Abstract

The application of optical projection tomography to in-vivo experiments is limited by specimen movement during the acquisition. We present a set of mathematical correction methods applied to the acquired data stacks to correct for movement in both directions of the image plane. These methods have been applied to correct experimental data taken from in-vivo optical projection tomography experiments in Caenorhabditis elegans. Successful reconstructions for both fluorescence and white light (absorption) measurements are shown. Since no difference between movement of the animal and movement of the rotation axis is made, this approach at the same time removes artifacts due to mechanical drifts and errors in the assumed center of rotation.

© 2010 OSA

Full Article  |  PDF Article

References

  • View by:
  • |
  • |
  • |

  1. M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
    [CrossRef] [PubMed]
  2. E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
    [CrossRef] [PubMed]
  3. S. T. Hess, T. P. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
    [CrossRef] [PubMed]
  4. L. M. Hirvonen, K. Wicker, O. Mandula, and R. Heintzmann, “Structured illumination microscopy of a living cell,” Eur. Biophys. J. 38(6), 807–812 (2009).
    [CrossRef] [PubMed]
  5. D. Baddeley, C. Batram, Y. Weiland, C. Cremer, and U. J. Birk, “Nanostructure analysis using spatially modulated illumination microscopy,” Nat. Protoc. 2(10), 2640–2646 (2007).
    [CrossRef] [PubMed]
  6. D. Baddeley, V. O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P. M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, and M. C. Cardoso, “Measurement of replication structures at the nanometer scale using super-resolution light microscopy,” Nucleic Acids Res. 38, 1–11 (2009).
    [PubMed]
  7. N. Ji, D. E. Milkie, and E. Betzig, “Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues,” Nat. Methods 7(2), 141–147 (2010).
    [CrossRef] [PubMed]
  8. W. Denk, J. H. Strickler, and W. W. Webb, “Two-photon laser scanning fluorescence microscopy,” Science 248(4951), 73–76 (1990).
    [CrossRef] [PubMed]
  9. C. Vinegoni, L. Fexon, P. F. Feruglio, M. Pivovarov, J. L. Figueiredo, M. Nahrendorf, A. Pozzo, A. Sbarbati, and R. Weissleder, “High throughput transmission optical projection tomography using low cost graphics processing unit,” Opt. Express 17(25), 22320–22332 (2009).
    [CrossRef] [PubMed]
  10. J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
    [CrossRef] [PubMed]
  11. J. Sharpe, “Optical projection tomography,” Annu. Rev. Biomed. Eng. 6(1), 209–228 (2004).
    [CrossRef] [PubMed]
  12. M. J. Boot, C. H. Westerberg, J. Sanz-Ezquerro, J. Cotterell, R. Schweitzer, M. Torres, and J. Sharpe, “In vitro whole-organ imaging: 4D quantification of growing mouse limb buds,” Nat. Methods 5(7), 609–612 (2008).
    [CrossRef] [PubMed]
  13. A. Darrell, H. Meyer, K. Marias, M. Brady, and J. Ripoll, “Weighted filtered backprojection for quantitative fluorescence optical projection tomography,” Phys. Med. Biol. 53(14), 3863–3881 (2008).
    [CrossRef] [PubMed]
  14. H. Meyer, A. Darrell, A. Metaxakis, C. Savakis, and J. Ripoll, “Optical Projection Tomography for In-Vivo Imaging of Drosophila melanogaster,” Microscopy and Analysis 22, 19–22 (2008).
  15. 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]
  16. J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
    [CrossRef] [PubMed]
  17. R. B. Schulz, J. Ripoll, and V. Ntziachristos, “Noncontact optical tomography of turbid media,” Opt. Lett. 28(18), 1701–1703 (2003).
    [CrossRef] [PubMed]
  18. A. Sarasa-Renedo, R. Favicchio, U. Birk, G. Zacharakis, C. Mamalaki, and J. Ripoll, “Source intensity profile in noncontact optical tomography,” Opt. Lett. 35(1), 34–36 (2010).
    [CrossRef]
  19. J. McGinty, K. B. Tahir, R. Laine, C. B. Talbot, C. Dunsby, M. A. A. Neil, L. Quintana, J. Swoger, J. Sharpe, and P. M. W. French, “Fluorescence lifetime optical projection tomography,” J Biophotonics 1(5), 390–394 (2008).
    [CrossRef] [PubMed]
  20. J. Culver, W. Akers, and S. Achilefu, “Multimodality molecular imaging with combined optical and SPECT/PET modalities,” J. Nucl. Med. 49(2), 169–172 (2008).
    [CrossRef] [PubMed]
  21. C. Vinegoni, D. Razansky, J. L. Figueiredo, L. Fexon, M. Pivovarov, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Born normalization for fluorescence optical projection tomography for whole heart imaging,” J. Vis. Exp. 28(28), 1389 (2009).
    [PubMed]
  22. A. Bassi, D. Brida, C. D'Andrea, G. Valentini, S. De Silvestri, G. Cerullo, and R. Cubeddu, “Time gated optical projection tomography for 3D imaging of highly scattering biological models,” in Biomedical Optics, OSA Technical Digest (CD) (Optical Society of America, 2010), p. BTuF5.
  23. J. R. Walls, J. G. Sled, J. Sharpe, and R. M. Henkelman, “Resolution improvement in emission optical projection tomography,” Phys. Med. Biol. 52(10), 2775–2790 (2007).
    [CrossRef] [PubMed]
  24. U. J. Birk, A. Darrell, N. Konstantinides, A. Sarasa-Renedo, and J. Ripoll, “Improved Reconstructions and Generalized Filtered Back Projection for Optical Projection Tomography,” Appl. Opt. submitted.
  25. A. Katsevich, “An accurate approximate algorithm for motion compensation in two-dimensional tomography,” Inverse Probl. 26(6), 065007 (2010).
    [CrossRef]
  26. U. J. Birk, A. Darrell, N. Konstantinides, and J. Ripoll, “Correction of Lateral Movement and Spherical Aberrations in Optical Projection Tomography,” in Biomedical Optics, OSA Technical Digest (CD) (Optical Society of America, 2010), p. BTuF6.
  27. S. Brenner, “The genetics of Caenorhabditis elegans,” Genetics 77(1), 71–94 (1974).
    [PubMed]
  28. J. R. Walls, J. G. Sled, J. Sharpe, and R. M. Henkelman, “Correction of artefacts in optical projection tomography,” Phys. Med. Biol. 50(19), 4645–4665 (2005).
    [CrossRef] [PubMed]
  29. Quantitative Imaging Group at the Faculty of Applied Sciences, Delft University of Technology, “DIPimage & DIPlib,” http://www.diplib.org/ .
  30. J. C. Crocker and D. G. Grier, “Methods of Digital Video Microscopy for Colloidal Studies,” J. Colloid Interface Sci. 179(1), 298–310 (1996).
    [CrossRef]
  31. L. R. Barnden, J. Dickson, and B. F. Hutton, “Detection and validation of the body edge in low count emission tomography images,” Comput. Methods Programs Biomed. 84(2-3), 153–161 (2006).
    [CrossRef] [PubMed]
  32. A. C. Kak, and M. Slaney, Principles of Computerized Tomographic Imaging (IEEE Service Center, 1988).
  33. D. Baddeley, Y. Weiland, C. Batram, U. Birk, and C. Cremer, “Model based precision structural measurements on barely resolved objects,” J. Microsc. 237(1), 70–78 (2010).
    [CrossRef] [PubMed]

