachristos, “Surface Reconstruction for free-space 360 degrees fluorescence molecular tomography and the effects of animal motion,” IEEE Trans. Med. Imaging 27(2), 188–194 (2008).
[CrossRef] [PubMed]

2007

N. C. Deliolanis, T. Lasser, D. Hyde, A. Soubret, J. Ripoll, and V. Ntziachristos, “Free-space fluorescence molecular tomography utilizing 360° geometry projections,” Opt. Lett. 32(4), 382–384 (2007).
[CrossRef] [PubMed]

D. Shcherbo, E. M. Merzlyak, T. V. Chepurnykh, A. F. Fradkov, G. V. Ermakova, E. A. Solovieva, K. A. Lukyanov, E. A. Bogdanova, A. G. Zaraisky, S. Lukyanov, and D. M. Chudakov, “Bright far-red fluorescent protein for whole-body imaging,” Nat. Methods 4(9), 741–746 (2007).
[CrossRef] [PubMed]

2006

I. V. Turchin, V. I. Plehanov, A. G. Orlova, V. A. Kamenskiy, M. S. Kleshnin, M. V. Shirmanova, N. M. Shakhova, I. V. Balalaeva, and A. P. Savitskiy, “Fluorescence diffuse tomography of small animals with DsRed2 fluorescent protein,” Laser Phys. 16(5), 741–746 (2006).
[CrossRef]

B. N. G. Giepmans, S. R. Adams, M. H. Ellisman, and R. Y. Tsien, “The fluorescent toolbox for assessing protein location and function,” Science 312(5771), 217–224 (2006).
[CrossRef] [PubMed]

H. Kishimoto, T. Kojima, Y. Watanabe, S. Kagawa, T. Fujiwara, F. Uno, F. Teraishi, S. Kyo, H. Mizuguchi, Y. Hashimoto, Y. Urata, N. Tanaka, and T. Fujiwara, “In vivo imaging of lymph node metastasis with telomerase-specific replication-selective adenovirus,” Nat. Med. 12(10), 1213–1219 (2006).
[CrossRef] [PubMed]

M. J. Niedre, G. M. Turner, and V. Ntziachristos, “Time-resolved imaging of optical coefficients through murine chest cavities,” J. Biomed. Opt. 11(6), 064017 (2006).
[CrossRef] [PubMed]

2005

G. Alexandrakis, F. R. Rannou, and A. F. Chatziioannou, “Tomographic bioluminescence imaging by use of a combined optical-PET (OPET) system: a computer simulation feasibility study,” Phys. Med. Biol. 50(17), 4225–4241 (2005).
[CrossRef] [PubMed]

B. Brooksby, S. Srinivasan, S. D. Jiang, H. Dehghani, B. W. Pogue, K. D. Paulsen, J. Weaver, C. Kogel, and S. P. Poplack, “Spectral priors improve near-infrared diffuse tomography more than spatial priors,” Opt. Lett. 30(15), 1968–1970 (2005).
[CrossRef] [PubMed]

A. J. Chaudhari, F. Darvas, J. R. Bading, R. A. Moats, P. S. Conti, D. J. Smith, S. R. Cherry, and R. M. Leahy, “Hyperspectral and multispectral bioluminescence optical tomography for small animal imaging,” Phys. Med. Biol. 50(23), 5421–5441 (2005).
[CrossRef] [PubMed]

F. Helmchen and W. Denk, “Deep tissue two-photon microscopy,” Nat. Methods 2(12), 932–940 (2005).
[CrossRef] [PubMed]

G. Zacharakis, H. Kambara, H. Shih, J. Ripoll, J. Grimm, Y. Saeki, R. Weissleder, and V. Ntziachristos, “Volumetric tomography of fluorescent proteins through small animals in vivo,” Proc. Natl. Acad. Sci. U.S.A. 102(51), 18252–18257 (2005).
[CrossRef] [PubMed]

2004

N. C. Shaner, R. E. Campbell, P. A. Steinbach, B. N. G. Giepmans, A. E. Palmer, and R. Y. Tsien, “Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein,” Nat. Biotechnol. 22(12), 1567–1572 (2004).
[CrossRef] [PubMed]

L. Wang, W. C. Jackson, P. A. Steinbach, and R. Y. Tsien, “Evolution of new nonantibody proteins via iterative somatic hypermutation,” Proc. Natl. Acad. Sci. U.S.A. 101(48), 16745–16749 (2004).
[CrossRef] [PubMed]

M. Sena-Esteves, J. C. Tebbets, S. Steffens, T. Crombleholme, and A. W. Flake, “Optimized large-scale production of high titer lentivirus vector pseudotypes,” J. Virol. Methods 122(2), 131–139 (2004).
[CrossRef] [PubMed]

2003

2002

R. E. Campbell, O. Tour, A. E. Palmer, P. A. Steinbach, G. S. Baird, D. A. Zacharias, and R. Y. Tsien, “A monomeric red fluorescent protein,” Proc. Natl. Acad. Sci. U.S.A. 99(12), 7877–7882 (2002).
[CrossRef] [PubMed]

R. K. Jain, L. L. Munn, and D. Fukumura, “Dissecting tumour pathophysiology using intravital microscopy,” Nat. Rev. Cancer 2(4), 266–276 (2002).
[CrossRef] [PubMed]

2001

2000

M. Yang, E. Baranov, P. Jiang, F. X. Sun, X. M. Li, L. N. Li, S. Hasegawa, M. Bouvet, M. Al-Tuwaijri, T. Chishima, H. Shimada, A. R. Moossa, S. Penman, and R. M. Hoffman, “Whole-body optical imaging of green fluorescent protein-expressing tumors and metastases,” Proc. Natl. Acad. Sci. U.S.A. 97(3), 1206–1211 (2000).
[CrossRef] [PubMed]

L. Lüdemann, B. Hamm, and C. Zimmer, “Pharmacokinetic analysis of glioma compartments with dynamic Gd-DTPA-enhanced magnetic resonance imaging,” Magn. Reson. Imaging 18(10), 1201–1214 (2000).
[CrossRef] [PubMed]

1998

H. Du, R. C. A. Fuh, J. Z. Li, L. A. Corkan, and J. S. Lindsey, “PhotochemCAD: A computer-aided design and research tool in photochemistry,” Photochem. Photobiol. 68, 141–142 (1998).

1990

W. F. Cheong, S. A. Prahl, and A. J. Welch, “A review of the optical properties of biological tissues,” IEEE J. Quantum Electron. 26(12), 2166–2185 (1990).
[CrossRef]

1987

M. Potmesil, “Generating octree models of 3d objects from their silhouettes in a sequence of images,” Comput. Vis. Graph. Image Process. 40(1), 1–29 (1987).
[CrossRef]

Adams, S. R.

B. N. G. Giepmans, S. R. Adams, M. H. Ellisman, and R. Y. Tsien, “The fluorescent toolbox for assessing protein location and function,” Science 312(5771), 217–224 (2006).
[CrossRef] [PubMed]

Aguilera, T. A.

X. Shu, A. Royant, M. Z. Lin, T. A. Aguilera, V. Lev-Ram, P. A. Steinbach, and R. Y. Tsien, “Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome,” Science 324(5928), 804–807 (2009).
[CrossRef] [PubMed]

Ahn, S.

Alexandrakis, G.

G. Alexandrakis, F. R. Rannou, and A. F. Chatziioannou, “Tomographic bioluminescence imaging by use of a combined optical-PET (OPET) system: a computer simulation feasibility study,” Phys. Med. Biol. 50(17), 4225–4241 (2005).
[CrossRef] [PubMed]

Al-Tuwaijri, M.

M. Yang, E. Baranov, P. Jiang, F. X. Sun, X. M. Li, L. N. Li, S. Hasegawa, M. Bouvet, M. Al-Tuwaijri, T. Chishima, H. Shimada, A. R. Moossa, S. Penman, and R. M. Hoffman, “Whole-body optical imaging of green fluorescent protein-expressing tumors and metastases,” Proc. Natl. Acad. Sci. U.S.A. 97(3), 1206–1211 (2000).
[CrossRef] [PubMed]

Arridge, S. R.

Arslanbaeva, L. R.

I. V. Turchin, V. A. Kamensky, V. I. Plehanov, A. G. Orlova, M. S. Kleshnin, I. I. Fiks, M. V. Shirmanova, I. G. Meerovich, L. R. Arslanbaeva, V. V. Jerdeva, and A. P. Savitsky, “Fluorescence diffuse tomography for detection of red fluorescent protein expressed tumors in small animals,” J. Biomed. Opt. 13(4), 041310 (2008).
[CrossRef] [PubMed]

Bading, J. R.

A. J. Chaudhari, F. Darvas, J. R. Bading, R. A. Moats, P. S. Conti, D. J. Smith, S. R. Cherry, and R. M. Leahy, “Hyperspectral and multispectral bioluminescence optical tomography for small animal imaging,” Phys. Med. Biol. 50(23), 5421–5441 (2005).
[CrossRef] [PubMed]

Badr, C.

T. Wurdinger, C. Badr, L. Pike, R. de Kleine, R. Weissleder, X. O. Breakefield, and B. A. Tannous, “A secreted luciferase for ex vivo monitoring of in vivo processes,” Nat. Methods 5(2), 171–173 (2008).
[CrossRef] [PubMed]

Baird, G. S.

R. E. Campbell, O. Tour, A. E. Palmer, P. A. Steinbach, G. S. Baird, D. A. Zacharias, and R. Y. Tsien, “A monomeric red fluorescent protein,” Proc. Natl. Acad. Sci. U.S.A. 99(12), 7877–7882 (2002).
[CrossRef] [PubMed]

Balalaeva, I. V.

I. V. Turchin, V. I. Plehanov, A. G. Orlova, V. A. Kamenskiy, M. S. Kleshnin, M. V. Shirmanova, N. M. Shakhova, I. V. Balalaeva, and A. P. Savitskiy, “Fluorescence diffuse tomography of small animals with DsRed2 fluorescent protein,” Laser Phys. 16(5), 741–746 (2006).
[CrossRef]

Baranov, E.

M. Yang, E. Baranov, P. Jiang, F. X. Sun, X. M. Li, L. N. Li, S. Hasegawa, M. Bouvet, M. Al-Tuwaijri, T. Chishima, H. Shimada, A. R. Moossa, S. Penman, and R. M. Hoffman, “Whole-body optical imaging of green fluorescent protein-expressing tumors and metastases,” Proc. Natl. Acad. Sci. U.S.A. 97(3), 1206–1211 (2000).
[CrossRef] [PubMed]

Bewersdorf, J.

K. S. Morozova, K. D. Piatkevich, T. J. Gould, J. H. Zhang, J. Bewersdorf, and V. V. Verkhusha, “Far-red fluorescent protein excitable with red lasers for flow cytometry and superresolution STED nanoscopy,” Biophys. J. 99(2), L13–L15 (2010).
[CrossRef] [PubMed]

Bogdanova, E. A.

