Abstract

We implement the use of a graphics processing unit (GPU) in order to achieve real time data processing for high-throughput transmission optical projection tomography imaging. By implementing the GPU we have obtained a 300 fold performance enhancement in comparison to a CPU workstation implementation. This enables to obtain on-the-fly reconstructions enabling for high throughput imaging.

© 2009 OSA

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  1. V. Ntziachristos, J. Ripoll, L. V. Wang, and R. Weissleder, “Looking and listening to light: the evolution of whole-body photonic imaging,” Nat. Biotechnol. 23(3), 313–320 (2005).
    [CrossRef] [PubMed]
  2. D. Razansky, M. Distel, C. Vinegoni, R. Ma, N. Perrimon, R. W. Köster, and V. Ntziachristos, “Multispectral opto-acoustic tomography of deep-seated fluorescent proteins in vivo,” Nat. Photonics 3(7), 412–417 (2009).
    [CrossRef]
  3. 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 (2007).
    [CrossRef] [PubMed]
  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]
  5. H. S. Sakhalkar and M. Oldham, “Fast, high-resolution 3D dosimetry utilizing a novel optical-CT scanner incorporating tertiary telecentric collimation,” Med. Phys. 35(1), 101–111 (2008).
    [CrossRef] [PubMed]
  6. J. Radon, “On the determination of function from their integrals along certain manifolds,” Ber. Saechs. Akad. Wiss, Leipzig Math. Phys. Kl. 69, 262–277 (1917).
  7. R. M. Mersereau and A. V. Oppenheim, “Digital reconstruction of multidimensional signals from their projections,” Proc. IEEE 62(10), 1319–1338 (1974).
    [CrossRef]
  8. R. M. Mersereau, “Direct Fourier transform techniques in 3-D image reconstruction,” Comput. Biol. Med. 6(4), 247–258 (1976).
    [CrossRef] [PubMed]
  9. H. Stark, J. W. Woods, I. Paul, and R. Hingorani, “An investigation of computerized tomography by direct Fourier inversion and optimum interpolation,” IEEE Trans. Biomed. Eng. 28(7), 496–505 (1981).
    [CrossRef] [PubMed]
  10. R. M. Lewitt, “Reconstruction algorithms: Transform methods,” Proc. IEEE 71(3), 390–408 (1983).
    [CrossRef]
  11. J. D. O’Sullivan, “A fast sinc function gridding algorithm for fourier inversion in computer tomography,” IEEE Trans. Med. Imaging 4(4), 200–207 (1985).
    [CrossRef] [PubMed]
  12. S. Matej and I. Bajla, “A high-speed reconstruction from projections using direct Fourier method with optimized parameters-an experimental analysis,” IEEE Trans. Med. Imaging 9(4), 421–429 (1990).
    [CrossRef] [PubMed]
  13. H. Schomberg and J. Timmer, “The gridding method for image reconstruction by Fourier transformation,” IEEE Trans. Med. Imaging 14(3), 596–607 (1995).
    [CrossRef] [PubMed]
  14. A. Brandt, J. Mann, M. Brodski, and M. Galun, “A fast and accurate multilevel inversion of the radon transform,” SIAM J. Appl. Math. 60(2), 437–462 (2000).
    [CrossRef]
  15. S. Basu and Y. Bresler, “O(N(2)log(2)N) filtered backprojection reconstruction algorithm for tomography,” IEEE Trans. Image Process. 9(10), 1760–1773 (2000).
    [CrossRef] [PubMed]
  16. G. C. Sharp, N. Kandasamy, H. Singh, and M. Folkert, “GPU-based streaming architectures for fast cone-beam CT image reconstruction and demons deformable registration,” Phys. Med. Biol. 52(19), 5771–5783 (2007).
    [CrossRef] [PubMed]
  17. T. Shimobaba, Y. Sato, J. Miura, M. Takenouchi, and T. Ito, “Real-time digital holographic microscopy using the graphic processing unit,” Opt. Express 16(16), 11776–11781 (2008).
    [CrossRef] [PubMed]
  18. K. Mueller, F. Xu, and N. Neophytou, “Why do GPUs work so well for acceleration of CT? SPIE Electronic Imaging '07,” Keynote, Computational Imaging V, San Jose, (2007).
  19. H. Scherl, B. Keck, M. Kowarschik, and J. Hornegger, “Fast GPU-Based CT Reconstruction using the Common Unified Device Architecture (CUDA),” Nuclear Science Symposium Conference Record 6, 4464–4466 (2007).
  20. P. B. Noël, A. Walczak, K. R. Hoffmann, J. Xu, J. J. Corso, and S. Schafer, “Clinical Evaluation of GPU-Based Cone Beam Computed Tomography,” Proc. of High-Performance Medical Image Computing and Computer-Aided Intervention (HP-MICCAI), (2008).
  21. J. B. T. M. Roerdink and M. A. Westenbrg, “Data-parallel tomographyc reconstruction: a comparison of filtered backprojection and direct fourier reconstruction,” Parallel Comput. 24(14), 2129–2142 (1998).
    [CrossRef]
  22. NVIDIA Corporation. CUDA Programming Guide (manual), February (2007).
  23. J. Nickolls, I. Buck, M. Garland, and K. Skadron, “Scalable parallel programming with CUDA,” Queueing Syst. 6, 40–53 (2008).
  24. J. Nickolls and I. Buck, “NVIDIA CUDA software and GPU parallel computing architecture,” Microprocessor Forum, May (2007).
  25. S. Ryoo, C. I. Rodrigues, S. S. Stone, S. S. Baghsorkhi, S. Z.Ueng, J. A. Stratton, and W. W. Hwu “Program Optimization Space Pruning for a Multithreaded GPU,” Proc. of the sixth annual IEEE/ACM int. symp. on Code gen. and opt, (2008).
  26. C. Vinegoni, D. Razansky, L. Fexon, J. L. Figueiredo, M. Pivovarov, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Born normalization for fluorescence optical projection tomography for whole heart imaging,” J Vis Exp. 28, 1389 (2009).
  27. C. Vinegoni, D. Razansky, J. L. Figueiredo, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Normalized Born ratio for fluorescence optical projection tomography,” Opt. Lett. 34(3), 319–321 (2009).
    [CrossRef] [PubMed]
  28. 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]