2010 (4)

N. Ji, D. E. Milkie, and E. Betzig, “Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues,” Nat. Methods 7(2), 141–147 (2010).
[CrossRef] [PubMed]

A. Sarasa-Renedo, R. Favicchio, U. Birk, G. Zacharakis, C. Mamalaki, and J. Ripoll, “Source intensity profile in noncontact optical tomography,” Opt. Lett. 35(1), 34–36 (2010).
[CrossRef]

A. Katsevich, “An accurate approximate algorithm for motion compensation in two-dimensional tomography,” Inverse Probl. 26(6), 065007 (2010).
[CrossRef]

D. Baddeley, Y. Weiland, C. Batram, U. Birk, and C. Cremer, “Model based precision structural measurements on barely resolved objects,” J. Microsc. 237(1), 70–78 (2010).
[CrossRef] [PubMed]

2009 (4)

C. Vinegoni, D. Razansky, J. L. Figueiredo, L. Fexon, M. Pivovarov, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Born normalization for fluorescence optical projection tomography for whole heart imaging,” J. Vis. Exp. 28(28), 1389 (2009).
[PubMed]

D. Baddeley, V. O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P. M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, and M. C. Cardoso, “Measurement of replication structures at the nanometer scale using super-resolution light microscopy,” Nucleic Acids Res. 38, 1–11 (2009).
[PubMed]

C. Vinegoni, L. Fexon, P. F. Feruglio, M. Pivovarov, J. L. Figueiredo, M. Nahrendorf, A. Pozzo, A. Sbarbati, and R. Weissleder, “High throughput transmission optical projection tomography using low cost graphics processing unit,” Opt. Express 17(25), 22320–22332 (2009).
[CrossRef] [PubMed]

L. M. Hirvonen, K. Wicker, O. Mandula, and R. Heintzmann, “Structured illumination microscopy of a living cell,” Eur. Biophys. J. 38(6), 807–812 (2009).
[CrossRef] [PubMed]

2008 (6)

J. McGinty, K. B. Tahir, R. Laine, C. B. Talbot, C. Dunsby, M. A. A. Neil, L. Quintana, J. Swoger, J. Sharpe, and P. M. W. French, “Fluorescence lifetime optical projection tomography,” J Biophotonics 1(5), 390–394 (2008).
[CrossRef] [PubMed]

J. Culver, W. Akers, and S. Achilefu, “Multimodality molecular imaging with combined optical and SPECT/PET modalities,” J. Nucl. Med. 49(2), 169–172 (2008).
[CrossRef] [PubMed]

M. J. Boot, C. H. Westerberg, J. Sanz-Ezquerro, J. Cotterell, R. Schweitzer, M. Torres, and J. Sharpe, “In vitro whole-organ imaging: 4D quantification of growing mouse limb buds,” Nat. Methods 5(7), 609–612 (2008).
[CrossRef] [PubMed]

A. Darrell, H. Meyer, K. Marias, M. Brady, and J. Ripoll, “Weighted filtered backprojection for quantitative fluorescence optical projection tomography,” Phys. Med. Biol. 53(14), 3863–3881 (2008).
[CrossRef] [PubMed]

H. Meyer, A. Darrell, A. Metaxakis, C. Savakis, and J. Ripoll, “Optical Projection Tomography for In-Vivo Imaging of Drosophila melanogaster,” Microscopy and Analysis 22, 19–22 (2008).

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]

2007 (2)

D. Baddeley, C. Batram, Y. Weiland, C. Cremer, and U. J. Birk, “Nanostructure analysis using spatially modulated illumination microscopy,” Nat. Protoc. 2(10), 2640–2646 (2007).
[CrossRef] [PubMed]

J. R. Walls, J. G. Sled, J. Sharpe, and R. M. Henkelman, “Resolution improvement in emission optical projection tomography,” Phys. Med. Biol. 52(10), 2775–2790 (2007).
[CrossRef] [PubMed]

2006 (4)

L. R. Barnden, J. Dickson, and B. F. Hutton, “Detection and validation of the body edge in low count emission tomography images,” Comput. Methods Programs Biomed. 84(2-3), 153–161 (2006).
[CrossRef] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[CrossRef] [PubMed]

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

S. T. Hess, T. P. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[CrossRef] [PubMed]

2005 (1)

J. R. Walls, J. G. Sled, J. Sharpe, and R. M. Henkelman, “Correction of artefacts in optical projection tomography,” Phys. Med. Biol. 50(19), 4645–4665 (2005).
[CrossRef] [PubMed]

2004 (2)

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

J. Sharpe, “Optical projection tomography,” Annu. Rev. Biomed. Eng. 6(1), 209–228 (2004).
[CrossRef] [PubMed]

2003 (1)

2002 (1)

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[CrossRef] [PubMed]

1996 (1)

J. C. Crocker and D. G. Grier, “Methods of Digital Video Microscopy for Colloidal Studies,” J. Colloid Interface Sci. 179(1), 298–310 (1996).
[CrossRef]

1990 (1)

W. Denk, J. H. Strickler, and W. W. Webb, “Two-photon laser scanning fluorescence microscopy,” Science 248(4951), 73–76 (1990).
[CrossRef] [PubMed]

1974 (1)

S. Brenner, “The genetics of Caenorhabditis elegans,” Genetics 77(1), 71–94 (1974).
[PubMed]

Achilefu, S.

J. Culver, W. Akers, and S. Achilefu, “Multimodality molecular imaging with combined optical and SPECT/PET modalities,” J. Nucl. Med. 49(2), 169–172 (2008).
[CrossRef] [PubMed]

Ahlgren, U.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[CrossRef] [PubMed]

Akers, W.