D. Shcherbo, E. M. Merzlyak, T. V. Chepurnykh, A. F. Fradkov, G. V. Ermakova, E. A. Solovieva, K. A. Lukyanov, E. A. Bogdanova, A. G. Zaraisky, S. Lukyanov, and D. M. Chudakov, “Bright far-red fluorescent protein for whole-body imaging,” Nat. Methods 4(9), 741–746 (2007).
[CrossRef] [PubMed]

Bouvet, M.

M. Yang, E. Baranov, P. Jiang, F. X. Sun, X. M. Li, L. N. Li, S. Hasegawa, M. Bouvet, M. Al-Tuwaijri, T. Chishima, H. Shimada, A. R. Moossa, S. Penman, and R. M. Hoffman, “Whole-body optical imaging of green fluorescent protein-expressing tumors and metastases,” Proc. Natl. Acad. Sci. U.S.A. 97(3), 1206–1211 (2000).
[CrossRef] [PubMed]

Breakefield, X. O.

T. Wurdinger, C. Badr, L. Pike, R. de Kleine, R. Weissleder, X. O. Breakefield, and B. A. Tannous, “A secreted luciferase for ex vivo monitoring of in vivo processes,” Nat. Methods 5(2), 171–173 (2008).
[CrossRef] [PubMed]

Britanova, O. V.

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

Brooksby, B.

Campbell, R. E.

N. C. Shaner, R. E. Campbell, P. A. Steinbach, B. N. G. Giepmans, A. E. Palmer, and R. Y. Tsien, “Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein,” Nat. Biotechnol. 22(12), 1567–1572 (2004).
[CrossRef] [PubMed]

R. E. Campbell, O. Tour, A. E. Palmer, P. A. Steinbach, G. S. Baird, D. A. Zacharias, and R. Y. Tsien, “A monomeric red fluorescent protein,” Proc. Natl. Acad. Sci. U.S.A. 99(12), 7877–7882 (2002).
[CrossRef] [PubMed]

Chatziioannou, A. F.

G. Alexandrakis, F. R. Rannou, and A. F. Chatziioannou, “Tomographic bioluminescence imaging by use of a combined optical-PET (OPET) system: a computer simulation feasibility study,” Phys. Med. Biol. 50(17), 4225–4241 (2005).
[CrossRef] [PubMed]

Chaudhari, A. J.

A. J. Chaudhari, F. Darvas, J. R. Bading, R. A. Moats, P. S. Conti, D. J. Smith, S. R. Cherry, and R. M. Leahy, “Hyperspectral and multispectral bioluminescence optical tomography for small animal imaging,” Phys. Med. Biol. 50(23), 5421–5441 (2005).
[CrossRef] [PubMed]

Cheong, W. F.

W. F. Cheong, S. A. Prahl, and A. J. Welch, “A review of the optical properties of biological tissues,” IEEE J. Quantum Electron. 26(12), 2166–2185 (1990).
[CrossRef]

Chepurnykh, T. V.

D. Shcherbo, C. S. Murphy, G. V. Ermakova, E. A. Solovieva, T. V. Chepurnykh, A. S. Shcheglov, V. V. Verkhusha, V. Z. Pletnev, K. L. Hazelwood, P. M. Roche, S. Lukyanov, A. G. Zaraisky, M. W. Davidson, and D. M. Chudakov, “Far-red fluorescent tags for protein imaging in living tissues,” Biochem. J. 418(3), 567–574 (2009).
[CrossRef] [PubMed]

D. Shcherbo, E. M. Merzlyak, T. V. Chepurnykh, A. F. Fradkov, G. V. Ermakova, E. A. Solovieva, K. A. Lukyanov, E. A. Bogdanova, A. G. Zaraisky, S. Lukyanov, and D. M. Chudakov, “Bright far-red fluorescent protein for whole-body imaging,” Nat. Methods 4(9), 741–746 (2007).
[CrossRef] [PubMed]

Cherry, S. R.

C. Q. Li, G. S. Mitchell, J. Dutta, S. Ahn, R. M. Leahy, and S. R. Cherry, “A three-dimensional multispectral fluorescence optical tomography imaging system for small animals based on a conical mirror design,” Opt. Express 17(9), 7571–7585 (2009).
[CrossRef] [PubMed]

A. J. Chaudhari, F. Darvas, J. R. Bading, R. A. Moats, P. S. Conti, D. J. Smith, S. R. Cherry, and R. M. Leahy, “Hyperspectral and multispectral bioluminescence optical tomography for small animal imaging,” Phys. Med. Biol. 50(23), 5421–5441 (2005).
[CrossRef] [PubMed]

Chishima, T.

M. Yang, E. Baranov, P. Jiang, F. X. Sun, X. M. Li, L. N. Li, S. Hasegawa, M. Bouvet, M. Al-Tuwaijri, T. Chishima, H. Shimada, A. R. Moossa, S. Penman, and R. M. Hoffman, “Whole-body optical imaging of green fluorescent protein-expressing tumors and metastases,” Proc. Natl. Acad. Sci. U.S.A. 97(3), 1206–1211 (2000).
[CrossRef] [PubMed]

Choe, R.

Chudakov, D. M.

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

D. Shcherbo, C. S. Murphy, G. V. Ermakova, E. A. Solovieva, T. V. Chepurnykh, A. S. Shcheglov, V. V. Verkhusha, V. Z. Pletnev, K. L. Hazelwood, P. M. Roche, S. Lukyanov, A. G. Zaraisky, M. W. Davidson, and D. M. Chudakov, “Far-red fluorescent tags for protein imaging in living tissues,” Biochem. J. 418(3), 567–574 (2009).
[CrossRef] [PubMed]

D. Shcherbo, E. M. Merzlyak, T. V. Chepurnykh, A. F. Fradkov, G. V. Ermakova, E. A. Solovieva, K. A. Lukyanov, E. A. Bogdanova, A. G. Zaraisky, S. Lukyanov, and D. M. Chudakov, “Bright far-red fluorescent protein for whole-body imaging,” Nat. Methods 4(9), 741–746 (2007).
[CrossRef] [PubMed]

Conti, P. S.

A. J. Chaudhari, F. Darvas, J. R. Bading, R. A. Moats, P. S. Conti, D. J. Smith, S. R. Cherry, and R. M. Leahy, “Hyperspectral and multispectral bioluminescence optical tomography for small animal imaging,” Phys. Med. Biol. 50(23), 5421–5441 (2005).
[CrossRef] [PubMed]

Corkan, L. A.

H. Du, R. C. A. Fuh, J. Z. Li, L. A. Corkan, and J. S. Lindsey, “PhotochemCAD: A computer-aided design and research tool in photochemistry,” Photochem. Photobiol. 68, 141–142 (1998).

Corlu, A.

Crombleholme, T.

M. Sena-Esteves, J. C. Tebbets, S. Steffens, T. Crombleholme, and A. W. Flake, “Optimized large-scale production of high titer lentivirus vector pseudotypes,” J. Virol. Methods 122(2), 131–139 (2004).
[CrossRef] [PubMed]

Darvas, F.

A. J. Chaudhari, F. Darvas, J. R. Bading, R. A. Moats, P. S. Conti, D. J. Smith, S. R. Cherry, and R. M. Leahy, “Hyperspectral and multispectral bioluminescence optical tomography for small animal imaging,” Phys. Med. Biol. 50(23), 5421–5441 (2005).
[CrossRef] [PubMed]

Davidson, M. W.

D. Shcherbo, C. S. Murphy, G. V. Ermakova, E. A. Solovieva, T. V. Chepurnykh, A. S. Shcheglov, V. V. Verkhusha, V. Z. Pletnev, K. L. Hazelwood, P. M. Roche, S. Lukyanov, A. G. Zaraisky, M. W. Davidson, and D. M. Chudakov, “Far-red fluorescent tags for protein imaging in living tissues,” Biochem. J. 418(3), 567–574 (2009).
[CrossRef] [PubMed]

de Kleine, R.

T. Wurdinger, C. Badr, L. Pike, R. de Kleine, R. Weissleder, X. O. Breakefield, and B. A. Tannous, “A secreted luciferase for ex vivo monitoring of in vivo processes,” Nat. Methods 5(2), 171–173 (2008).
[CrossRef] [PubMed]

Dehghani, H.

Deliolanis, N. C.

N. C. Deliolanis, R. Kasmieh, T. Wurdinger, B. A. Tannous, K. Shah, and V. Ntziachristos, “Performance of the red-shifted fluorescent proteins in deep-tissue molecular imaging applications,” J. Biomed. Opt. 13(4), 044008 (2008).
[CrossRef] [PubMed]

N. C. Deliolanis, T. Lasser, D. Hyde, A. Soubret, J. Ripoll, and V. Ntziachristos, “Free-space fluorescence molecular tomography utilizing 360° geometry projections,” Opt. Lett. 32(4), 382–384 (2007).
[CrossRef] [PubMed]

Denk, W.

F. Helmchen and W. Denk, “Deep tissue two-photon microscopy,” Nat. Methods 2(12), 932–940 (2005).
[CrossRef] [PubMed]

Du, H.

H. Du, R. C. A. Fuh, J. Z. Li, L. A. Corkan, and J. S. Lindsey, “PhotochemCAD: A computer-aided design and research tool in photochemistry,” Photochem. Photobiol. 68, 141–142 (1998).

Durduran, T.

Dutta, J.

Ellisman, M. H.

B. N. G. Giepmans, S. R. Adams, M. H. Ellisman, and R. Y. Tsien, “The fluorescent toolbox for assessing protein location and function,” Science 312(5771), 217–224 (2006).
[CrossRef] [PubMed]

Ermakova, G. V.

D. Shcherbo, C. S. Murphy, G. V. Ermakova, E. A. Solovieva, T. V. Chepurnykh, A. S. Shcheglov, V. V. Verkhusha, V. Z. Pletnev, K. L. Hazelwood, P. M. Roche, S. Lukyanov, A. G. Zaraisky, M. W. Davidson, and D. M. Chudakov, “Far-red fluorescent tags for protein imaging in living tissues,” Biochem. J. 418(3), 567–574 (2009).
[CrossRef] [PubMed]

D. Shcherbo, E. M. Merzlyak, T. V. Chepurnykh, A. F. Fradkov, G. V. Ermakova, E. A. Solovieva, K. A. Lukyanov, E. A. Bogdanova, A. G. Zaraisky, S. Lukyanov, and D. M. Chudakov, “Bright far-red fluorescent protein for whole-body imaging,” Nat. Methods 4(9), 741–746 (2007).
[CrossRef] [PubMed]

Fiks, I. I.

I. V. Turchin, V. A. Kamensky, V. I. Plehanov, A. G. Orlova, M. S. Kleshnin, I. I. Fiks, M. V. Shirmanova, I. G. Meerovich, L. R. Arslanbaeva, V. V. Jerdeva, and A. P. Savitsky, “Fluorescence diffuse tomography for detection of red fluorescent protein expressed tumors in small animals,” J. Biomed. Opt. 13(4), 041310 (2008).
[CrossRef] [PubMed]

Flake, A. W.

M. Sena-Esteves, J. C. Tebbets, S. Steffens, T. Crombleholme, and A. W. Flake, “Optimized large-scale production of high titer lentivirus vector pseudotypes,” J. Virol. Methods 122(2), 131–139 (2004).
[CrossRef] [PubMed]

Fradkov, A. F.