2009

D. Razansky, M. Distel, C. Vinegoni, R. Ma, N. Perrimon, R. W. Köster, and V. Ntziachristos, “Multispectral opto-acoustic tomography of deep-seated fluorescent proteins in vivo,” Nat. Photonics 3(7), 412–417 (2009).
[CrossRef]

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

C. Vinegoni, D. Razansky, J. L. Figueiredo, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Normalized Born ratio for fluorescence optical projection tomography,” Opt. Lett. 34(3), 319–321 (2009).
[CrossRef] [PubMed]

2008

J. Nickolls, I. Buck, M. Garland, and K. Skadron, “Scalable parallel programming with CUDA,” Queueing Syst. 6, 40–53 (2008).

T. Shimobaba, Y. Sato, J. Miura, M. Takenouchi, and T. Ito, “Real-time digital holographic microscopy using the graphic processing unit,” Opt. Express 16(16), 11776–11781 (2008).
[CrossRef] [PubMed]

H. S. Sakhalkar and M. Oldham, “Fast, high-resolution 3D dosimetry utilizing a novel optical-CT scanner incorporating tertiary telecentric collimation,” Med. Phys. 35(1), 101–111 (2008).
[CrossRef] [PubMed]

2007

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 (2007).
[CrossRef] [PubMed]

G. C. Sharp, N. Kandasamy, H. Singh, and M. Folkert, “GPU-based streaming architectures for fast cone-beam CT image reconstruction and demons deformable registration,” Phys. Med. Biol. 52(19), 5771–5783 (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]

2005

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

2002

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]

2000

A. Brandt, J. Mann, M. Brodski, and M. Galun, “A fast and accurate multilevel inversion of the radon transform,” SIAM J. Appl. Math. 60(2), 437–462 (2000).
[CrossRef]

S. Basu and Y. Bresler, “O(N(2)log(2)N) filtered backprojection reconstruction algorithm for tomography,” IEEE Trans. Image Process. 9(10), 1760–1773 (2000).
[CrossRef] [PubMed]

1998

J. B. T. M. Roerdink and M. A. Westenbrg, “Data-parallel tomographyc reconstruction: a comparison of filtered backprojection and direct fourier reconstruction,” Parallel Comput. 24(14), 2129–2142 (1998).
[CrossRef]

1995

H. Schomberg and J. Timmer, “The gridding method for image reconstruction by Fourier transformation,” IEEE Trans. Med. Imaging 14(3), 596–607 (1995).
[CrossRef] [PubMed]

