Abstract

We demonstrate real time off-axis Quantitative Phase Imaging (QPI) using a phase reconstruction algorithm based on NVIDIA’s CUDA programming model. The phase unwrapping component is based on Goldstein’s algorithm. By mapping the process of extracting phase information and unwrapping to GPU, we are able to speed up the whole procedure by more than 18.8× with respect to CPU processing and ultimately achieve video rate for mega-pixel images. Our CUDA implementation also supports processing of multiple images simultaneously. This enables our imaging system to support high speed, high throughput, and real-time image acquisition and visualization.

© 2011 OSA

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  1. G. Popescu, in Methods in Cell Biology, B. P. Jena, ed. (Academic Press, San Diego, 2008), pp. 87–115.
  2. C. Depeursinge, “Digital holography applied to microscopy,” in Digital Holography and Three-Dimensional Display, T.-C. Poon, ed. (Springer, 2006), p. 98.
  3. D. C. Ghiglia and M. D. Pritt, Two-Dimensional Phase Unwrapping: Theory, Algorithms, and Software (Wiley, New York, 1998).
  4. G. Popescu, T. Ikeda, R. R. Dasari, and M. S. Feld, “Diffraction phase microscopy for quantifying cell structure and dynamics,” Opt. Lett. 31(6), 775–777 (2006).
    [CrossRef] [PubMed]
  5. D. Kirk and W.-m. Hwu, Programming Massively Parallel Processors Hands-on With CUDA (Morgan Kaufmann, Burlington, MA, 2010).
  6. P. A. Karasev, D. P. Campbell, and M. A. Richards, “Obtaining a 35x speedup in 2d phase unwrapping using commodity graphics processors,” in 2007 IEEE Radar Conference (IEEE, 2007), pp. 574–578.
  7. P. Mistry, S. Braganza, D. Kaeli, and M. Leeser, Accelerating Phase Unwrapping and Affine Transformations for Optical Quadrature Microscopy Using CUDA (ACM, Washington, D.C., 2009), pp. 28–37.
  8. G. Popescu, L. P. Deflores, J. C. Vaughan, K. Badizadegan, H. Iwai, R. R. Dasari, and M. S. Feld, “Fourier phase microscopy for investigation of biological structures and dynamics,” Opt. Lett. 29(21), 2503–2505 (2004).
    [CrossRef] [PubMed]
  9. T. Ikeda, G. Popescu, R. R. Dasari, and M. S. Feld, “Hilbert phase microscopy for investigating fast dynamics in transparent systems,” Opt. Lett. 30(10), 1165–1167 (2005).
    [CrossRef] [PubMed]
  10. Y. K. Park, C. A. Best, K. Badizadegan, R. R. Dasari, M. S. Feld, T. Kuriabova, M. L. Henle, A. J. Levine, and G. Popescu, “Measurement of red blood cell mechanics during morphological changes,” Proc. Natl. Acad. Sci. U.S.A. 107(15), 6731–6736 (2010).
    [CrossRef] [PubMed]
  11. Y. K. Park, M. Diez-Silva, G. Popescu, G. Lykotrafitis, W. Choi, M. S. Feld, and S. Suresh, “Refractive index maps and membrane dynamics of human red blood cells parasitized by Plasmodium falciparum,” Proc. Natl. Acad. Sci. U.S.A. 105(37), 13730–13735 (2008).
    [CrossRef] [PubMed]
  12. H. F. Ding, Z. Wang, F. Nguyen, S. A. Boppart, and G. Popescu, “Fourier transform light scattering of inhomogeneous and dynamic structures,” Phys. Rev. Lett. 101(23), 238102 (2008).
    [CrossRef] [PubMed]
  13. NVIDIA, NVIDIA CUFFT Library.
  14. NVIDIA, NVIDIA CUDA Programming Guide 3.2 (2010).

2010

Y. K. Park, C. A. Best, K. Badizadegan, R. R. Dasari, M. S. Feld, T. Kuriabova, M. L. Henle, A. J. Levine, and G. Popescu, “Measurement of red blood cell mechanics during morphological changes,” Proc. Natl. Acad. Sci. U.S.A. 107(15), 6731–6736 (2010).
[CrossRef] [PubMed]

2008

Y. K. Park, M. Diez-Silva, G. Popescu, G. Lykotrafitis, W. Choi, M. S. Feld, and S. Suresh, “Refractive index maps and membrane dynamics of human red blood cells parasitized by Plasmodium falciparum,” Proc. Natl. Acad. Sci. U.S.A. 105(37), 13730–13735 (2008).
[CrossRef] [PubMed]

H. F. Ding, Z. Wang, F. Nguyen, S. A. Boppart, and G. Popescu, “Fourier transform light scattering of inhomogeneous and dynamic structures,” Phys. Rev. Lett. 101(23), 238102 (2008).
[CrossRef] [PubMed]

2006

2005

2004

Badizadegan, K.