J. Culver, W. Akers, and S. Achilefu, “Multimodality molecular imaging with combined optical and SPECT/PET modalities,” J. Nucl. Med. 49(2), 169–172 (2008).
[CrossRef] [PubMed]

Baddeley, D.

D. Baddeley, Y. Weiland, C. Batram, U. Birk, and C. Cremer, “Model based precision structural measurements on barely resolved objects,” J. Microsc. 237(1), 70–78 (2010).
[CrossRef] [PubMed]

D. Baddeley, V. O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P. M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, and M. C. Cardoso, “Measurement of replication structures at the nanometer scale using super-resolution light microscopy,” Nucleic Acids Res. 38, 1–11 (2009).
[PubMed]

D. Baddeley, C. Batram, Y. Weiland, C. Cremer, and U. J. Birk, “Nanostructure analysis using spatially modulated illumination microscopy,” Nat. Protoc. 2(10), 2640–2646 (2007).
[CrossRef] [PubMed]

Baldock, R.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[CrossRef] [PubMed]

Barnden, L. R.

L. R. Barnden, J. Dickson, and B. F. Hutton, “Detection and validation of the body edge in low count emission tomography images,” Comput. Methods Programs Biomed. 84(2-3), 153–161 (2006).
[CrossRef] [PubMed]

Bates, M.

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[CrossRef] [PubMed]

Batram, C.

D. Baddeley, Y. Weiland, C. Batram, U. Birk, and C. Cremer, “Model based precision structural measurements on barely resolved objects,” J. Microsc. 237(1), 70–78 (2010).
[CrossRef] [PubMed]

D. Baddeley, C. Batram, Y. Weiland, C. Cremer, and U. J. Birk, “Nanostructure analysis using spatially modulated illumination microscopy,” Nat. Protoc. 2(10), 2640–2646 (2007).
[CrossRef] [PubMed]

Betzig, E.

N. Ji, D. E. Milkie, and E. Betzig, “Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues,” Nat. Methods 7(2), 141–147 (2010).
[CrossRef] [PubMed]

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Birk, U.

D. Baddeley, Y. Weiland, C. Batram, U. Birk, and C. Cremer, “Model based precision structural measurements on barely resolved objects,” J. Microsc. 237(1), 70–78 (2010).
[CrossRef] [PubMed]

A. Sarasa-Renedo, R. Favicchio, U. Birk, G. Zacharakis, C. Mamalaki, and J. Ripoll, “Source intensity profile in noncontact optical tomography,” Opt. Lett. 35(1), 34–36 (2010).
[CrossRef]

D. Baddeley, V. O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P. M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, and M. C. Cardoso, “Measurement of replication structures at the nanometer scale using super-resolution light microscopy,” Nucleic Acids Res. 38, 1–11 (2009).
[PubMed]

Birk, U. J.

D. Baddeley, C. Batram, Y. Weiland, C. Cremer, and U. J. Birk, “Nanostructure analysis using spatially modulated illumination microscopy,” Nat. Protoc. 2(10), 2640–2646 (2007).
[CrossRef] [PubMed]

U. J. Birk, A. Darrell, N. Konstantinides, A. Sarasa-Renedo, and J. Ripoll, “Improved Reconstructions and Generalized Filtered Back Projection for Optical Projection Tomography,” Appl. Opt. submitted.

Bonifacino, J. S.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Boot, M. J.

M. J. Boot, C. H. Westerberg, J. Sanz-Ezquerro, J. Cotterell, R. Schweitzer, M. Torres, and J. Sharpe, “In vitro whole-organ imaging: 4D quantification of growing mouse limb buds,” Nat. Methods 5(7), 609–612 (2008).
[CrossRef] [PubMed]

Brady, M.

A. Darrell, H. Meyer, K. Marias, M. Brady, and J. Ripoll, “Weighted filtered backprojection for quantitative fluorescence optical projection tomography,” Phys. Med. Biol. 53(14), 3863–3881 (2008).
[CrossRef] [PubMed]

Brenner, S.

S. Brenner, “The genetics of Caenorhabditis elegans,” Genetics 77(1), 71–94 (1974).
[PubMed]

Cardoso, M. C.

D. Baddeley, V. O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P. M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, and M. C. Cardoso, “Measurement of replication structures at the nanometer scale using super-resolution light microscopy,” Nucleic Acids Res. 38, 1–11 (2009).
[PubMed]

Carlton, P. M.

D. Baddeley, V. O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P. M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, and M. C. Cardoso, “Measurement of replication structures at the nanometer scale using super-resolution light microscopy,” Nucleic Acids Res. 38, 1–11 (2009).
[PubMed]

Chagin, V. O.

D. Baddeley, V. O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P. M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, and M. C. Cardoso, “Measurement of replication structures at the nanometer scale using super-resolution light microscopy,” Nucleic Acids Res. 38, 1–11 (2009).
[PubMed]

Cotterell, J.

M. J. Boot, C. H. Westerberg, J. Sanz-Ezquerro, J. Cotterell, R. Schweitzer, M. Torres, and J. Sharpe, “In vitro whole-organ imaging: 4D quantification of growing mouse limb buds,” Nat. Methods 5(7), 609–612 (2008).
[CrossRef] [PubMed]

Cremer, C.

D. Baddeley, Y. Weiland, C. Batram, U. Birk, and C. Cremer, “Model based precision structural measurements on barely resolved objects,” J. Microsc. 237(1), 70–78 (2010).
[CrossRef] [PubMed]

D. Baddeley, V. O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P. M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, and M. C. Cardoso, “Measurement of replication structures at the nanometer scale using super-resolution light microscopy,” Nucleic Acids Res. 38, 1–11 (2009).
[PubMed]

D. Baddeley, C. Batram, Y. Weiland, C. Cremer, and U. J. Birk, “Nanostructure analysis using spatially modulated illumination microscopy,” Nat. Protoc. 2(10), 2640–2646 (2007).
[CrossRef] [PubMed]

Crocker, J. C.

J. C. Crocker and D. G. Grier, “Methods of Digital Video Microscopy for Colloidal Studies,” J. Colloid Interface Sci. 179(1), 298–310 (1996).
[CrossRef]

Culver, J.

J. Culver, W. Akers, and S. Achilefu, “Multimodality molecular imaging with combined optical and SPECT/PET modalities,” J. Nucl. Med. 49(2), 169–172 (2008).
[CrossRef] [PubMed]

Darrell, A.

A. Darrell, H. Meyer, K. Marias, M. Brady, and J. Ripoll, “Weighted filtered backprojection for quantitative fluorescence optical projection tomography,” Phys. Med. Biol. 53(14), 3863–3881 (2008).
[CrossRef] [PubMed]

H. Meyer, A. Darrell, A. Metaxakis, C. Savakis, and J. Ripoll, “Optical Projection Tomography for In-Vivo Imaging of Drosophila melanogaster,” Microscopy and Analysis 22, 19–22 (2008).