D. Shcherbo, E. M. Merzlyak, T. V. Chepurnykh, A. F. Fradkov, G. V. Ermakova, E. A. Solovieva, K. A. Lukyanov, E. A. Bogdanova, A. G. Zaraisky, S. Lukyanov, and D. M. Chudakov, “Bright far-red fluorescent protein for whole-body imaging,” Nat. Methods 4(9), 741–746 (2007).
[CrossRef] [PubMed]

Fuh, R. C. A.

H. Du, R. C. A. Fuh, J. Z. Li, L. A. Corkan, and J. S. Lindsey, “PhotochemCAD: A computer-aided design and research tool in photochemistry,” Photochem. Photobiol. 68, 141–142 (1998).

Fujiwara, T.

H. Kishimoto, T. Kojima, Y. Watanabe, S. Kagawa, T. Fujiwara, F. Uno, F. Teraishi, S. Kyo, H. Mizuguchi, Y. Hashimoto, Y. Urata, N. Tanaka, and T. Fujiwara, “In vivo imaging of lymph node metastasis with telomerase-specific replication-selective adenovirus,” Nat. Med. 12(10), 1213–1219 (2006).
[CrossRef] [PubMed]

H. Kishimoto, T. Kojima, Y. Watanabe, S. Kagawa, T. Fujiwara, F. Uno, F. Teraishi, S. Kyo, H. Mizuguchi, Y. Hashimoto, Y. Urata, N. Tanaka, and T. Fujiwara, “In vivo imaging of lymph node metastasis with telomerase-specific replication-selective adenovirus,” Nat. Med. 12(10), 1213–1219 (2006).
[CrossRef] [PubMed]

Fukumura, D.

R. K. Jain, L. L. Munn, and D. Fukumura, “Dissecting tumour pathophysiology using intravital microscopy,” Nat. Rev. Cancer 2(4), 266–276 (2002).
[CrossRef] [PubMed]

Giepmans, B. N. G.

B. N. G. Giepmans, S. R. Adams, M. H. Ellisman, and R. Y. Tsien, “The fluorescent toolbox for assessing protein location and function,” Science 312(5771), 217–224 (2006).
[CrossRef] [PubMed]

N. C. Shaner, R. E. Campbell, P. A. Steinbach, B. N. G. Giepmans, A. E. Palmer, and R. Y. Tsien, “Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein,” Nat. Biotechnol. 22(12), 1567–1572 (2004).
[CrossRef] [PubMed]

Gorodnicheva, T. V.

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

Gould, T. J.

K. S. Morozova, K. D. Piatkevich, T. J. Gould, J. H. Zhang, J. Bewersdorf, and V. V. Verkhusha, “Far-red fluorescent protein excitable with red lasers for flow cytometry and superresolution STED nanoscopy,” Biophys. J. 99(2), L13–L15 (2010).
[CrossRef] [PubMed]

Grimm, J.

G. Zacharakis, H. Kambara, H. Shih, J. Ripoll, J. Grimm, Y. Saeki, R. Weissleder, and V. Ntziachristos, “Volumetric tomography of fluorescent proteins through small animals in vivo,” Proc. Natl. Acad. Sci. U.S.A. 102(51), 18252–18257 (2005).
[CrossRef] [PubMed]

Hamm, B.

L. Lüdemann, B. Hamm, and C. Zimmer, “Pharmacokinetic analysis of glioma compartments with dynamic Gd-DTPA-enhanced magnetic resonance imaging,” Magn. Reson. Imaging 18(10), 1201–1214 (2000).
[CrossRef] [PubMed]

Hasegawa, S.

M. Yang, E. Baranov, P. Jiang, F. X. Sun, X. M. Li, L. N. Li, S. Hasegawa, M. Bouvet, M. Al-Tuwaijri, T. Chishima, H. Shimada, A. R. Moossa, S. Penman, and R. M. Hoffman, “Whole-body optical imaging of green fluorescent protein-expressing tumors and metastases,” Proc. Natl. Acad. Sci. U.S.A. 97(3), 1206–1211 (2000).
[CrossRef] [PubMed]

Hashimoto, Y.

H. Kishimoto, T. Kojima, Y. Watanabe, S. Kagawa, T. Fujiwara, F. Uno, F. Teraishi, S. Kyo, H. Mizuguchi, Y. Hashimoto, Y. Urata, N. Tanaka, and T. Fujiwara, “In vivo imaging of lymph node metastasis with telomerase-specific replication-selective adenovirus,” Nat. Med. 12(10), 1213–1219 (2006).
[CrossRef] [PubMed]

Hazelwood, K. L.

D. Shcherbo, C. S. Murphy, G. V. Ermakova, E. A. Solovieva, T. V. Chepurnykh, A. S. Shcheglov, V. V. Verkhusha, V. Z. Pletnev, K. L. Hazelwood, P. M. Roche, S. Lukyanov, A. G. Zaraisky, M. W. Davidson, and D. M. Chudakov, “Far-red fluorescent tags for protein imaging in living tissues,” Biochem. J. 418(3), 567–574 (2009).
[CrossRef] [PubMed]

Helmchen, F.

F. Helmchen and W. Denk, “Deep tissue two-photon microscopy,” Nat. Methods 2(12), 932–940 (2005).
[CrossRef] [PubMed]

Hillman, E. M. C.

Hoffman, R. M.

M. Yang, E. Baranov, P. Jiang, F. X. Sun, X. M. Li, L. N. Li, S. Hasegawa, M. Bouvet, M. Al-Tuwaijri, T. Chishima, H. Shimada, A. R. Moossa, S. Penman, and R. M. Hoffman, “Whole-body optical imaging of green fluorescent protein-expressing tumors and metastases,” Proc. Natl. Acad. Sci. U.S.A. 97(3), 1206–1211 (2000).
[CrossRef] [PubMed]

Hyde, D.

Jackson, W. C.

L. Wang, W. C. Jackson, P. A. Steinbach, and R. Y. Tsien, “Evolution of new nonantibody proteins via iterative somatic hypermutation,” Proc. Natl. Acad. Sci. U.S.A. 101(48), 16745–16749 (2004).
[CrossRef] [PubMed]

Jain, R. K.

R. K. Jain, L. L. Munn, and D. Fukumura, “Dissecting tumour pathophysiology using intravital microscopy,” Nat. Rev. Cancer 2(4), 266–276 (2002).
[CrossRef] [PubMed]

Jerdeva, V. V.

I. V. Turchin, V. A. Kamensky, V. I. Plehanov, A. G. Orlova, M. S. Kleshnin, I. I. Fiks, M. V. Shirmanova, I. G. Meerovich, L. R. Arslanbaeva, V. V. Jerdeva, and A. P. Savitsky, “Fluorescence diffuse tomography for detection of red fluorescent protein expressed tumors in small animals,” J. Biomed. Opt. 13(4), 041310 (2008).
[CrossRef] [PubMed]

Jiang, P.

M. Yang, E. Baranov, P. Jiang, F. X. Sun, X. M. Li, L. N. Li, S. Hasegawa, M. Bouvet, M. Al-Tuwaijri, T. Chishima, H. Shimada, A. R. Moossa, S. Penman, and R. M. Hoffman, “Whole-body optical imaging of green fluorescent protein-expressing tumors and metastases,” Proc. Natl. Acad. Sci. U.S.A. 97(3), 1206–1211 (2000).
[CrossRef] [PubMed]

Jiang, S. D.

Kagawa, S.

H. Kishimoto, T. Kojima, Y. Watanabe, S. Kagawa, T. Fujiwara, F. Uno, F. Teraishi, S. Kyo, H. Mizuguchi, Y. Hashimoto, Y. Urata, N. Tanaka, and T. Fujiwara, “In vivo imaging of lymph node metastasis with telomerase-specific replication-selective adenovirus,” Nat. Med. 12(10), 1213–1219 (2006).
[CrossRef] [PubMed]

Kambara, H.

G. Zacharakis, H. Kambara, H. Shih, J. Ripoll, J. Grimm, Y. Saeki, R. Weissleder, and V. Ntziachristos, “Volumetric tomography of fluorescent proteins through small animals in vivo,” Proc. Natl. Acad. Sci. U.S.A. 102(51), 18252–18257 (2005).
[CrossRef] [PubMed]

Kamenskiy, V. A.

I. V. Turchin, V. I. Plehanov, A. G. Orlova, V. A. Kamenskiy, M. S. Kleshnin, M. V. Shirmanova, N. M. Shakhova, I. V. Balalaeva, and A. P. Savitskiy, “Fluorescence diffuse tomography of small animals with DsRed2 fluorescent protein,” Laser Phys. 16(5), 741–746 (2006).
[CrossRef]

Kamensky, V. A.

I. V. Turchin, V. A. Kamensky, V. I. Plehanov, A. G. Orlova, M. S. Kleshnin, I. I. Fiks, M. V. Shirmanova, I. G. Meerovich, L. R. Arslanbaeva, V. V. Jerdeva, and A. P. Savitsky, “Fluorescence diffuse tomography for detection of red fluorescent protein expressed tumors in small animals,” J. Biomed. Opt. 13(4), 041310 (2008).
[CrossRef] [PubMed]

Kasmieh, R.

N. C. Deliolanis, R. Kasmieh, T. Wurdinger, B. A. Tannous, K. Shah, and V. Ntziachristos, “Performance of the red-shifted fluorescent proteins in deep-tissue molecular imaging applications,” J. Biomed. Opt. 13(4), 044008 (2008).
[CrossRef] [PubMed]

Kishimoto, H.

H. Kishimoto, T. Kojima, Y. Watanabe, S. Kagawa, T. Fujiwara, F. Uno, F. Teraishi, S. Kyo, H. Mizuguchi, Y. Hashimoto, Y. Urata, N. Tanaka, and T. Fujiwara, “In vivo imaging of lymph node metastasis with telomerase-specific replication-selective adenovirus,” Nat. Med. 12(10), 1213–1219 (2006).
[CrossRef] [PubMed]

Kleshnin, M. S.

I. V. Turchin, V. A. Kamensky, V. I. Plehanov, A. G. Orlova, M. S. Kleshnin, I. I. Fiks, M. V. Shirmanova, I. G. Meerovich, L. R. Arslanbaeva, V. V. Jerdeva, and A. P. Savitsky, “Fluorescence diffuse tomography for detection of red fluorescent protein expressed tumors in small animals,” J. Biomed. Opt. 13(4), 041310 (2008).
[CrossRef] [PubMed]

I. V. Turchin, V. I. Plehanov, A. G. Orlova, V. A. Kamenskiy, M. S. Kleshnin, M. V. Shirmanova, N. M. Shakhova, I. V. Balalaeva, and A. P. Savitskiy, “Fluorescence diffuse tomography of small animals with DsRed2 fluorescent protein,” Laser Phys. 16(5), 741–746 (2006).
[CrossRef]

Kogel, C.

Kojima, T.