1990

S. Matej and I. Bajla, “A high-speed reconstruction from projections using direct Fourier method with optimized parameters-an experimental analysis,” IEEE Trans. Med. Imaging 9(4), 421–429 (1990).
[CrossRef] [PubMed]

1985

J. D. O’Sullivan, “A fast sinc function gridding algorithm for fourier inversion in computer tomography,” IEEE Trans. Med. Imaging 4(4), 200–207 (1985).
[CrossRef] [PubMed]

1983

R. M. Lewitt, “Reconstruction algorithms: Transform methods,” Proc. IEEE 71(3), 390–408 (1983).
[CrossRef]

1981

H. Stark, J. W. Woods, I. Paul, and R. Hingorani, “An investigation of computerized tomography by direct Fourier inversion and optimum interpolation,” IEEE Trans. Biomed. Eng. 28(7), 496–505 (1981).
[CrossRef] [PubMed]

1976

R. M. Mersereau, “Direct Fourier transform techniques in 3-D image reconstruction,” Comput. Biol. Med. 6(4), 247–258 (1976).
[CrossRef] [PubMed]

1974

R. M. Mersereau and A. V. Oppenheim, “Digital reconstruction of multidimensional signals from their projections,” Proc. IEEE 62(10), 1319–1338 (1974).
[CrossRef]

1917

J. Radon, “On the determination of function from their integrals along certain manifolds,” Ber. Saechs. Akad. Wiss, Leipzig Math. Phys. Kl. 69, 262–277 (1917).

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]

Bajla, I.

S. Matej and I. Bajla, “A high-speed reconstruction from projections using direct Fourier method with optimized parameters-an experimental analysis,” IEEE Trans. Med. Imaging 9(4), 421–429 (1990).
[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]

Basu, S.

S. Basu and Y. Bresler, “O(N(2)log(2)N) filtered backprojection reconstruction algorithm for tomography,” IEEE Trans. Image Process. 9(10), 1760–1773 (2000).
[CrossRef] [PubMed]

Brandt, A.

A. Brandt, J. Mann, M. Brodski, and M. Galun, “A fast and accurate multilevel inversion of the radon transform,” SIAM J. Appl. Math. 60(2), 437–462 (2000).
[CrossRef]

Bresler, Y.

S. Basu and Y. Bresler, “O(N(2)log(2)N) filtered backprojection reconstruction algorithm for tomography,” IEEE Trans. Image Process. 9(10), 1760–1773 (2000).
[CrossRef] [PubMed]

Brodski, M.

A. Brandt, J. Mann, M. Brodski, and M. Galun, “A fast and accurate multilevel inversion of the radon transform,” SIAM J. Appl. Math. 60(2), 437–462 (2000).
[CrossRef]

Buck, I.

J. Nickolls, I. Buck, M. Garland, and K. Skadron, “Scalable parallel programming with CUDA,” Queueing Syst. 6, 40–53 (2008).

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]

Distel, M.

D. Razansky, M. Distel, C. Vinegoni, R. Ma, N. Perrimon, R. W. Köster, and V. Ntziachristos, “Multispectral opto-acoustic tomography of deep-seated fluorescent proteins in vivo,” Nat. Photonics 3(7), 412–417 (2009).
[CrossRef]

Fexon, L.

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

Figueiredo, J. L.

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

C. Vinegoni, D. Razansky, J. L. Figueiredo, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Normalized Born ratio for fluorescence optical projection tomography,” Opt. Lett. 34(3), 319–321 (2009).
[CrossRef] [PubMed]

Folkert, M.

G. C. Sharp, N. Kandasamy, H. Singh, and M. Folkert, “GPU-based streaming architectures for fast cone-beam CT image reconstruction and demons deformable registration,” Phys. Med. Biol. 52(19), 5771–5783 (2007).
[CrossRef] [PubMed]

Galun, M.

A. Brandt, J. Mann, M. Brodski, and M. Galun, “A fast and accurate multilevel inversion of the radon transform,” SIAM J. Appl. Math. 60(2), 437–462 (2000).
[CrossRef]

Garland, M.

J. Nickolls, I. Buck, M. Garland, and K. Skadron, “Scalable parallel programming with CUDA,” Queueing Syst. 6, 40–53 (2008).

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]

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]

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]

Hingorani, R.