U. J. Birk, A. Darrell, N. Konstantinides, A. Sarasa-Renedo, and J. Ripoll, “Improved Reconstructions and Generalized Filtered Back Projection for Optical Projection Tomography,” Appl. Opt. submitted.

Davidson, D.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[CrossRef] [PubMed]

Davidson, M. W.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Del Bene, F.

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

Denk, W.

W. Denk, J. H. Strickler, and W. W. Webb, “Two-photon laser scanning fluorescence microscopy,” Science 248(4951), 73–76 (1990).
[CrossRef] [PubMed]

Dickson, J.

L. R. Barnden, J. Dickson, and B. F. Hutton, “Detection and validation of the body edge in low count emission tomography images,” Comput. Methods Programs Biomed. 84(2-3), 153–161 (2006).
[CrossRef] [PubMed]

Domaing, P.

D. Baddeley, V. O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P. M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, and M. C. Cardoso, “Measurement of replication structures at the nanometer scale using super-resolution light microscopy,” Nucleic Acids Res. 38, 1–11 (2009).
[PubMed]

Dunsby, C.

J. McGinty, K. B. Tahir, R. Laine, C. B. Talbot, C. Dunsby, M. A. A. Neil, L. Quintana, J. Swoger, J. Sharpe, and P. M. W. French, “Fluorescence lifetime optical projection tomography,” J Biophotonics 1(5), 390–394 (2008).
[CrossRef] [PubMed]

Favicchio, R.

Feruglio, P. F.

Fexon, L.

C. Vinegoni, L. Fexon, P. F. Feruglio, M. Pivovarov, J. L. Figueiredo, M. Nahrendorf, A. Pozzo, A. Sbarbati, and R. Weissleder, “High throughput transmission optical projection tomography using low cost graphics processing unit,” Opt. Express 17(25), 22320–22332 (2009).
[CrossRef] [PubMed]

C. Vinegoni, D. Razansky, J. L. Figueiredo, L. Fexon, M. Pivovarov, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Born normalization for fluorescence optical projection tomography for whole heart imaging,” J. Vis. Exp. 28(28), 1389 (2009).
[PubMed]

Figueiredo, J. L.

C. Vinegoni, D. Razansky, J. L. Figueiredo, L. Fexon, M. Pivovarov, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Born normalization for fluorescence optical projection tomography for whole heart imaging,” J. Vis. Exp. 28(28), 1389 (2009).
[PubMed]

C. Vinegoni, L. Fexon, P. F. Feruglio, M. Pivovarov, J. L. Figueiredo, M. Nahrendorf, A. Pozzo, A. Sbarbati, and R. Weissleder, “High throughput transmission optical projection tomography using low cost graphics processing unit,” Opt. Express 17(25), 22320–22332 (2009).
[CrossRef] [PubMed]

French, P. M. W.

J. McGinty, K. B. Tahir, R. Laine, C. B. Talbot, C. Dunsby, M. A. A. Neil, L. Quintana, J. Swoger, J. Sharpe, and P. M. W. French, “Fluorescence lifetime optical projection tomography,” J Biophotonics 1(5), 390–394 (2008).
[CrossRef] [PubMed]

Gahl, A.

D. Baddeley, V. O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P. M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, and M. C. Cardoso, “Measurement of replication structures at the nanometer scale using super-resolution light microscopy,” Nucleic Acids Res. 38, 1–11 (2009).
[PubMed]

Girirajan, T. P.

S. T. Hess, T. P. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[CrossRef] [PubMed]

Grier, D. G.

J. C. Crocker and D. G. Grier, “Methods of Digital Video Microscopy for Colloidal Studies,” J. Colloid Interface Sci. 179(1), 298–310 (1996).
[CrossRef]

Hecksher-Sørensen, J.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[CrossRef] [PubMed]

Heintzmann, R.

L. M. Hirvonen, K. Wicker, O. Mandula, and R. Heintzmann, “Structured illumination microscopy of a living cell,” Eur. Biophys. J. 38(6), 807–812 (2009).
[CrossRef] [PubMed]

Henkelman, R. M.

J. R. Walls, J. G. Sled, J. Sharpe, and R. M. Henkelman, “Resolution improvement in emission optical projection tomography,” Phys. Med. Biol. 52(10), 2775–2790 (2007).
[CrossRef] [PubMed]

J. R. Walls, J. G. Sled, J. Sharpe, and R. M. Henkelman, “Correction of artefacts in optical projection tomography,” Phys. Med. Biol. 50(19), 4645–4665 (2005).
[CrossRef] [PubMed]

Hess, H. F.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Hess, S. T.

S. T. Hess, T. P. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[CrossRef] [PubMed]

Hill, B.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[CrossRef] [PubMed]

Hirvonen, L. M.

L. M. Hirvonen, K. Wicker, O. Mandula, and R. Heintzmann, “Structured illumination microscopy of a living cell,” Eur. Biophys. J. 38(6), 807–812 (2009).
[CrossRef] [PubMed]

Huisken, J.

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

Hutton, B. F.

L. R. Barnden, J. Dickson, and B. F. Hutton, “Detection and validation of the body edge in low count emission tomography images,” Comput. Methods Programs Biomed. 84(2-3), 153–161 (2006).
[CrossRef] [PubMed]

Ji, N.

N. Ji, D. E. Milkie, and E. Betzig, “Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues,” Nat. Methods 7(2), 141–147 (2010).
[CrossRef] [PubMed]

Katsevich, A.

A. Katsevich, “An accurate approximate algorithm for motion compensation in two-dimensional tomography,” Inverse Probl. 26(6), 065007 (2010).
[CrossRef]

Konstantinides, N.

U. J. Birk, A. Darrell, N. Konstantinides, A. Sarasa-Renedo, and J. Ripoll, “Improved Reconstructions and Generalized Filtered Back Projection for Optical Projection Tomography,” Appl. Opt. submitted.

Laine, R.

J. McGinty, K. B. Tahir, R. Laine, C. B. Talbot, C. Dunsby, M. A. A. Neil, L. Quintana, J. Swoger, J. Sharpe, and P. M. W. French, “Fluorescence lifetime optical projection tomography,” J Biophotonics 1(5), 390–394 (2008).
[CrossRef] [PubMed]

Leonhardt, H.