H. Kishimoto, T. Kojima, Y. Watanabe, S. Kagawa, T. Fujiwara, F. Uno, F. Teraishi, S. Kyo, H. Mizuguchi, Y. Hashimoto, Y. Urata, N. Tanaka, and T. Fujiwara, “In vivo imaging of lymph node metastasis with telomerase-specific replication-selective adenovirus,” Nat. Med. 12(10), 1213–1219 (2006).
[CrossRef] [PubMed]

Kyo, S.

H. Kishimoto, T. Kojima, Y. Watanabe, S. Kagawa, T. Fujiwara, F. Uno, F. Teraishi, S. Kyo, H. Mizuguchi, Y. Hashimoto, Y. Urata, N. Tanaka, and T. Fujiwara, “In vivo imaging of lymph node metastasis with telomerase-specific replication-selective adenovirus,” Nat. Med. 12(10), 1213–1219 (2006).
[CrossRef] [PubMed]

Lasser, T.

T. Lasser, A. Soubret, J. Ripoll, and V. Ntziachristos, “Surface Reconstruction for free-space 360 degrees fluorescence molecular tomography and the effects of animal motion,” IEEE Trans. Med. Imaging 27(2), 188–194 (2008).
[CrossRef] [PubMed]

N. C. Deliolanis, T. Lasser, D. Hyde, A. Soubret, J. Ripoll, and V. Ntziachristos, “Free-space fluorescence molecular tomography utilizing 360° geometry projections,” Opt. Lett. 32(4), 382–384 (2007).
[CrossRef] [PubMed]

Leahy, R. M.

C. Q. Li, G. S. Mitchell, J. Dutta, S. Ahn, R. M. Leahy, and S. R. Cherry, “A three-dimensional multispectral fluorescence optical tomography imaging system for small animals based on a conical mirror design,” Opt. Express 17(9), 7571–7585 (2009).
[CrossRef] [PubMed]

A. J. Chaudhari, F. Darvas, J. R. Bading, R. A. Moats, P. S. Conti, D. J. Smith, S. R. Cherry, and R. M. Leahy, “Hyperspectral and multispectral bioluminescence optical tomography for small animal imaging,” Phys. Med. Biol. 50(23), 5421–5441 (2005).
[CrossRef] [PubMed]

Lev-Ram, V.

X. Shu, A. Royant, M. Z. Lin, T. A. Aguilera, V. Lev-Ram, P. A. Steinbach, and R. Y. Tsien, “Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome,” Science 324(5928), 804–807 (2009).
[CrossRef] [PubMed]

Li, C. Q.

Li, J. Z.

H. Du, R. C. A. Fuh, J. Z. Li, L. A. Corkan, and J. S. Lindsey, “PhotochemCAD: A computer-aided design and research tool in photochemistry,” Photochem. Photobiol. 68, 141–142 (1998).

Li, L. N.

M. Yang, E. Baranov, P. Jiang, F. X. Sun, X. M. Li, L. N. Li, S. Hasegawa, M. Bouvet, M. Al-Tuwaijri, T. Chishima, H. Shimada, A. R. Moossa, S. Penman, and R. M. Hoffman, “Whole-body optical imaging of green fluorescent protein-expressing tumors and metastases,” Proc. Natl. Acad. Sci. U.S.A. 97(3), 1206–1211 (2000).
[CrossRef] [PubMed]

Li, X. M.

M. Yang, E. Baranov, P. Jiang, F. X. Sun, X. M. Li, L. N. Li, S. Hasegawa, M. Bouvet, M. Al-Tuwaijri, T. Chishima, H. Shimada, A. R. Moossa, S. Penman, and R. M. Hoffman, “Whole-body optical imaging of green fluorescent protein-expressing tumors and metastases,” Proc. Natl. Acad. Sci. U.S.A. 97(3), 1206–1211 (2000).
[CrossRef] [PubMed]

Lin, M. Z.

X. Shu, A. Royant, M. Z. Lin, T. A. Aguilera, V. Lev-Ram, P. A. Steinbach, and R. Y. Tsien, “Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome,” Science 324(5928), 804–807 (2009).
[CrossRef] [PubMed]

Lindsey, J. S.

H. Du, R. C. A. Fuh, J. Z. Li, L. A. Corkan, and J. S. Lindsey, “PhotochemCAD: A computer-aided design and research tool in photochemistry,” Photochem. Photobiol. 68, 141–142 (1998).

Loschenov, V. B.

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

Lüdemann, L.

L. Lüdemann, B. Hamm, and C. Zimmer, “Pharmacokinetic analysis of glioma compartments with dynamic Gd-DTPA-enhanced magnetic resonance imaging,” Magn. Reson. Imaging 18(10), 1201–1214 (2000).
[CrossRef] [PubMed]

Luker, G. D.

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

Luker, K. E.

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

Lukyanov, K. A.

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

D. Shcherbo, E. M. Merzlyak, T. V. Chepurnykh, A. F. Fradkov, G. V. Ermakova, E. A. Solovieva, K. A. Lukyanov, E. A. Bogdanova, A. G. Zaraisky, S. Lukyanov, and D. M. Chudakov, “Bright far-red fluorescent protein for whole-body imaging,” Nat. Methods 4(9), 741–746 (2007).
[CrossRef] [PubMed]

Lukyanov, S.

D. Shcherbo, C. S. Murphy, G. V. Ermakova, E. A. Solovieva, T. V. Chepurnykh, A. S. Shcheglov, V. V. Verkhusha, V. Z. Pletnev, K. L. Hazelwood, P. M. Roche, S. Lukyanov, A. G. Zaraisky, M. W. Davidson, and D. M. Chudakov, “Far-red fluorescent tags for protein imaging in living tissues,” Biochem. J. 418(3), 567–574 (2009).
[CrossRef] [PubMed]

D. Shcherbo, E. M. Merzlyak, T. V. Chepurnykh, A. F. Fradkov, G. V. Ermakova, E. A. Solovieva, K. A. Lukyanov, E. A. Bogdanova, A. G. Zaraisky, S. Lukyanov, and D. M. Chudakov, “Bright far-red fluorescent protein for whole-body imaging,” Nat. Methods 4(9), 741–746 (2007).
[CrossRef] [PubMed]

Meerovich, I. G.

I. V. Turchin, V. A. Kamensky, V. I. Plehanov, A. G. Orlova, M. S. Kleshnin, I. I. Fiks, M. V. Shirmanova, I. G. Meerovich, L. R. Arslanbaeva, V. V. Jerdeva, and A. P. Savitsky, “Fluorescence diffuse tomography for detection of red fluorescent protein expressed tumors in small animals,” J. Biomed. Opt. 13(4), 041310 (2008).
[CrossRef] [PubMed]

Merzlyak, E. M.

D. Shcherbo, E. M. Merzlyak, T. V. Chepurnykh, A. F. Fradkov, G. V. Ermakova, E. A. Solovieva, K. A. Lukyanov, E. A. Bogdanova, A. G. Zaraisky, S. Lukyanov, and D. M. Chudakov, “Bright far-red fluorescent protein for whole-body imaging,” Nat. Methods 4(9), 741–746 (2007).
[CrossRef] [PubMed]

Mitchell, G. S.

Mizuguchi, H.

H. Kishimoto, T. Kojima, Y. Watanabe, S. Kagawa, T. Fujiwara, F. Uno, F. Teraishi, S. Kyo, H. Mizuguchi, Y. Hashimoto, Y. Urata, N. Tanaka, and T. Fujiwara, “In vivo imaging of lymph node metastasis with telomerase-specific replication-selective adenovirus,” Nat. Med. 12(10), 1213–1219 (2006).
[CrossRef] [PubMed]

Moats, R. A.

A. J. Chaudhari, F. Darvas, J. R. Bading, R. A. Moats, P. S. Conti, D. J. Smith, S. R. Cherry, and R. M. Leahy, “Hyperspectral and multispectral bioluminescence optical tomography for small animal imaging,” Phys. Med. Biol. 50(23), 5421–5441 (2005).
[CrossRef] [PubMed]

Moossa, A. R.

M. Yang, E. Baranov, P. Jiang, F. X. Sun, X. M. Li, L. N. Li, S. Hasegawa, M. Bouvet, M. Al-Tuwaijri, T. Chishima, H. Shimada, A. R. Moossa, S. Penman, and R. M. Hoffman, “Whole-body optical imaging of green fluorescent protein-expressing tumors and metastases,” Proc. Natl. Acad. Sci. U.S.A. 97(3), 1206–1211 (2000).
[CrossRef] [PubMed]

Morozova, K. S.

K. S. Morozova, K. D. Piatkevich, T. J. Gould, J. H. Zhang, J. Bewersdorf, and V. V. Verkhusha, “Far-red fluorescent protein excitable with red lasers for flow cytometry and superresolution STED nanoscopy,” Biophys. J. 99(2), L13–L15 (2010).
[CrossRef] [PubMed]

Munn, L. L.

R. K. Jain, L. L. Munn, and D. Fukumura, “Dissecting tumour pathophysiology using intravital microscopy,” Nat. Rev. Cancer 2(4), 266–276 (2002).
[CrossRef] [PubMed]

Murphy, C. S.

D. Shcherbo, C. S. Murphy, G. V. Ermakova, E. A. Solovieva, T. V. Chepurnykh, A. S. Shcheglov, V. V. Verkhusha, V. Z. Pletnev, K. L. Hazelwood, P. M. Roche, S. Lukyanov, A. G. Zaraisky, M. W. Davidson, and D. M. Chudakov, “Far-red fluorescent tags for protein imaging in living tissues,” Biochem. J. 418(3), 567–574 (2009).
[CrossRef] [PubMed]

Niedre, M. J.

M. J. Niedre, G. M. Turner, and V. Ntziachristos, “Time-resolved imaging of optical coefficients through murine chest cavities,” J. Biomed. Opt. 11(6), 064017 (2006).
[CrossRef] [PubMed]

Ntziachristos, V.

N. C. Deliolanis, R. Kasmieh, T. Wurdinger, B. A. Tannous, K. Shah, and V. Ntziachristos, “Performance of the red-shifted fluorescent proteins in deep-tissue molecular imaging applications,” J. Biomed. Opt. 13(4), 044008 (2008).
[CrossRef] [PubMed]

T. Lasser, A. Soubret, J. Ripoll, and V. Ntziachristos, “Surface Reconstruction for free-space 360 degrees fluorescence molecular tomography and the effects of animal motion,” IEEE Trans. Med. Imaging 27(2), 188–194 (2008).
[CrossRef] [PubMed]

N. C. Deliolanis, T. Lasser, D. Hyde, A. Soubret, J. Ripoll, and V. Ntziachristos, “Free-space fluorescence molecular tomography utilizing 360° geometry projections,” Opt. Lett. 32(4), 382–384 (2007).
[CrossRef] [PubMed]

M. J. Niedre, G. M. Turner, and V. Ntziachristos, “Time-resolved imaging of optical coefficients through murine chest cavities,” J. Biomed. Opt. 11(6), 064017 (2006).
[CrossRef] [PubMed]

G. Zacharakis, H. Kambara, H. Shih, J. Ripoll, J. Grimm, Y. Saeki, R. Weissleder, and V. Ntziachristos, “Volumetric tomography of fluorescent proteins through small animals in vivo,” Proc. Natl. Acad. Sci. U.S.A. 102(51), 18252–18257 (2005).
[CrossRef] [PubMed]

R. Weissleder and V. Ntziachristos, “Shedding light onto live molecular targets,” Nat. Med. 9(1), 123–128 (2003).
[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]

Orlova, A. G.