H. Stark, J. W. Woods, I. Paul, and R. Hingorani, “An investigation of computerized tomography by direct Fourier inversion and optimum interpolation,” IEEE Trans. Biomed. Eng. 28(7), 496–505 (1981).
[CrossRef] [PubMed]

Ito, T.

Kandasamy, N.

G. C. Sharp, N. Kandasamy, H. Singh, and M. Folkert, “GPU-based streaming architectures for fast cone-beam CT image reconstruction and demons deformable registration,” Phys. Med. Biol. 52(19), 5771–5783 (2007).
[CrossRef] [PubMed]

Köster, R. W.

D. Razansky, M. Distel, C. Vinegoni, R. Ma, N. Perrimon, R. W. Köster, and V. Ntziachristos, “Multispectral opto-acoustic tomography of deep-seated fluorescent proteins in vivo,” Nat. Photonics 3(7), 412–417 (2009).
[CrossRef]

Lewitt, R. M.

R. M. Lewitt, “Reconstruction algorithms: Transform methods,” Proc. IEEE 71(3), 390–408 (1983).
[CrossRef]

Ma, R.

D. Razansky, M. Distel, C. Vinegoni, R. Ma, N. Perrimon, R. W. Köster, and V. Ntziachristos, “Multispectral opto-acoustic tomography of deep-seated fluorescent proteins in vivo,” Nat. Photonics 3(7), 412–417 (2009).
[CrossRef]

Mann, J.

A. Brandt, J. Mann, M. Brodski, and M. Galun, “A fast and accurate multilevel inversion of the radon transform,” SIAM J. Appl. Math. 60(2), 437–462 (2000).
[CrossRef]

Matej, S.

S. Matej and I. Bajla, “A high-speed reconstruction from projections using direct Fourier method with optimized parameters-an experimental analysis,” IEEE Trans. Med. Imaging 9(4), 421–429 (1990).
[CrossRef] [PubMed]

Mersereau, R. M.

R. M. Mersereau, “Direct Fourier transform techniques in 3-D image reconstruction,” Comput. Biol. Med. 6(4), 247–258 (1976).
[CrossRef] [PubMed]

R. M. Mersereau and A. V. Oppenheim, “Digital reconstruction of multidimensional signals from their projections,” Proc. IEEE 62(10), 1319–1338 (1974).
[CrossRef]

Miura, J.

Nahrendorf, M.

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

C. Vinegoni, D. Razansky, J. L. Figueiredo, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Normalized Born ratio for fluorescence optical projection tomography,” Opt. Lett. 34(3), 319–321 (2009).
[CrossRef] [PubMed]

Nickolls, J.

J. Nickolls, I. Buck, M. Garland, and K. Skadron, “Scalable parallel programming with CUDA,” Queueing Syst. 6, 40–53 (2008).

Ntziachristos, V.

D. Razansky, M. Distel, C. Vinegoni, R. Ma, N. Perrimon, R. W. Köster, and V. Ntziachristos, “Multispectral opto-acoustic tomography of deep-seated fluorescent proteins in vivo,” Nat. Photonics 3(7), 412–417 (2009).
[CrossRef]

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

C. Vinegoni, D. Razansky, J. L. Figueiredo, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Normalized Born ratio for fluorescence optical projection tomography,” Opt. Lett. 34(3), 319–321 (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 (2007).
[CrossRef] [PubMed]

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

O’Sullivan, J. D.

J. D. O’Sullivan, “A fast sinc function gridding algorithm for fourier inversion in computer tomography,” IEEE Trans. Med. Imaging 4(4), 200–207 (1985).
[CrossRef] [PubMed]

Oldham, M.

H. S. Sakhalkar and M. Oldham, “Fast, high-resolution 3D dosimetry utilizing a novel optical-CT scanner incorporating tertiary telecentric collimation,” Med. Phys. 35(1), 101–111 (2008).
[CrossRef] [PubMed]

Oppenheim, A. V.

R. M. Mersereau and A. V. Oppenheim, “Digital reconstruction of multidimensional signals from their projections,” Proc. IEEE 62(10), 1319–1338 (1974).
[CrossRef]

Paul, I.

H. Stark, J. W. Woods, I. Paul, and R. Hingorani, “An investigation of computerized tomography by direct Fourier inversion and optimum interpolation,” IEEE Trans. Biomed. Eng. 28(7), 496–505 (1981).
[CrossRef] [PubMed]

Perrimon, N.