D. Baddeley, V. O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P. M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, and M. C. Cardoso, “Measurement of replication structures at the nanometer scale using super-resolution light microscopy,” Nucleic Acids Res. 38, 1–11 (2009).
[PubMed]

Lindwasser, O. W.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Lippincott-Schwartz, J.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Mamalaki, C.

Mandula, O.

L. M. Hirvonen, K. Wicker, O. Mandula, and R. Heintzmann, “Structured illumination microscopy of a living cell,” Eur. Biophys. J. 38(6), 807–812 (2009).
[CrossRef] [PubMed]

Marias, K.

A. Darrell, H. Meyer, K. Marias, M. Brady, and J. Ripoll, “Weighted filtered backprojection for quantitative fluorescence optical projection tomography,” Phys. Med. Biol. 53(14), 3863–3881 (2008).
[CrossRef] [PubMed]

Martin, S.

D. Baddeley, V. O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P. M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, and M. C. Cardoso, “Measurement of replication structures at the nanometer scale using super-resolution light microscopy,” Nucleic Acids Res. 38, 1–11 (2009).
[PubMed]

Mason, M. D.

S. T. Hess, T. P. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[CrossRef] [PubMed]

McGinty, J.

J. McGinty, K. B. Tahir, R. Laine, C. B. Talbot, C. Dunsby, M. A. A. Neil, L. Quintana, J. Swoger, J. Sharpe, and P. M. W. French, “Fluorescence lifetime optical projection tomography,” J Biophotonics 1(5), 390–394 (2008).
[CrossRef] [PubMed]

Metaxakis, A.

H. Meyer, A. Darrell, A. Metaxakis, C. Savakis, and J. Ripoll, “Optical Projection Tomography for In-Vivo Imaging of Drosophila melanogaster,” Microscopy and Analysis 22, 19–22 (2008).

Meyer, H.

H. Meyer, A. Darrell, A. Metaxakis, C. Savakis, and J. Ripoll, “Optical Projection Tomography for In-Vivo Imaging of Drosophila melanogaster,” Microscopy and Analysis 22, 19–22 (2008).

A. Darrell, H. Meyer, K. Marias, M. Brady, and J. Ripoll, “Weighted filtered backprojection for quantitative fluorescence optical projection tomography,” Phys. Med. Biol. 53(14), 3863–3881 (2008).
[CrossRef] [PubMed]

Milkie, D. E.

N. Ji, D. E. Milkie, and E. Betzig, “Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues,” Nat. Methods 7(2), 141–147 (2010).
[CrossRef] [PubMed]

Nahrendorf, M.

C. Vinegoni, D. Razansky, J. L. Figueiredo, L. Fexon, M. Pivovarov, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Born normalization for fluorescence optical projection tomography for whole heart imaging,” J. Vis. Exp. 28(28), 1389 (2009).
[PubMed]

C. Vinegoni, L. Fexon, P. F. Feruglio, M. Pivovarov, J. L. Figueiredo, M. Nahrendorf, A. Pozzo, A. Sbarbati, and R. Weissleder, “High throughput transmission optical projection tomography using low cost graphics processing unit,” Opt. Express 17(25), 22320–22332 (2009).
[CrossRef] [PubMed]

Neil, M. A. A.

J. McGinty, K. B. Tahir, R. Laine, C. B. Talbot, C. Dunsby, M. A. A. Neil, L. Quintana, J. Swoger, J. Sharpe, and P. M. W. French, “Fluorescence lifetime optical projection tomography,” J Biophotonics 1(5), 390–394 (2008).
[CrossRef] [PubMed]

Ntziachristos, V.

C. Vinegoni, D. Razansky, J. L. Figueiredo, L. Fexon, M. Pivovarov, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Born normalization for fluorescence optical projection tomography for whole heart imaging,” J. Vis. Exp. 28(28), 1389 (2009).
[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]

R. B. Schulz, J. Ripoll, and V. Ntziachristos, “Noncontact optical tomography of turbid media,” Opt. Lett. 28(18), 1701–1703 (2003).
[CrossRef] [PubMed]

Olenych, S.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Patterson, G. H.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Perrimon, N.

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]

Perry, P.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[CrossRef] [PubMed]

Pitsouli, C.

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]

Pivovarov, M.

C. Vinegoni, L. Fexon, P. F. Feruglio, M. Pivovarov, J. L. Figueiredo, M. Nahrendorf, A. Pozzo, A. Sbarbati, and R. Weissleder, “High throughput transmission optical projection tomography using low cost graphics processing unit,” Opt. Express 17(25), 22320–22332 (2009).
[CrossRef] [PubMed]

C. Vinegoni, D. Razansky, J. L. Figueiredo, L. Fexon, M. Pivovarov, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Born normalization for fluorescence optical projection tomography for whole heart imaging,” J. Vis. Exp. 28(28), 1389 (2009).
[PubMed]

Pombo, A.

D. Baddeley, V. O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P. M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, and M. C. Cardoso, “Measurement of replication structures at the nanometer scale using super-resolution light microscopy,” Nucleic Acids Res. 38, 1–11 (2009).
[PubMed]

Pozzo, A.

Quintana, L.

J. McGinty, K. B. Tahir, R. Laine, C. B. Talbot, C. Dunsby, M. A. A. Neil, L. Quintana, J. Swoger, J. Sharpe, and P. M. W. French, “Fluorescence lifetime optical projection tomography,” J Biophotonics 1(5), 390–394 (2008).
[CrossRef] [PubMed]

Razansky, D.

C. Vinegoni, D. Razansky, J. L. Figueiredo, L. Fexon, M. Pivovarov, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Born normalization for fluorescence optical projection tomography for whole heart imaging,” J. Vis. Exp. 28(28), 1389 (2009).
[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]

Ripoll, J.

A. Sarasa-Renedo, R. Favicchio, U. Birk, G. Zacharakis, C. Mamalaki, and J. Ripoll, “Source intensity profile in noncontact optical tomography,” Opt. Lett. 35(1), 34–36 (2010).
[CrossRef]

H. Meyer, A. Darrell, A. Metaxakis, C. Savakis, and J. Ripoll, “Optical Projection Tomography for In-Vivo Imaging of Drosophila melanogaster,” Microscopy and Analysis 22, 19–22 (2008).

A. Darrell, H. Meyer, K. Marias, M. Brady, and J. Ripoll, “Weighted filtered backprojection for quantitative fluorescence optical projection tomography,” Phys. Med. Biol. 53(14), 3863–3881 (2008).
[CrossRef] [PubMed]

R. B. Schulz, J. Ripoll, and V. Ntziachristos, “Noncontact optical tomography of turbid media,” Opt. Lett. 28(18), 1701–1703 (2003).
[CrossRef] [PubMed]

U. J. Birk, A. Darrell, N. Konstantinides, A. Sarasa-Renedo, and J. Ripoll, “Improved Reconstructions and Generalized Filtered Back Projection for Optical Projection Tomography,” Appl. Opt. submitted.