I. V. Turchin, V. A. Kamensky, V. I. Plehanov, A. G. Orlova, M. S. Kleshnin, I. I. Fiks, M. V. Shirmanova, I. G. Meerovich, L. R. Arslanbaeva, V. V. Jerdeva, and A. P. Savitsky, “Fluorescence diffuse tomography for detection of red fluorescent protein expressed tumors in small animals,” J. Biomed. Opt. 13(4), 041310 (2008).
[CrossRef] [PubMed]

I. V. Turchin, V. I. Plehanov, A. G. Orlova, V. A. Kamenskiy, M. S. Kleshnin, M. V. Shirmanova, N. M. Shakhova, I. V. Balalaeva, and A. P. Savitskiy, “Fluorescence diffuse tomography of small animals with DsRed2 fluorescent protein,” Laser Phys. 16(5), 741–746 (2006).
[CrossRef]

Palmer, A. E.

N. C. Shaner, R. E. Campbell, P. A. Steinbach, B. N. G. Giepmans, A. E. Palmer, and R. Y. Tsien, “Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein,” Nat. Biotechnol. 22(12), 1567–1572 (2004).
[CrossRef] [PubMed]

R. E. Campbell, O. Tour, A. E. Palmer, P. A. Steinbach, G. S. Baird, D. A. Zacharias, and R. Y. Tsien, “A monomeric red fluorescent protein,” Proc. Natl. Acad. Sci. U.S.A. 99(12), 7877–7882 (2002).
[CrossRef] [PubMed]

Paulsen, K. D.

Penman, S.

M. Yang, E. Baranov, P. Jiang, F. X. Sun, X. M. Li, L. N. Li, S. Hasegawa, M. Bouvet, M. Al-Tuwaijri, T. Chishima, H. Shimada, A. R. Moossa, S. Penman, and R. M. Hoffman, “Whole-body optical imaging of green fluorescent protein-expressing tumors and metastases,” Proc. Natl. Acad. Sci. U.S.A. 97(3), 1206–1211 (2000).
[CrossRef] [PubMed]

Piatkevich, K. D.

K. S. Morozova, K. D. Piatkevich, T. J. Gould, J. H. Zhang, J. Bewersdorf, and V. V. Verkhusha, “Far-red fluorescent protein excitable with red lasers for flow cytometry and superresolution STED nanoscopy,” Biophys. J. 99(2), L13–L15 (2010).
[CrossRef] [PubMed]

Pike, L.

T. Wurdinger, C. Badr, L. Pike, R. de Kleine, R. Weissleder, X. O. Breakefield, and B. A. Tannous, “A secreted luciferase for ex vivo monitoring of in vivo processes,” Nat. Methods 5(2), 171–173 (2008).
[CrossRef] [PubMed]

Pittet, M. J.

R. Weissleder and M. J. Pittet, “Imaging in the era of molecular oncology,” Nature 452(7187), 580–589 (2008).
[CrossRef] [PubMed]

Plehanov, V. I.

I. V. Turchin, V. A. Kamensky, V. I. Plehanov, A. G. Orlova, M. S. Kleshnin, I. I. Fiks, M. V. Shirmanova, I. G. Meerovich, L. R. Arslanbaeva, V. V. Jerdeva, and A. P. Savitsky, “Fluorescence diffuse tomography for detection of red fluorescent protein expressed tumors in small animals,” J. Biomed. Opt. 13(4), 041310 (2008).
[CrossRef] [PubMed]

I. V. Turchin, V. I. Plehanov, A. G. Orlova, V. A. Kamenskiy, M. S. Kleshnin, M. V. Shirmanova, N. M. Shakhova, I. V. Balalaeva, and A. P. Savitskiy, “Fluorescence diffuse tomography of small animals with DsRed2 fluorescent protein,” Laser Phys. 16(5), 741–746 (2006).
[CrossRef]

Pletnev, V. Z.

D. Shcherbo, C. S. Murphy, G. V. Ermakova, E. A. Solovieva, T. V. Chepurnykh, A. S. Shcheglov, V. V. Verkhusha, V. Z. Pletnev, K. L. Hazelwood, P. M. Roche, S. Lukyanov, A. G. Zaraisky, M. W. Davidson, and D. M. Chudakov, “Far-red fluorescent tags for protein imaging in living tissues,” Biochem. J. 418(3), 567–574 (2009).
[CrossRef] [PubMed]

Pogue, B. W.

Poplack, S. P.

Potmesil, M.

M. Potmesil, “Generating octree models of 3d objects from their silhouettes in a sequence of images,” Comput. Vis. Graph. Image Process. 40(1), 1–29 (1987).
[CrossRef]

Prahl, S. A.

W. F. Cheong, S. A. Prahl, and A. J. Welch, “A review of the optical properties of biological tissues,” IEEE J. Quantum Electron. 26(12), 2166–2185 (1990).
[CrossRef]

Rannou, F. R.

G. Alexandrakis, F. R. Rannou, and A. F. Chatziioannou, “Tomographic bioluminescence imaging by use of a combined optical-PET (OPET) system: a computer simulation feasibility study,” Phys. Med. Biol. 50(17), 4225–4241 (2005).
[CrossRef] [PubMed]

Ripoll, J.

T. Lasser, A. Soubret, J. Ripoll, and V. Ntziachristos, “Surface Reconstruction for free-space 360 degrees fluorescence molecular tomography and the effects of animal motion,” IEEE Trans. Med. Imaging 27(2), 188–194 (2008).
[CrossRef] [PubMed]

N. C. Deliolanis, T. Lasser, D. Hyde, A. Soubret, J. Ripoll, and V. Ntziachristos, “Free-space fluorescence molecular tomography utilizing 360° geometry projections,” Opt. Lett. 32(4), 382–384 (2007).
[CrossRef] [PubMed]

G. Zacharakis, H. Kambara, H. Shih, J. Ripoll, J. Grimm, Y. Saeki, R. Weissleder, and V. Ntziachristos, “Volumetric tomography of fluorescent proteins through small animals in vivo,” Proc. Natl. Acad. Sci. U.S.A. 102(51), 18252–18257 (2005).
[CrossRef] [PubMed]

Roche, P. M.

D. Shcherbo, C. S. Murphy, G. V. Ermakova, E. A. Solovieva, T. V. Chepurnykh, A. S. Shcheglov, V. V. Verkhusha, V. Z. Pletnev, K. L. Hazelwood, P. M. Roche, S. Lukyanov, A. G. Zaraisky, M. W. Davidson, and D. M. Chudakov, “Far-red fluorescent tags for protein imaging in living tissues,” Biochem. J. 418(3), 567–574 (2009).
[CrossRef] [PubMed]

Royant, A.

X. Shu, A. Royant, M. Z. Lin, T. A. Aguilera, V. Lev-Ram, P. A. Steinbach, and R. Y. Tsien, “Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome,” Science 324(5928), 804–807 (2009).
[CrossRef] [PubMed]

Ryabova, A. V.

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

Saeki, Y.

G. Zacharakis, H. Kambara, H. Shih, J. Ripoll, J. Grimm, Y. Saeki, R. Weissleder, and V. Ntziachristos, “Volumetric tomography of fluorescent proteins through small animals in vivo,” Proc. Natl. Acad. Sci. U.S.A. 102(51), 18252–18257 (2005).
[CrossRef] [PubMed]

Savitskiy, A. P.

I. V. Turchin, V. I. Plehanov, A. G. Orlova, V. A. Kamenskiy, M. S. Kleshnin, M. V. Shirmanova, N. M. Shakhova, I. V. Balalaeva, and A. P. Savitskiy, “Fluorescence diffuse tomography of small animals with DsRed2 fluorescent protein,” Laser Phys. 16(5), 741–746 (2006).
[CrossRef]

Savitsky, A. P.

I. V. Turchin, V. A. Kamensky, V. I. Plehanov, A. G. Orlova, M. S. Kleshnin, I. I. Fiks, M. V. Shirmanova, I. G. Meerovich, L. R. Arslanbaeva, V. V. Jerdeva, and A. P. Savitsky, “Fluorescence diffuse tomography for detection of red fluorescent protein expressed tumors in small animals,” J. Biomed. Opt. 13(4), 041310 (2008).
[CrossRef] [PubMed]

Schmidt, B. T.

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

Schweiger, M.

Sena-Esteves, M.

M. Sena-Esteves, J. C. Tebbets, S. Steffens, T. Crombleholme, and A. W. Flake, “Optimized large-scale production of high titer lentivirus vector pseudotypes,” J. Virol. Methods 122(2), 131–139 (2004).
[CrossRef] [PubMed]

Shah, K.

N. C. Deliolanis, R. Kasmieh, T. Wurdinger, B. A. Tannous, K. Shah, and V. Ntziachristos, “Performance of the red-shifted fluorescent proteins in deep-tissue molecular imaging applications,” J. Biomed. Opt. 13(4), 044008 (2008).
[CrossRef] [PubMed]

Shakhova, N. M.

I. V. Turchin, V. I. Plehanov, A. G. Orlova, V. A. Kamenskiy, M. S. Kleshnin, M. V. Shirmanova, N. M. Shakhova, I. V. Balalaeva, and A. P. Savitskiy, “Fluorescence diffuse tomography of small animals with DsRed2 fluorescent protein,” Laser Phys. 16(5), 741–746 (2006).
[CrossRef]

Shaner, N. C.

N. C. Shaner, R. E. Campbell, P. A. Steinbach, B. N. G. Giepmans, A. E. Palmer, and R. Y. Tsien, “Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein,” Nat. Biotechnol. 22(12), 1567–1572 (2004).
[CrossRef] [PubMed]

Shcheglov, A. S.

D. Shcherbo, C. S. Murphy, G. V. Ermakova, E. A. Solovieva, T. V. Chepurnykh, A. S. Shcheglov, V. V. Verkhusha, V. Z. Pletnev, K. L. Hazelwood, P. M. Roche, S. Lukyanov, A. G. Zaraisky, M. W. Davidson, and D. M. Chudakov, “Far-red fluorescent tags for protein imaging in living tissues,” Biochem. J. 418(3), 567–574 (2009).
[CrossRef] [PubMed]

Shcherbo, D.

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

D. Shcherbo, C. S. Murphy, G. V. Ermakova, E. A. Solovieva, T. V. Chepurnykh, A. S. Shcheglov, V. V. Verkhusha, V. Z. Pletnev, K. L. Hazelwood, P. M. Roche, S. Lukyanov, A. G. Zaraisky, M. W. Davidson, and D. M. Chudakov, “Far-red fluorescent tags for protein imaging in living tissues,” Biochem. J. 418(3), 567–574 (2009).
[CrossRef] [PubMed]

D. Shcherbo, E. M. Merzlyak, T. V. Chepurnykh, A. F. Fradkov, G. V. Ermakova, E. A. Solovieva, K. A. Lukyanov, E. A. Bogdanova, A. G. Zaraisky, S. Lukyanov, and D. M. Chudakov, “Bright far-red fluorescent protein for whole-body imaging,” Nat. Methods 4(9), 741–746 (2007).
[CrossRef] [PubMed]

Shemiakina, I. I.