D. Razansky, M. Distel, C. Vinegoni, R. Ma, N. Perrimon, R. W. Köster, and V. Ntziachristos, “Multispectral opto-acoustic tomography of deep-seated fluorescent proteins in vivo,” Nat. Photonics 3(7), 412–417 (2009).
[CrossRef]

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 (2007).
[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 (2007).
[CrossRef] [PubMed]

Pivovarov, M.

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

Radon, J.

J. Radon, “On the determination of function from their integrals along certain manifolds,” Ber. Saechs. Akad. Wiss, Leipzig Math. Phys. Kl. 69, 262–277 (1917).

Razansky, D.

C. Vinegoni, D. Razansky, J. L. Figueiredo, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Normalized Born ratio for fluorescence optical projection tomography,” Opt. Lett. 34(3), 319–321 (2009).
[CrossRef] [PubMed]

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

D. Razansky, M. Distel, C. Vinegoni, R. Ma, N. Perrimon, R. W. Köster, and V. Ntziachristos, “Multispectral opto-acoustic tomography of deep-seated fluorescent proteins in vivo,” Nat. Photonics 3(7), 412–417 (2009).
[CrossRef]

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 (2007).
[CrossRef] [PubMed]

Ripoll, J.

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

Roerdink, J. B. T. M.

J. B. T. M. Roerdink and M. A. Westenbrg, “Data-parallel tomographyc reconstruction: a comparison of filtered backprojection and direct fourier reconstruction,” Parallel Comput. 24(14), 2129–2142 (1998).
[CrossRef]

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]

Sakhalkar, H. S.

H. S. Sakhalkar and M. Oldham, “Fast, high-resolution 3D dosimetry utilizing a novel optical-CT scanner incorporating tertiary telecentric collimation,” Med. Phys. 35(1), 101–111 (2008).
[CrossRef] [PubMed]

Sato, Y.

Schomberg, H.

H. Schomberg and J. Timmer, “The gridding method for image reconstruction by Fourier transformation,” IEEE Trans. Med. Imaging 14(3), 596–607 (1995).
[CrossRef] [PubMed]

Sharp, G. C.

G. C. Sharp, N. Kandasamy, H. Singh, and M. Folkert, “GPU-based streaming architectures for fast cone-beam CT image reconstruction and demons deformable registration,” Phys. Med. Biol. 52(19), 5771–5783 (2007).
[CrossRef] [PubMed]

Sharpe, J.

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. 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]

Shimobaba, T.

Singh, H.

G. C. Sharp, N. Kandasamy, H. Singh, and M. Folkert, “GPU-based streaming architectures for fast cone-beam CT image reconstruction and demons deformable registration,” Phys. Med. Biol. 52(19), 5771–5783 (2007).
[CrossRef] [PubMed]

Skadron, K.

J. Nickolls, I. Buck, M. Garland, and K. Skadron, “Scalable parallel programming with CUDA,” Queueing Syst. 6, 40–53 (2008).

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]

Stark, H.

H. Stark, J. W. Woods, I. Paul, and R. Hingorani, “An investigation of computerized tomography by direct Fourier inversion and optimum interpolation,” IEEE Trans. Biomed. Eng. 28(7), 496–505 (1981).
[CrossRef] [PubMed]

Takenouchi, M.

Timmer, J.

H. Schomberg and J. Timmer, “The gridding method for image reconstruction by Fourier transformation,” IEEE Trans. Med. Imaging 14(3), 596–607 (1995).
[CrossRef] [PubMed]

Vinegoni, C.

C. Vinegoni, D. Razansky, J. L. Figueiredo, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Normalized Born ratio for fluorescence optical projection tomography,” Opt. Lett. 34(3), 319–321 (2009).
[CrossRef] [PubMed]

D. Razansky, M. Distel, C. Vinegoni, R. Ma, N. Perrimon, R. W. Köster, and V. Ntziachristos, “Multispectral opto-acoustic tomography of deep-seated fluorescent proteins in vivo,” Nat. Photonics 3(7), 412–417 (2009).
[CrossRef]

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

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 (2007).
[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]

Wang, L. V.

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

Weissleder, R.