Ross, A.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[CrossRef] [PubMed]

Rust, M. J.

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[CrossRef] [PubMed]

Sanz-Ezquerro, J.

M. J. Boot, C. H. Westerberg, J. Sanz-Ezquerro, J. Cotterell, R. Schweitzer, M. Torres, and J. Sharpe, “In vitro whole-organ imaging: 4D quantification of growing mouse limb buds,” Nat. Methods 5(7), 609–612 (2008).
[CrossRef] [PubMed]

Sarasa-Renedo, A.

A. Sarasa-Renedo, R. Favicchio, U. Birk, G. Zacharakis, C. Mamalaki, and J. Ripoll, “Source intensity profile in noncontact optical tomography,” Opt. Lett. 35(1), 34–36 (2010).
[CrossRef]

U. J. Birk, A. Darrell, N. Konstantinides, A. Sarasa-Renedo, and J. Ripoll, “Improved Reconstructions and Generalized Filtered Back Projection for Optical Projection Tomography,” Appl. Opt. submitted.

Savakis, C.

H. Meyer, A. Darrell, A. Metaxakis, C. Savakis, and J. Ripoll, “Optical Projection Tomography for In-Vivo Imaging of Drosophila melanogaster,” Microscopy and Analysis 22, 19–22 (2008).

Sbarbati, A.

Schermelleh, L.

D. Baddeley, V. O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P. M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, and M. C. Cardoso, “Measurement of replication structures at the nanometer scale using super-resolution light microscopy,” Nucleic Acids Res. 38, 1–11 (2009).
[PubMed]

Schulz, R. B.

Schweitzer, R.

M. J. Boot, C. H. Westerberg, J. Sanz-Ezquerro, J. Cotterell, R. Schweitzer, M. Torres, and J. Sharpe, “In vitro whole-organ imaging: 4D quantification of growing mouse limb buds,” Nat. Methods 5(7), 609–612 (2008).
[CrossRef] [PubMed]

Sharpe, J.

M. J. Boot, C. H. Westerberg, J. Sanz-Ezquerro, J. Cotterell, R. Schweitzer, M. Torres, and J. Sharpe, “In vitro whole-organ imaging: 4D quantification of growing mouse limb buds,” Nat. Methods 5(7), 609–612 (2008).
[CrossRef] [PubMed]

J. McGinty, K. B. Tahir, R. Laine, C. B. Talbot, C. Dunsby, M. A. A. Neil, L. Quintana, J. Swoger, J. Sharpe, and P. M. W. French, “Fluorescence lifetime optical projection tomography,” J Biophotonics 1(5), 390–394 (2008).
[CrossRef] [PubMed]

J. R. Walls, J. G. Sled, J. Sharpe, and R. M. Henkelman, “Resolution improvement in emission optical projection tomography,” Phys. Med. Biol. 52(10), 2775–2790 (2007).
[CrossRef] [PubMed]

J. R. Walls, J. G. Sled, J. Sharpe, and R. M. Henkelman, “Correction of artefacts in optical projection tomography,” Phys. Med. Biol. 50(19), 4645–4665 (2005).
[CrossRef] [PubMed]

J. Sharpe, “Optical projection tomography,” Annu. Rev. Biomed. Eng. 6(1), 209–228 (2004).
[CrossRef] [PubMed]

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[CrossRef] [PubMed]

Sled, J. G.

J. R. Walls, J. G. Sled, J. Sharpe, and R. M. Henkelman, “Resolution improvement in emission optical projection tomography,” Phys. Med. Biol. 52(10), 2775–2790 (2007).
[CrossRef] [PubMed]

J. R. Walls, J. G. Sled, J. Sharpe, and R. M. Henkelman, “Correction of artefacts in optical projection tomography,” Phys. Med. Biol. 50(19), 4645–4665 (2005).
[CrossRef] [PubMed]

Sougrat, R.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Stelzer, E. H.

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

Strickler, J. H.

W. Denk, J. H. Strickler, and W. W. Webb, “Two-photon laser scanning fluorescence microscopy,” Science 248(4951), 73–76 (1990).
[CrossRef] [PubMed]

Swoger, J.

J. McGinty, K. B. Tahir, R. Laine, C. B. Talbot, C. Dunsby, M. A. A. Neil, L. Quintana, J. Swoger, J. Sharpe, and P. M. W. French, “Fluorescence lifetime optical projection tomography,” J Biophotonics 1(5), 390–394 (2008).
[CrossRef] [PubMed]

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

Tahir, K. B.

J. McGinty, K. B. Tahir, R. Laine, C. B. Talbot, C. Dunsby, M. A. A. Neil, L. Quintana, J. Swoger, J. Sharpe, and P. M. W. French, “Fluorescence lifetime optical projection tomography,” J Biophotonics 1(5), 390–394 (2008).
[CrossRef] [PubMed]

Talbot, C. B.

J. McGinty, K. B. Tahir, R. Laine, C. B. Talbot, C. Dunsby, M. A. A. Neil, L. Quintana, J. Swoger, J. Sharpe, and P. M. W. French, “Fluorescence lifetime optical projection tomography,” J Biophotonics 1(5), 390–394 (2008).
[CrossRef] [PubMed]

Torres, M.

M. J. Boot, C. H. Westerberg, J. Sanz-Ezquerro, J. Cotterell, R. Schweitzer, M. Torres, and J. Sharpe, “In vitro whole-organ imaging: 4D quantification of growing mouse limb buds,” Nat. Methods 5(7), 609–612 (2008).
[CrossRef] [PubMed]

Vinegoni, C.

C. Vinegoni, D. Razansky, J. L. Figueiredo, L. Fexon, M. Pivovarov, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Born normalization for fluorescence optical projection tomography for whole heart imaging,” J. Vis. Exp. 28(28), 1389 (2009).
[PubMed]

C. Vinegoni, L. Fexon, P. F. Feruglio, M. Pivovarov, J. L. Figueiredo, M. Nahrendorf, A. Pozzo, A. Sbarbati, and R. Weissleder, “High throughput transmission optical projection tomography using low cost graphics processing unit,” Opt. Express 17(25), 22320–22332 (2009).
[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]

Walls, J. R.