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

Shidlovskiy, K. M.

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

Shih, H.

G. Zacharakis, H. Kambara, H. Shih, J. Ripoll, J. Grimm, Y. Saeki, R. Weissleder, and V. Ntziachristos, “Volumetric tomography of fluorescent proteins through small animals in vivo,” Proc. Natl. Acad. Sci. U.S.A. 102(51), 18252–18257 (2005).
[CrossRef] [PubMed]

Shimada, H.

M. Yang, E. Baranov, P. Jiang, F. X. Sun, X. M. Li, L. N. Li, S. Hasegawa, M. Bouvet, M. Al-Tuwaijri, T. Chishima, H. Shimada, A. R. Moossa, S. Penman, and R. M. Hoffman, “Whole-body optical imaging of green fluorescent protein-expressing tumors and metastases,” Proc. Natl. Acad. Sci. U.S.A. 97(3), 1206–1211 (2000).
[CrossRef] [PubMed]

Shirmanova, M. V.

I. V. Turchin, V. A. Kamensky, V. I. Plehanov, A. G. Orlova, M. S. Kleshnin, I. I. Fiks, M. V. Shirmanova, I. G. Meerovich, L. R. Arslanbaeva, V. V. Jerdeva, and A. P. Savitsky, “Fluorescence diffuse tomography for detection of red fluorescent protein expressed tumors in small animals,” J. Biomed. Opt. 13(4), 041310 (2008).
[CrossRef] [PubMed]

I. V. Turchin, V. I. Plehanov, A. G. Orlova, V. A. Kamenskiy, M. S. Kleshnin, M. V. Shirmanova, N. M. Shakhova, I. V. Balalaeva, and A. P. Savitskiy, “Fluorescence diffuse tomography of small animals with DsRed2 fluorescent protein,” Laser Phys. 16(5), 741–746 (2006).
[CrossRef]

Shu, X.

X. Shu, A. Royant, M. Z. Lin, T. A. Aguilera, V. Lev-Ram, P. A. Steinbach, and R. Y. Tsien, “Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome,” Science 324(5928), 804–807 (2009).
[CrossRef] [PubMed]

Smith, D. J.

A. J. Chaudhari, F. Darvas, J. R. Bading, R. A. Moats, P. S. Conti, D. J. Smith, S. R. Cherry, and R. M. Leahy, “Hyperspectral and multispectral bioluminescence optical tomography for small animal imaging,” Phys. Med. Biol. 50(23), 5421–5441 (2005).
[CrossRef] [PubMed]

Solovieva, E. A.

D. Shcherbo, C. S. Murphy, G. V. Ermakova, E. A. Solovieva, T. V. Chepurnykh, A. S. Shcheglov, V. V. Verkhusha, V. Z. Pletnev, K. L. Hazelwood, P. M. Roche, S. Lukyanov, A. G. Zaraisky, M. W. Davidson, and D. M. Chudakov, “Far-red fluorescent tags for protein imaging in living tissues,” Biochem. J. 418(3), 567–574 (2009).
[CrossRef] [PubMed]

D. Shcherbo, E. M. Merzlyak, T. V. Chepurnykh, A. F. Fradkov, G. V. Ermakova, E. A. Solovieva, K. A. Lukyanov, E. A. Bogdanova, A. G. Zaraisky, S. Lukyanov, and D. M. Chudakov, “Bright far-red fluorescent protein for whole-body imaging,” Nat. Methods 4(9), 741–746 (2007).
[CrossRef] [PubMed]

Soubret, A.

T. Lasser, A. Soubret, J. Ripoll, and V. Ntziachristos, “Surface Reconstruction for free-space 360 degrees fluorescence molecular tomography and the effects of animal motion,” IEEE Trans. Med. Imaging 27(2), 188–194 (2008).
[CrossRef] [PubMed]

N. C. Deliolanis, T. Lasser, D. Hyde, A. Soubret, J. Ripoll, and V. Ntziachristos, “Free-space fluorescence molecular tomography utilizing 360° geometry projections,” Opt. Lett. 32(4), 382–384 (2007).
[CrossRef] [PubMed]

Souslova, E. A.

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

Srinivasan, S.

Steffens, S.

M. Sena-Esteves, J. C. Tebbets, S. Steffens, T. Crombleholme, and A. W. Flake, “Optimized large-scale production of high titer lentivirus vector pseudotypes,” J. Virol. Methods 122(2), 131–139 (2004).
[CrossRef] [PubMed]

Steinbach, P. A.

X. Shu, A. Royant, M. Z. Lin, T. A. Aguilera, V. Lev-Ram, P. A. Steinbach, and R. Y. Tsien, “Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome,” Science 324(5928), 804–807 (2009).
[CrossRef] [PubMed]

L. Wang, W. C. Jackson, P. A. Steinbach, and R. Y. Tsien, “Evolution of new nonantibody proteins via iterative somatic hypermutation,” Proc. Natl. Acad. Sci. U.S.A. 101(48), 16745–16749 (2004).
[CrossRef] [PubMed]

N. C. Shaner, R. E. Campbell, P. A. Steinbach, B. N. G. Giepmans, A. E. Palmer, and R. Y. Tsien, “Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein,” Nat. Biotechnol. 22(12), 1567–1572 (2004).
[CrossRef] [PubMed]

R. E. Campbell, O. Tour, A. E. Palmer, P. A. Steinbach, G. S. Baird, D. A. Zacharias, and R. Y. Tsien, “A monomeric red fluorescent protein,” Proc. Natl. Acad. Sci. U.S.A. 99(12), 7877–7882 (2002).
[CrossRef] [PubMed]

Strukova, L.

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

Sun, F. X.

M. Yang, E. Baranov, P. Jiang, F. X. Sun, X. M. Li, L. N. Li, S. Hasegawa, M. Bouvet, M. Al-Tuwaijri, T. Chishima, H. Shimada, A. R. Moossa, S. Penman, and R. M. Hoffman, “Whole-body optical imaging of green fluorescent protein-expressing tumors and metastases,” Proc. Natl. Acad. Sci. U.S.A. 97(3), 1206–1211 (2000).
[CrossRef] [PubMed]

Tanaka, N.

H. Kishimoto, T. Kojima, Y. Watanabe, S. Kagawa, T. Fujiwara, F. Uno, F. Teraishi, S. Kyo, H. Mizuguchi, Y. Hashimoto, Y. Urata, N. Tanaka, and T. Fujiwara, “In vivo imaging of lymph node metastasis with telomerase-specific replication-selective adenovirus,” Nat. Med. 12(10), 1213–1219 (2006).
[CrossRef] [PubMed]

Tannous, B. A.

N. C. Deliolanis, R. Kasmieh, T. Wurdinger, B. A. Tannous, K. Shah, and V. Ntziachristos, “Performance of the red-shifted fluorescent proteins in deep-tissue molecular imaging applications,” J. Biomed. Opt. 13(4), 044008 (2008).
[CrossRef] [PubMed]

T. Wurdinger, C. Badr, L. Pike, R. de Kleine, R. Weissleder, X. O. Breakefield, and B. A. Tannous, “A secreted luciferase for ex vivo monitoring of in vivo processes,” Nat. Methods 5(2), 171–173 (2008).
[CrossRef] [PubMed]

Tebbets, J. C.

M. Sena-Esteves, J. C. Tebbets, S. Steffens, T. Crombleholme, and A. W. Flake, “Optimized large-scale production of high titer lentivirus vector pseudotypes,” J. Virol. Methods 122(2), 131–139 (2004).
[CrossRef] [PubMed]

Teraishi, F.

H. Kishimoto, T. Kojima, Y. Watanabe, S. Kagawa, T. Fujiwara, F. Uno, F. Teraishi, S. Kyo, H. Mizuguchi, Y. Hashimoto, Y. Urata, N. Tanaka, and T. Fujiwara, “In vivo imaging of lymph node metastasis with telomerase-specific replication-selective adenovirus,” Nat. Med. 12(10), 1213–1219 (2006).
[CrossRef] [PubMed]

Tour, O.

R. E. Campbell, O. Tour, A. E. Palmer, P. A. Steinbach, G. S. Baird, D. A. Zacharias, and R. Y. Tsien, “A monomeric red fluorescent protein,” Proc. Natl. Acad. Sci. U.S.A. 99(12), 7877–7882 (2002).
[CrossRef] [PubMed]

Tsien, R. Y.

X. Shu, A. Royant, M. Z. Lin, T. A. Aguilera, V. Lev-Ram, P. A. Steinbach, and R. Y. Tsien, “Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome,” Science 324(5928), 804–807 (2009).
[CrossRef] [PubMed]

B. N. G. Giepmans, S. R. Adams, M. H. Ellisman, and R. Y. Tsien, “The fluorescent toolbox for assessing protein location and function,” Science 312(5771), 217–224 (2006).
[CrossRef] [PubMed]

L. Wang, W. C. Jackson, P. A. Steinbach, and R. Y. Tsien, “Evolution of new nonantibody proteins via iterative somatic hypermutation,” Proc. Natl. Acad. Sci. U.S.A. 101(48), 16745–16749 (2004).
[CrossRef] [PubMed]

N. C. Shaner, R. E. Campbell, P. A. Steinbach, B. N. G. Giepmans, A. E. Palmer, and R. Y. Tsien, “Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein,” Nat. Biotechnol. 22(12), 1567–1572 (2004).
[CrossRef] [PubMed]

R. E. Campbell, O. Tour, A. E. Palmer, P. A. Steinbach, G. S. Baird, D. A. Zacharias, and R. Y. Tsien, “A monomeric red fluorescent protein,” Proc. Natl. Acad. Sci. U.S.A. 99(12), 7877–7882 (2002).
[CrossRef] [PubMed]

Turchin, I. V.

I. V. Turchin, V. A. Kamensky, V. I. Plehanov, A. G. Orlova, M. S. Kleshnin, I. I. Fiks, M. V. Shirmanova, I. G. Meerovich, L. R. Arslanbaeva, V. V. Jerdeva, and A. P. Savitsky, “Fluorescence diffuse tomography for detection of red fluorescent protein expressed tumors in small animals,” J. Biomed. Opt. 13(4), 041310 (2008).
[CrossRef] [PubMed]

I. V. Turchin, V. I. Plehanov, A. G. Orlova, V. A. Kamenskiy, M. S. Kleshnin, M. V. Shirmanova, N. M. Shakhova, I. V. Balalaeva, and A. P. Savitskiy, “Fluorescence diffuse tomography of small animals with DsRed2 fluorescent protein,” Laser Phys. 16(5), 741–746 (2006).
[CrossRef]

Turner, G. M.

M. J. Niedre, G. M. Turner, and V. Ntziachristos, “Time-resolved imaging of optical coefficients through murine chest cavities,” J. Biomed. Opt. 11(6), 064017 (2006).
[CrossRef] [PubMed]

Uno, F.