C. Vinegoni, D. Razansky, J. L. Figueiredo, M. Nahrendorf, V. Ntziachristos, and R. Weissleder, “Normalized Born ratio for fluorescence optical projection tomography,” Opt. Lett. 34(3), 319–321 (2009).
[CrossRef] [PubMed]

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

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

Westenbrg, M. A.

J. B. T. M. Roerdink and M. A. Westenbrg, “Data-parallel tomographyc reconstruction: a comparison of filtered backprojection and direct fourier reconstruction,” Parallel Comput. 24(14), 2129–2142 (1998).
[CrossRef]

Woods, J. W.

H. Stark, J. W. Woods, I. Paul, and R. Hingorani, “An investigation of computerized tomography by direct Fourier inversion and optimum interpolation,” IEEE Trans. Biomed. Eng. 28(7), 496–505 (1981).
[CrossRef] [PubMed]

Ber. Saechs. Akad. Wiss, Leipzig Math. Phys. Kl.

J. Radon, “On the determination of function from their integrals along certain manifolds,” Ber. Saechs. Akad. Wiss, Leipzig Math. Phys. Kl. 69, 262–277 (1917).

Comput. Biol. Med.

R. M. Mersereau, “Direct Fourier transform techniques in 3-D image reconstruction,” Comput. Biol. Med. 6(4), 247–258 (1976).
[CrossRef] [PubMed]

IEEE Trans. Biomed. Eng.

H. Stark, J. W. Woods, I. Paul, and R. Hingorani, “An investigation of computerized tomography by direct Fourier inversion and optimum interpolation,” IEEE Trans. Biomed. Eng. 28(7), 496–505 (1981).
[CrossRef] [PubMed]

IEEE Trans. Image Process.

S. Basu and Y. Bresler, “O(N(2)log(2)N) filtered backprojection reconstruction algorithm for tomography,” IEEE Trans. Image Process. 9(10), 1760–1773 (2000).
[CrossRef] [PubMed]

IEEE Trans. Med. Imaging

J. D. O’Sullivan, “A fast sinc function gridding algorithm for fourier inversion in computer tomography,” IEEE Trans. Med. Imaging 4(4), 200–207 (1985).
[CrossRef] [PubMed]

S. Matej and I. Bajla, “A high-speed reconstruction from projections using direct Fourier method with optimized parameters-an experimental analysis,” IEEE Trans. Med. Imaging 9(4), 421–429 (1990).
[CrossRef] [PubMed]

H. Schomberg and J. Timmer, “The gridding method for image reconstruction by Fourier transformation,” IEEE Trans. Med. Imaging 14(3), 596–607 (1995).
[CrossRef] [PubMed]

J Vis Exp.

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

Med. Phys.

H. S. Sakhalkar and M. Oldham, “Fast, high-resolution 3D dosimetry utilizing a novel optical-CT scanner incorporating tertiary telecentric collimation,” Med. Phys. 35(1), 101–111 (2008).
[CrossRef] [PubMed]

Nat. Biotechnol.

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

Nat. Methods

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 (2007).
[CrossRef] [PubMed]

Nat. Photonics

D. Razansky, M. Distel, C. Vinegoni, R. Ma, N. Perrimon, R. W. Köster, and V. Ntziachristos, “Multispectral opto-acoustic tomography of deep-seated fluorescent proteins in vivo,” Nat. Photonics 3(7), 412–417 (2009).
[CrossRef]

Opt. Express

Opt. Lett.

Parallel Comput.

J. B. T. M. Roerdink and M. A. Westenbrg, “Data-parallel tomographyc reconstruction: a comparison of filtered backprojection and direct fourier reconstruction,” Parallel Comput. 24(14), 2129–2142 (1998).
[CrossRef]

Phys. Med. Biol.

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]

G. C. Sharp, N. Kandasamy, H. Singh, and M. Folkert, “GPU-based streaming architectures for fast cone-beam CT image reconstruction and demons deformable registration,” Phys. Med. Biol. 52(19), 5771–5783 (2007).
[CrossRef] [PubMed]

Proc. IEEE

R. M. Lewitt, “Reconstruction algorithms: Transform methods,” Proc. IEEE 71(3), 390–408 (1983).
[CrossRef]

R. M. Mersereau and A. V. Oppenheim, “Digital reconstruction of multidimensional signals from their projections,” Proc. IEEE 62(10), 1319–1338 (1974).
[CrossRef]

Queueing Syst.

J. Nickolls, I. Buck, M. Garland, and K. Skadron, “Scalable parallel programming with CUDA,” Queueing Syst. 6, 40–53 (2008).