J. R. Walls, J. G. Sled, J. Sharpe, and R. M. Henkelman, “Resolution improvement in emission optical projection tomography,” Phys. Med. Biol. 52(10), 2775–2790 (2007).
[CrossRef] [PubMed]

J. R. Walls, J. G. Sled, J. Sharpe, and R. M. Henkelman, “Correction of artefacts in optical projection tomography,” Phys. Med. Biol. 50(19), 4645–4665 (2005).
[CrossRef] [PubMed]

Webb, W. W.

W. Denk, J. H. Strickler, and W. W. Webb, “Two-photon laser scanning fluorescence microscopy,” Science 248(4951), 73–76 (1990).
[CrossRef] [PubMed]

Weiland, Y.

D. Baddeley, Y. Weiland, C. Batram, U. Birk, and C. Cremer, “Model based precision structural measurements on barely resolved objects,” J. Microsc. 237(1), 70–78 (2010).
[CrossRef] [PubMed]

D. Baddeley, C. Batram, Y. Weiland, C. Cremer, and U. J. Birk, “Nanostructure analysis using spatially modulated illumination microscopy,” Nat. Protoc. 2(10), 2640–2646 (2007).
[CrossRef] [PubMed]

Weissleder, R.

C. Vinegoni, L. Fexon, P. F. Feruglio, M. Pivovarov, J. L. Figueiredo, M. Nahrendorf, A. Pozzo, A. Sbarbati, and R. Weissleder, “High throughput transmission optical projection tomography using low cost graphics processing unit,” Opt. Express 17(25), 22320–22332 (2009).
[CrossRef] [PubMed]

C. Vinegoni, D. Razansky, J. L. Figueiredo, L. Fexon, M. Pivovarov, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Born normalization for fluorescence optical projection tomography for whole heart imaging,” J. Vis. Exp. 28(28), 1389 (2009).
[PubMed]

Westerberg, C. H.

M. J. Boot, C. H. Westerberg, J. Sanz-Ezquerro, J. Cotterell, R. Schweitzer, M. Torres, and J. Sharpe, “In vitro whole-organ imaging: 4D quantification of growing mouse limb buds,” Nat. Methods 5(7), 609–612 (2008).
[CrossRef] [PubMed]

Wicker, K.

L. M. Hirvonen, K. Wicker, O. Mandula, and R. Heintzmann, “Structured illumination microscopy of a living cell,” Eur. Biophys. J. 38(6), 807–812 (2009).
[CrossRef] [PubMed]

Wittbrodt, J.

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

Zacharakis, G.

Zhuang, X.

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[CrossRef] [PubMed]

Annu. Rev. Biomed. Eng. (1)

J. Sharpe, “Optical projection tomography,” Annu. Rev. Biomed. Eng. 6(1), 209–228 (2004).
[CrossRef] [PubMed]

Appl. Opt. (1)

U. J. Birk, A. Darrell, N. Konstantinides, A. Sarasa-Renedo, and J. Ripoll, “Improved Reconstructions and Generalized Filtered Back Projection for Optical Projection Tomography,” Appl. Opt. submitted.

Biophys. J. (1)

S. T. Hess, T. P. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J. 91(11), 4258–4272 (2006).
[CrossRef] [PubMed]

Comput. Methods Programs Biomed. (1)

L. R. Barnden, J. Dickson, and B. F. Hutton, “Detection and validation of the body edge in low count emission tomography images,” Comput. Methods Programs Biomed. 84(2-3), 153–161 (2006).
[CrossRef] [PubMed]

Eur. Biophys. J. (1)

L. M. Hirvonen, K. Wicker, O. Mandula, and R. Heintzmann, “Structured illumination microscopy of a living cell,” Eur. Biophys. J. 38(6), 807–812 (2009).
[CrossRef] [PubMed]

Genetics (1)

S. Brenner, “The genetics of Caenorhabditis elegans,” Genetics 77(1), 71–94 (1974).
[PubMed]

Inverse Probl. (1)

A. Katsevich, “An accurate approximate algorithm for motion compensation in two-dimensional tomography,” Inverse Probl. 26(6), 065007 (2010).
[CrossRef]

J Biophotonics (1)

J. McGinty, K. B. Tahir, R. Laine, C. B. Talbot, C. Dunsby, M. A. A. Neil, L. Quintana, J. Swoger, J. Sharpe, and P. M. W. French, “Fluorescence lifetime optical projection tomography,” J Biophotonics 1(5), 390–394 (2008).
[CrossRef] [PubMed]

J. Colloid Interface Sci. (1)

J. C. Crocker and D. G. Grier, “Methods of Digital Video Microscopy for Colloidal Studies,” J. Colloid Interface Sci. 179(1), 298–310 (1996).
[CrossRef]

J. Microsc. (1)

D. Baddeley, Y. Weiland, C. Batram, U. Birk, and C. Cremer, “Model based precision structural measurements on barely resolved objects,” J. Microsc. 237(1), 70–78 (2010).
[CrossRef] [PubMed]

J. Nucl. Med. (1)

J. Culver, W. Akers, and S. Achilefu, “Multimodality molecular imaging with combined optical and SPECT/PET modalities,” J. Nucl. Med. 49(2), 169–172 (2008).
[CrossRef] [PubMed]

J. Vis. Exp. (1)

C. Vinegoni, D. Razansky, J. L. Figueiredo, L. Fexon, M. Pivovarov, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Born normalization for fluorescence optical projection tomography for whole heart imaging,” J. Vis. Exp. 28(28), 1389 (2009).
[PubMed]

Microscopy and Analysis (1)

H. Meyer, A. Darrell, A. Metaxakis, C. Savakis, and J. Ripoll, “Optical Projection Tomography for In-Vivo Imaging of Drosophila melanogaster,” Microscopy and Analysis 22, 19–22 (2008).

Nat. Methods (4)

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]

M. J. Boot, C. H. Westerberg, J. Sanz-Ezquerro, J. Cotterell, R. Schweitzer, M. Torres, and J. Sharpe, “In vitro whole-organ imaging: 4D quantification of growing mouse limb buds,” Nat. Methods 5(7), 609–612 (2008).
[CrossRef] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3(10), 793–796 (2006).
[CrossRef] [PubMed]

N. Ji, D. E. Milkie, and E. Betzig, “Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues,” Nat. Methods 7(2), 141–147 (2010).
[CrossRef] [PubMed]

Nat. Protoc. (1)

D. Baddeley, C. Batram, Y. Weiland, C. Cremer, and U. J. Birk, “Nanostructure analysis using spatially modulated illumination microscopy,” Nat. Protoc. 2(10), 2640–2646 (2007).
[CrossRef] [PubMed]

Nucleic Acids Res. (1)

D. Baddeley, V. O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P. M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, and M. C. Cardoso, “Measurement of replication structures at the nanometer scale using super-resolution light microscopy,” Nucleic Acids Res. 38, 1–11 (2009).
[PubMed]