H. Kishimoto, T. Kojima, Y. Watanabe, S. Kagawa, T. Fujiwara, F. Uno, F. Teraishi, S. Kyo, H. Mizuguchi, Y. Hashimoto, Y. Urata, N. Tanaka, and T. Fujiwara, “In vivo imaging of lymph node metastasis with telomerase-specific replication-selective adenovirus,” Nat. Med. 12(10), 1213–1219 (2006).
[CrossRef] [PubMed]

Urata, Y.

H. Kishimoto, T. Kojima, Y. Watanabe, S. Kagawa, T. Fujiwara, F. Uno, F. Teraishi, S. Kyo, H. Mizuguchi, Y. Hashimoto, Y. Urata, N. Tanaka, and T. Fujiwara, “In vivo imaging of lymph node metastasis with telomerase-specific replication-selective adenovirus,” Nat. Med. 12(10), 1213–1219 (2006).
[CrossRef] [PubMed]

Verkhusha, V. V.

K. S. Morozova, K. D. Piatkevich, T. J. Gould, J. H. Zhang, J. Bewersdorf, and V. V. Verkhusha, “Far-red fluorescent protein excitable with red lasers for flow cytometry and superresolution STED nanoscopy,” Biophys. J. 99(2), L13–L15 (2010).
[CrossRef] [PubMed]

D. Shcherbo, C. S. Murphy, G. V. Ermakova, E. A. Solovieva, T. V. Chepurnykh, A. S. Shcheglov, V. V. Verkhusha, V. Z. Pletnev, K. L. Hazelwood, P. M. Roche, S. Lukyanov, A. G. Zaraisky, M. W. Davidson, and D. M. Chudakov, “Far-red fluorescent tags for protein imaging in living tissues,” Biochem. J. 418(3), 567–574 (2009).
[CrossRef] [PubMed]

Wang, L.

L. Wang, W. C. Jackson, P. A. Steinbach, and R. Y. Tsien, “Evolution of new nonantibody proteins via iterative somatic hypermutation,” Proc. Natl. Acad. Sci. U.S.A. 101(48), 16745–16749 (2004).
[CrossRef] [PubMed]

Watanabe, Y.

H. Kishimoto, T. Kojima, Y. Watanabe, S. Kagawa, T. Fujiwara, F. Uno, F. Teraishi, S. Kyo, H. Mizuguchi, Y. Hashimoto, Y. Urata, N. Tanaka, and T. Fujiwara, “In vivo imaging of lymph node metastasis with telomerase-specific replication-selective adenovirus,” Nat. Med. 12(10), 1213–1219 (2006).
[CrossRef] [PubMed]

Weaver, J.

Weissleder, R.

T. Wurdinger, C. Badr, L. Pike, R. de Kleine, R. Weissleder, X. O. Breakefield, and B. A. Tannous, “A secreted luciferase for ex vivo monitoring of in vivo processes,” Nat. Methods 5(2), 171–173 (2008).
[CrossRef] [PubMed]

R. Weissleder and M. J. Pittet, “Imaging in the era of molecular oncology,” Nature 452(7187), 580–589 (2008).
[CrossRef] [PubMed]

G. Zacharakis, H. Kambara, H. Shih, J. Ripoll, J. Grimm, Y. Saeki, R. Weissleder, and V. Ntziachristos, “Volumetric tomography of fluorescent proteins through small animals in vivo,” Proc. Natl. Acad. Sci. U.S.A. 102(51), 18252–18257 (2005).
[CrossRef] [PubMed]

R. Weissleder and V. Ntziachristos, “Shedding light onto live molecular targets,” Nat. Med. 9(1), 123–128 (2003).
[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]

Welch, A. J.

W. F. Cheong, S. A. Prahl, and A. J. Welch, “A review of the optical properties of biological tissues,” IEEE J. Quantum Electron. 26(12), 2166–2185 (1990).
[CrossRef]

Wurdinger, T.

T. Wurdinger, C. Badr, L. Pike, R. de Kleine, R. Weissleder, X. O. Breakefield, and B. A. Tannous, “A secreted luciferase for ex vivo monitoring of in vivo processes,” Nat. Methods 5(2), 171–173 (2008).
[CrossRef] [PubMed]

N. C. Deliolanis, R. Kasmieh, T. Wurdinger, B. A. Tannous, K. Shah, and V. Ntziachristos, “Performance of the red-shifted fluorescent proteins in deep-tissue molecular imaging applications,” J. Biomed. Opt. 13(4), 044008 (2008).
[CrossRef] [PubMed]

Yang, M.

M. Yang, E. Baranov, P. Jiang, F. X. Sun, X. M. Li, L. N. Li, S. Hasegawa, M. Bouvet, M. Al-Tuwaijri, T. Chishima, H. Shimada, A. R. Moossa, S. Penman, and R. M. Hoffman, “Whole-body optical imaging of green fluorescent protein-expressing tumors and metastases,” Proc. Natl. Acad. Sci. U.S.A. 97(3), 1206–1211 (2000).
[CrossRef] [PubMed]

Yodh, A. G.

Zacharakis, G.

G. Zacharakis, H. Kambara, H. Shih, J. Ripoll, J. Grimm, Y. Saeki, R. Weissleder, and V. Ntziachristos, “Volumetric tomography of fluorescent proteins through small animals in vivo,” Proc. Natl. Acad. Sci. U.S.A. 102(51), 18252–18257 (2005).
[CrossRef] [PubMed]

Zacharias, D. A.

R. E. Campbell, O. Tour, A. E. Palmer, P. A. Steinbach, G. S. Baird, D. A. Zacharias, and R. Y. Tsien, “A monomeric red fluorescent protein,” Proc. Natl. Acad. Sci. U.S.A. 99(12), 7877–7882 (2002).
[CrossRef] [PubMed]

Zaraisky, A. G.

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

D. Shcherbo, C. S. Murphy, G. V. Ermakova, E. A. Solovieva, T. V. Chepurnykh, A. S. Shcheglov, V. V. Verkhusha, V. Z. Pletnev, K. L. Hazelwood, P. M. Roche, S. Lukyanov, A. G. Zaraisky, M. W. Davidson, and D. M. Chudakov, “Far-red fluorescent tags for protein imaging in living tissues,” Biochem. J. 418(3), 567–574 (2009).
[CrossRef] [PubMed]

D. Shcherbo, E. M. Merzlyak, T. V. Chepurnykh, A. F. Fradkov, G. V. Ermakova, E. A. Solovieva, K. A. Lukyanov, E. A. Bogdanova, A. G. Zaraisky, S. Lukyanov, and D. M. Chudakov, “Bright far-red fluorescent protein for whole-body imaging,” Nat. Methods 4(9), 741–746 (2007).
[CrossRef] [PubMed]

Zhang, J. H.

K. S. Morozova, K. D. Piatkevich, T. J. Gould, J. H. Zhang, J. Bewersdorf, and V. V. Verkhusha, “Far-red fluorescent protein excitable with red lasers for flow cytometry and superresolution STED nanoscopy,” Biophys. J. 99(2), L13–L15 (2010).
[CrossRef] [PubMed]

Zimmer, C.

L. Lüdemann, B. Hamm, and C. Zimmer, “Pharmacokinetic analysis of glioma compartments with dynamic Gd-DTPA-enhanced magnetic resonance imaging,” Magn. Reson. Imaging 18(10), 1201–1214 (2000).
[CrossRef] [PubMed]

Biochem. J.

D. Shcherbo, C. S. Murphy, G. V. Ermakova, E. A. Solovieva, T. V. Chepurnykh, A. S. Shcheglov, V. V. Verkhusha, V. Z. Pletnev, K. L. Hazelwood, P. M. Roche, S. Lukyanov, A. G. Zaraisky, M. W. Davidson, and D. M. Chudakov, “Far-red fluorescent tags for protein imaging in living tissues,” Biochem. J. 418(3), 567–574 (2009).
[CrossRef] [PubMed]

Biophys. J.

K. S. Morozova, K. D. Piatkevich, T. J. Gould, J. H. Zhang, J. Bewersdorf, and V. V. Verkhusha, “Far-red fluorescent protein excitable with red lasers for flow cytometry and superresolution STED nanoscopy,” Biophys. J. 99(2), L13–L15 (2010).
[CrossRef] [PubMed]

Comput. Vis. Graph. Image Process.

M. Potmesil, “Generating octree models of 3d objects from their silhouettes in a sequence of images,” Comput. Vis. Graph. Image Process. 40(1), 1–29 (1987).
[CrossRef]

IEEE J. Quantum Electron.

W. F. Cheong, S. A. Prahl, and A. J. Welch, “A review of the optical properties of biological tissues,” IEEE J. Quantum Electron. 26(12), 2166–2185 (1990).
[CrossRef]

IEEE Trans. Med. Imaging

T. Lasser, A. Soubret, J. Ripoll, and V. Ntziachristos, “Surface Reconstruction for free-space 360 degrees fluorescence molecular tomography and the effects of animal motion,” IEEE Trans. Med. Imaging 27(2), 188–194 (2008).
[CrossRef] [PubMed]

J. Biomed. Opt.

M. J. Niedre, G. M. Turner, and V. Ntziachristos, “Time-resolved imaging of optical coefficients through murine chest cavities,” J. Biomed. Opt. 11(6), 064017 (2006).
[CrossRef] [PubMed]

N. C. Deliolanis, R. Kasmieh, T. Wurdinger, B. A. Tannous, K. Shah, and V. Ntziachristos, “Performance of the red-shifted fluorescent proteins in deep-tissue molecular imaging applications,” J. Biomed. Opt. 13(4), 044008 (2008).
[CrossRef] [PubMed]

I. V. Turchin, V. A. Kamensky, V. I. Plehanov, A. G. Orlova, M. S. Kleshnin, I. I. Fiks, M. V. Shirmanova, I. G. Meerovich, L. R. Arslanbaeva, V. V. Jerdeva, and A. P. Savitsky, “Fluorescence diffuse tomography for detection of red fluorescent protein expressed tumors in small animals,” J. Biomed. Opt. 13(4), 041310 (2008).
[CrossRef] [PubMed]

J. Virol. Methods

M. Sena-Esteves, J. C. Tebbets, S. Steffens, T. Crombleholme, and A. W. Flake, “Optimized large-scale production of high titer lentivirus vector pseudotypes,” J. Virol. Methods 122(2), 131–139 (2004).
[CrossRef] [PubMed]

Laser Phys.

I. V. Turchin, V. I. Plehanov, A. G. Orlova, V. A. Kamenskiy, M. S. Kleshnin, M. V. Shirmanova, N. M. Shakhova, I. V. Balalaeva, and A. P. Savitskiy, “Fluorescence diffuse tomography of small animals with DsRed2 fluorescent protein,” Laser Phys. 16(5), 741–746 (2006).
[CrossRef]

Magn. Reson. Imaging

L. Lüdemann, B. Hamm, and C. Zimmer, “Pharmacokinetic analysis of glioma compartments with dynamic Gd-DTPA-enhanced magnetic resonance imaging,” Magn. Reson. Imaging 18(10), 1201–1214 (2000).
[CrossRef] [PubMed]

Nat. Biotechnol.