Science

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]

SIAM J. Appl. Math.

A. Brandt, J. Mann, M. Brodski, and M. Galun, “A fast and accurate multilevel inversion of the radon transform,” SIAM J. Appl. Math. 60(2), 437–462 (2000).
[CrossRef]

Other

K. Mueller, F. Xu, and N. Neophytou, “Why do GPUs work so well for acceleration of CT? SPIE Electronic Imaging '07,” Keynote, Computational Imaging V, San Jose, (2007).

H. Scherl, B. Keck, M. Kowarschik, and J. Hornegger, “Fast GPU-Based CT Reconstruction using the Common Unified Device Architecture (CUDA),” Nuclear Science Symposium Conference Record 6, 4464–4466 (2007).

P. B. Noël, A. Walczak, K. R. Hoffmann, J. Xu, J. J. Corso, and S. Schafer, “Clinical Evaluation of GPU-Based Cone Beam Computed Tomography,” Proc. of High-Performance Medical Image Computing and Computer-Aided Intervention (HP-MICCAI), (2008).

J. Nickolls and I. Buck, “NVIDIA CUDA software and GPU parallel computing architecture,” Microprocessor Forum, May (2007).

S. Ryoo, C. I. Rodrigues, S. S. Stone, S. S. Baghsorkhi, S. Z.Ueng, J. A. Stratton, and W. W. Hwu “Program Optimization Space Pruning for a Multithreaded GPU,” Proc. of the sixth annual IEEE/ACM int. symp. on Code gen. and opt, (2008).

NVIDIA Corporation. CUDA Programming Guide (manual), February (2007).

Supplementary Material (1)

» Media 1: AVI (6120 KB)     

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Figures (10)

Fig. 1
Fig. 1

Experimental Setup. WLS white light source, BE beam expander, BPF band pass filters, ND optical density filters, S sample, TL telecentric lens imaging system.

Fig. 2
Fig. 2

Schematic of the coordinate system used for parallel-beam backprojection. Parallel projections Rf(θ,s) in the space domain of an object f(x,y) at different angles.

Fig. 3
Fig. 3

(a) Transillumination measurements. Parallel beams in the (x,y) plane are propagating from the source position xs to the detector position xd . (b) The attenuation along the direction of propagation for a beam with intensity I0 follows a Beer-Lambert law.

Fig. 4
Fig. 4

Scheme of the GPU implementation reconstruction algorithm.

Fig. 5
Fig. 5

Backprojection reconstruction process.

Fig. 6
Fig. 6

Scheme of the kernel executed on the CUDA-device.

Fig. 7
Fig. 7

Reconstructed image results for the absorption coefficient for 360 projections. Selected sections of the reconstructed images at three different planes (saggital (a), longitudinal (b), axial (c)) as shown in (d). (e) 3D rendering (Media 1). Size of each projection 1024x1024. Scale bar corresponds to 1 mm.

Fig. 8
Fig. 8

Sagittal (a), longitudinal (b), and axial (c) reconstructions obtained with projections taken every 10,5,3, and 1 degrees. Size of each projection 1024x1024. Scale bar corresponds to 1 mm.

Fig. 9
Fig. 9

On-the-fly sagittal (a) and axial (b) reconstructions with projections taken every one degree. The projections are displayed in real time during acquisition. Size of each projection 1024x1024. Scale bar corresponds to 1 mm.

Fig. 10
Fig. 10

Axial reconstructions obtained after the acquisition of 180 (a) or 360 (b) projections. (c) and (d) correspondent zoomed area. Histological section at approximately the same height (e). Size of each projection 1024x1024. Scale bar corresponds to 1 mm.

Tables (2)

Tables Icon

Table 1 Comparison of reconstruction times between GPU and CPU. Read and Write indicate the presence of actual reading and writing on the hard drive.

Tables Icon

Table 2 Comparison of reconstruction times between GPU and CPU (on-the-fly reconstructions). Read and Write indicate the presence of actual reading and writing on the hard drive.

Equations (3)

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

R ^ f ( θ , s ) = f ( x , y ) δ ( x cos θ + y sin θ ) d x d y
I ( x s , x d ) = I 0 e μ a L
f ( x , y ) = 0 π R θ * ( λ ) | λ | e i 2 π λ ( x cos θ + y sin θ ) d λ d θ

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