Opt. Express (1)

Opt. Lett. (2)

Phys. Med. Biol. (3)

A. Darrell, H. Meyer, K. Marias, M. Brady, and J. Ripoll, “Weighted filtered backprojection for quantitative fluorescence optical projection tomography,” Phys. Med. Biol. 53(14), 3863–3881 (2008).
[CrossRef] [PubMed]

J. R. Walls, J. G. Sled, J. Sharpe, and R. M. Henkelman, “Correction of artefacts in optical projection tomography,” Phys. Med. Biol. 50(19), 4645–4665 (2005).
[CrossRef] [PubMed]

J. R. Walls, J. G. Sled, J. Sharpe, and R. M. Henkelman, “Resolution improvement in emission optical projection tomography,” Phys. Med. Biol. 52(10), 2775–2790 (2007).
[CrossRef] [PubMed]

Science (4)

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[CrossRef] [PubMed]

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

W. Denk, J. H. Strickler, and W. W. Webb, “Two-photon laser scanning fluorescence microscopy,” Science 248(4951), 73–76 (1990).
[CrossRef] [PubMed]

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Other (4)

A. C. Kak, and M. Slaney, Principles of Computerized Tomographic Imaging (IEEE Service Center, 1988).

Quantitative Imaging Group at the Faculty of Applied Sciences, Delft University of Technology, “DIPimage & DIPlib,” http://www.diplib.org/ .

U. J. Birk, A. Darrell, N. Konstantinides, and J. Ripoll, “Correction of Lateral Movement and Spherical Aberrations in Optical Projection Tomography,” in Biomedical Optics, OSA Technical Digest (CD) (Optical Society of America, 2010), p. BTuF6.

A. Bassi, D. Brida, C. D'Andrea, G. Valentini, S. De Silvestri, G. Cerullo, and R. Cubeddu, “Time gated optical projection tomography for 3D imaging of highly scattering biological models,” in Biomedical Optics, OSA Technical Digest (CD) (Optical Society of America, 2010), p. BTuF5.

Supplementary Material (2)

» Media 1: MPG (1403 KB)     
» Media 2: MPG (933 KB)     

Cited By

OSA participates in CrossRef's Cited-By Linking service. Citing articles from OSA journals and other participating publishers are listed here.

Alert me when this article is cited.


Figures (7)

Fig. 1
Fig. 1

OPT setup: The capillary (C) with the specimen is placed in a bath (B). White light (LED2) passes a diffusor (D) before illuminating the sample. Fluorescence excitation is achieved by blue light (LED1) which is focused (L) and filtered (F1). The light detection system consists of an objective lens (OL), an iris (I), an emission filter (F2), a tube lens (TL), and a CCD camera. The focal plane of the objective lens is aligned with the center of the specimen.

Fig. 2
Fig. 2

Correction of longitudinal shifts in fluorescence images. a) 2D projection (raw data) as acquired in the experiment. The three arrows indicate the positions of the GFP expression loci of three touch neurons, which appear as point-like structures in the acquired images. b) The average z-displacement of the three expression loci in the 500 projections can be used to correct for longitudinal shifts.

Fig. 3
Fig. 3

Correction of lateral shifts. a) A 2D projection (raw data, autofluorescence of Parhyale hawaiensis, pseudo color). The blue lines indicate the positions of the capillary walls determined automatically. The dashed line indicates a position in which the object is highly structured, and the corresponding sinogram (b) indicates that the objects are rather small and approximately point-like. From a preliminary reconstruction of this sinogram, the positions of the extremities of the specimens can be estimated. c) The computer generated sinogram with objects at the same positions as those determined from b). By applying a least squares fit, the lateral shifts between the image b) and c) can be obtained, and used to correct for the lateral shifts.

Fig. 4
Fig. 4

Reconstructions of a single z-slice of OPT data taken from C. elegans. a) A theoretical experiment in which the center of rotation (COR) used for the reconstruction is offset by two pixels. b) Real experimental data most often shows two objects in the reconstruction, which cannot be overlaid by shifting the COR. c) After applying an optimization function in which the projections are shifted to yield the maximum variance of the intensities in the reconstructions: Several artifacts are visible e.g. where bright or dark objects have been smeared out (arrows). This reconstruction was then radon transformed, and the lateral shifts between the transformed reconstruction and the original projections were determined as described in the section “self-correcting approach”. Using these shifts as the refined correction for the lateral shifts, the reconstruction in d) was obtained.

Fig. 5
Fig. 5

Iterative correction of (in this case) lateral shifts using a self-correcting approach. The blue curve indicates the shifts found using one of the approaches described above. After applying these shifts to the individual projections, a reconstruction is calculated. Using a forward radon transform as in a virtual experiment, this reconstruction is rotated and projections are calculated for each angle. The shifts between the thus obtained projections and the original data are determined (red dotted curve). This data is smoothed to obtain the new lateral shifts (black curve, dashed).

Fig. 6
Fig. 6

Reconstructions of a data set taken from C. elegans in-vivo using the above correction methods. a) and b) show the mean intensity of the white light reconstruction (absorption) along the respective third axis. c) shows a 3D view of this data as volume rendering in gray (absorption). To emphasize the non-absorbing internal structure of the pharynx, an additional volume rendering of the inverted data set is shown in blue-green (Media 1); the inset shows the colormaps used for absorption values between zero and 1 = maximum absorption. d) shows the absorption (in gray) together with the reconstructed fluorescence data (in green) (Media 2). e) shows the xz-slice at y = 0 of the absorption as indicated in c).

Fig. 7
Fig. 7

Summary of the applied corrections for white light data (top half) and fluorescence data (bottom half). Left column: Raw z-y-data-slices of the 3D reconstruction before and after applying the correction methods. Right column: Shifts used to correct the projections prior to the reconstruction. First the longitudinal shifts were corrected, and then the lateral shifts. Slices of the reconstructions after correction for longitudinal and for lateral shifts are much sharper, and do not show ghost images, indicating an improved reconstruction.

Equations (3)

Equations on this page are rendered with MathJax. Learn more.

r i + 1 ( x , y , z ) = FBP [ p 0 ( y s y i ( θ ) , z s z i ( θ ) , θ ) ]
f ( θ ) = ( f y ( θ ) , f z ( θ ) ) = findshifts ( Radon [ r i + 1 ( x , y , z ) ] , p 0 ( y , z , θ ) )
s i + 1 ( θ ) = ( s y i + 1 ( θ ) , s z i + 1 ( θ ) ) = smooth [ f ( θ ) ]

Metrics