N. C. Shaner, R. E. Campbell, P. A. Steinbach, B. N. G. Giepmans, A. E. Palmer, and R. Y. Tsien, “Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein,” Nat. Biotechnol. 22(12), 1567–1572 (2004).
[CrossRef] [PubMed]

Nat. Med.

R. Weissleder and V. Ntziachristos, “Shedding light onto live molecular targets,” Nat. Med. 9(1), 123–128 (2003).
[CrossRef] [PubMed]

H. Kishimoto, T. Kojima, Y. Watanabe, S. Kagawa, T. Fujiwara, F. Uno, F. Teraishi, S. Kyo, H. Mizuguchi, Y. Hashimoto, Y. Urata, N. Tanaka, and T. Fujiwara, “In vivo imaging of lymph node metastasis with telomerase-specific replication-selective adenovirus,” Nat. Med. 12(10), 1213–1219 (2006).
[CrossRef] [PubMed]

Nat. Methods

F. Helmchen and W. Denk, “Deep tissue two-photon microscopy,” Nat. Methods 2(12), 932–940 (2005).
[CrossRef] [PubMed]

D. Shcherbo and I. I. Shemiakina IIA. V. Ryabova, K. E. Luker, B. T. Schmidt, E. A. Souslova, T. V. Gorodnicheva, L. Strukova, K. M. Shidlovskiy, O. V. Britanova, A. G. Zaraisky, K. A. Lukyanov, V. B. Loschenov, G. D. Luker, and D. M. Chudakov, “Near-infrared fluorescent proteins,” Nat. Methods 7(10), 827–829 (2010).
[CrossRef] [PubMed]

D. Shcherbo, E. M. Merzlyak, T. V. Chepurnykh, A. F. Fradkov, G. V. Ermakova, E. A. Solovieva, K. A. Lukyanov, E. A. Bogdanova, A. G. Zaraisky, S. Lukyanov, and D. M. Chudakov, “Bright far-red fluorescent protein for whole-body imaging,” Nat. Methods 4(9), 741–746 (2007).
[CrossRef] [PubMed]

T. Wurdinger, C. Badr, L. Pike, R. de Kleine, R. Weissleder, X. O. Breakefield, and B. A. Tannous, “A secreted luciferase for ex vivo monitoring of in vivo processes,” Nat. Methods 5(2), 171–173 (2008).
[CrossRef] [PubMed]

Nat. Rev. Cancer

R. K. Jain, L. L. Munn, and D. Fukumura, “Dissecting tumour pathophysiology using intravital microscopy,” Nat. Rev. Cancer 2(4), 266–276 (2002).
[CrossRef] [PubMed]

Nature

R. Weissleder and M. J. Pittet, “Imaging in the era of molecular oncology,” Nature 452(7187), 580–589 (2008).
[CrossRef] [PubMed]

Opt. Express

Opt. Lett.

Photochem. Photobiol.

H. Du, R. C. A. Fuh, J. Z. Li, L. A. Corkan, and J. S. Lindsey, “PhotochemCAD: A computer-aided design and research tool in photochemistry,” Photochem. Photobiol. 68, 141–142 (1998).

Phys. Med. Biol.

A. J. Chaudhari, F. Darvas, J. R. Bading, R. A. Moats, P. S. Conti, D. J. Smith, S. R. Cherry, and R. M. Leahy, “Hyperspectral and multispectral bioluminescence optical tomography for small animal imaging,” Phys. Med. Biol. 50(23), 5421–5441 (2005).
[CrossRef] [PubMed]

G. Alexandrakis, F. R. Rannou, and A. F. Chatziioannou, “Tomographic bioluminescence imaging by use of a combined optical-PET (OPET) system: a computer simulation feasibility study,” Phys. Med. Biol. 50(17), 4225–4241 (2005).
[CrossRef] [PubMed]

Proc. Natl. Acad. Sci. U.S.A.

L. Wang, W. C. Jackson, P. A. Steinbach, and R. Y. Tsien, “Evolution of new nonantibody proteins via iterative somatic hypermutation,” Proc. Natl. Acad. Sci. U.S.A. 101(48), 16745–16749 (2004).
[CrossRef] [PubMed]

G. Zacharakis, H. Kambara, H. Shih, J. Ripoll, J. Grimm, Y. Saeki, R. Weissleder, and V. Ntziachristos, “Volumetric tomography of fluorescent proteins through small animals in vivo,” Proc. Natl. Acad. Sci. U.S.A. 102(51), 18252–18257 (2005).
[CrossRef] [PubMed]

M. Yang, E. Baranov, P. Jiang, F. X. Sun, X. M. Li, L. N. Li, S. Hasegawa, M. Bouvet, M. Al-Tuwaijri, T. Chishima, H. Shimada, A. R. Moossa, S. Penman, and R. M. Hoffman, “Whole-body optical imaging of green fluorescent protein-expressing tumors and metastases,” Proc. Natl. Acad. Sci. U.S.A. 97(3), 1206–1211 (2000).
[CrossRef] [PubMed]

R. E. Campbell, O. Tour, A. E. Palmer, P. A. Steinbach, G. S. Baird, D. A. Zacharias, and R. Y. Tsien, “A monomeric red fluorescent protein,” Proc. Natl. Acad. Sci. U.S.A. 99(12), 7877–7882 (2002).
[CrossRef] [PubMed]

Science

X. Shu, A. Royant, M. Z. Lin, T. A. Aguilera, V. Lev-Ram, P. A. Steinbach, and R. Y. Tsien, “Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome,” Science 324(5928), 804–807 (2009).
[CrossRef] [PubMed]

B. N. G. Giepmans, S. R. Adams, M. H. Ellisman, and R. Y. Tsien, “The fluorescent toolbox for assessing protein location and function,” Science 312(5771), 217–224 (2006).
[CrossRef] [PubMed]

Other

A. Ishimaru, Wave Propagation and Scattering in Random Media (IEEE Press, 1997).

S. A. Prahl, “Optical Properties Spectra,” (2001), retrieved http://omlc.ogi.edu/spectra/ .

I. Georgakoudi, M. G. Muller, and M. S. Feld, “Intrinsic fluorescence spectroscopy of biological tissue,” in Fluorescence in Biomedicine, M. A. Mycek and B. Pogue, eds. (Marcel Decker, 2002), pp. 109–142.

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Figures (6)

Fig. 1
Fig. 1

Schematic of the experimental tomographic system (in free-space configuration).

Fig. 2
Fig. 2

Outline of the algorithmic implementation. Multicolored boxes denote multispectral data acquisition and processing.

Fig. 3
Fig. 3

Characteristic fluorescence and autofluorescence emission curves in deep tissue imaging. (a) In vivo relative spectral attenuation of light transmitted through 8 mm thick mouse tissue (upper left torso). Arrows indicate key wavelengths: blue – GFP excitation at 488 nm, green – GFP emission at 514 nm, orange – RFP excitation at 593 nm, and red bars – RFP emission 610-650 nm. The red arrow indicates the laser wavelength used for the calculation of the n-Born ratio. (b) normalized absorption and emission spectra for GFP and mCherry, (c) Normalized fluorescence of 106 U87dEGFR glioblastoma cells expressing FPs from deep tissue in transillumination mode. The orange shaded area indicates the intensity range of mCherry emission. The mCherry RFP emission was significantly higher when cells were closer to the excitation source (orange triangles pointing upward), than when they were closer to the detector (orange triangles pointing downward). GFP emission (cyan square) was essentially independent from the position. Black squares and lines indicate the autofluorescence intensity (control cells) and green squares and triangles show the emission of mCherry when excited at 532 nm. Data were normalized for relative FP brightness. (d) In vivo normalized autofluorescence emission in transillumination of 12 mm thick mouse tissue (upper center torso) when excited at 6 different laser lines ranging from 488 - 750 nm (see color legend). The measurements were normalized for spectral window bandwidth, laser power, exposure time, i.e. units are photon counts.nm−1mW−1.s−1. The continuous lines are spline interpolations.

Fig. 4
Fig. 4

Autofluorescence subtraction and normalization of raw transillumination images from a mouse head (dorsal view) with tumor expressing mCherry. – (Media 1) (a) Fluorescence image U f l at 620 nm when excited at 593 nm, (b), Autofluorescence image U a u at 620 nm excited at 532 nm, (c), Correction with autofluorescence subtraction U f l a U a u , (d) Normalization image of the head of the mouse at 635 nm, (e) n-Born ratio U n (cyan) overlaid on the reflectance image of the head (grayscale). (g) Autofluorescence corrected n-Born ratio U n overlaid on the reflectance image. (f) and (h) Density plots of all the uncorrected and corrected measurements, respectively, when each fluorescence pixel value is plotted vs the corresponding normalization pixel value (arbitrary units).

Fig. 5
Fig. 5

Multispectral fluorescence tomography reconstruction. (a) Schematic of the 3-wavelength n-Born ratio calculation. Here, s, m, and d are the source, mesh, and detector positions, respectively. Gsm, Gmd, and Gsd are the Green’s functions that model the corresponding propagating photon fields between s, m, and d. (b) Drawing of the cross section of the phantom containing 1% Intralipid and 1% whole blood. Small circles indicate the position of the two tubes containing 15 and 60 pmol of Texas Red fluorochrome. (c) A 3D view of the surface of the phantom with the positions of the sources (red crosses) and the detectors (blue circles) as projected on the surface. (d) Selected axial slices of the 3D single- and multi-spectral reconstructions of the fluorescence concentration (arbitrary units) of the two tubes inside the phantom. Black discs indicate the cross section of the phantom. (b) and (d) are on the same scale.

Fig. 6
Fig. 6

Representative example of intracranial U87dEGFR-mCherry glioblastoma reconstruction. (a) A 3D view of the surface of the mouse’s head, sources (red crosses) and detectors (blue circles) are projected on the surface. The black rectangle indicates the position of the axial slice 3. (b) A fluorescence epi-illumination image of histological section (slice #3) of the brain, blue – reflectance image at 593 nm, magenta – mCherry fluorescence emission at 620 nm when excited at 593 nm. (c) Single- and multi-spectral reconstructions of the mCherry fluorescence at the axial slice #3. (d) A series of axial slices of the mCherry tumor reconstructed fluorescence, and (e) Corresponding post-Gd-DTPA enhanced axial slices from the T1-weighted MRI series. Orange arrows indicate the position of the glioma. Colorbar for (c) and (d) is in arbitrary units. Dashed lines in (c) and (d) are visual guides to indicate the brain area.

Equations (5)

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U n B ( n ) = W ( m × n ) C ( m )
G 1 r D exp ( μ a D r )
W s d = G ( r s m , μ a λ e , μ s λ e ) G ( r m d , μ a λ f , μ s λ f ) G ( r s d , μ a λ n , μ s λ n )
[ U n b λ 1 ( n ) U n b λ 2 ( n ) U n b λ k ( n ) ] = [ W λ 1 ( m × n ) W λ 2 ( m × n ) W λ k ( m × n ) ] C ( m )
U n B = U f l a U a u | > 0 U n

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