Y. K. Park, C. A. Best, K. Badizadegan, R. R. Dasari, M. S. Feld, T. Kuriabova, M. L. Henle, A. J. Levine, and G. Popescu, “Measurement of red blood cell mechanics during morphological changes,” Proc. Natl. Acad. Sci. U.S.A. 107(15), 6731–6736 (2010).
[CrossRef] [PubMed]

G. Popescu, L. P. Deflores, J. C. Vaughan, K. Badizadegan, H. Iwai, R. R. Dasari, and M. S. Feld, “Fourier phase microscopy for investigation of biological structures and dynamics,” Opt. Lett. 29(21), 2503–2505 (2004).
[CrossRef] [PubMed]

Best, C. A.

Y. K. Park, C. A. Best, K. Badizadegan, R. R. Dasari, M. S. Feld, T. Kuriabova, M. L. Henle, A. J. Levine, and G. Popescu, “Measurement of red blood cell mechanics during morphological changes,” Proc. Natl. Acad. Sci. U.S.A. 107(15), 6731–6736 (2010).
[CrossRef] [PubMed]

Boppart, S. A.

H. F. Ding, Z. Wang, F. Nguyen, S. A. Boppart, and G. Popescu, “Fourier transform light scattering of inhomogeneous and dynamic structures,” Phys. Rev. Lett. 101(23), 238102 (2008).
[CrossRef] [PubMed]

Choi, W.

Y. K. Park, M. Diez-Silva, G. Popescu, G. Lykotrafitis, W. Choi, M. S. Feld, and S. Suresh, “Refractive index maps and membrane dynamics of human red blood cells parasitized by Plasmodium falciparum,” Proc. Natl. Acad. Sci. U.S.A. 105(37), 13730–13735 (2008).
[CrossRef] [PubMed]

Dasari, R. R.

Deflores, L. P.

Diez-Silva, M.

Y. K. Park, M. Diez-Silva, G. Popescu, G. Lykotrafitis, W. Choi, M. S. Feld, and S. Suresh, “Refractive index maps and membrane dynamics of human red blood cells parasitized by Plasmodium falciparum,” Proc. Natl. Acad. Sci. U.S.A. 105(37), 13730–13735 (2008).
[CrossRef] [PubMed]

Ding, H. F.

H. F. Ding, Z. Wang, F. Nguyen, S. A. Boppart, and G. Popescu, “Fourier transform light scattering of inhomogeneous and dynamic structures,” Phys. Rev. Lett. 101(23), 238102 (2008).
[CrossRef] [PubMed]

Feld, M. S.

Y. K. Park, C. A. Best, K. Badizadegan, R. R. Dasari, M. S. Feld, T. Kuriabova, M. L. Henle, A. J. Levine, and G. Popescu, “Measurement of red blood cell mechanics during morphological changes,” Proc. Natl. Acad. Sci. U.S.A. 107(15), 6731–6736 (2010).
[CrossRef] [PubMed]

Y. K. Park, M. Diez-Silva, G. Popescu, G. Lykotrafitis, W. Choi, M. S. Feld, and S. Suresh, “Refractive index maps and membrane dynamics of human red blood cells parasitized by Plasmodium falciparum,” Proc. Natl. Acad. Sci. U.S.A. 105(37), 13730–13735 (2008).
[CrossRef] [PubMed]

G. Popescu, T. Ikeda, R. R. Dasari, and M. S. Feld, “Diffraction phase microscopy for quantifying cell structure and dynamics,” Opt. Lett. 31(6), 775–777 (2006).
[CrossRef] [PubMed]

T. Ikeda, G. Popescu, R. R. Dasari, and M. S. Feld, “Hilbert phase microscopy for investigating fast dynamics in transparent systems,” Opt. Lett. 30(10), 1165–1167 (2005).
[CrossRef] [PubMed]

G. Popescu, L. P. Deflores, J. C. Vaughan, K. Badizadegan, H. Iwai, R. R. Dasari, and M. S. Feld, “Fourier phase microscopy for investigation of biological structures and dynamics,” Opt. Lett. 29(21), 2503–2505 (2004).
[CrossRef] [PubMed]

Henle, M. L.

Y. K. Park, C. A. Best, K. Badizadegan, R. R. Dasari, M. S. Feld, T. Kuriabova, M. L. Henle, A. J. Levine, and G. Popescu, “Measurement of red blood cell mechanics during morphological changes,” Proc. Natl. Acad. Sci. U.S.A. 107(15), 6731–6736 (2010).
[CrossRef] [PubMed]

Ikeda, T.

Iwai, H.

Kuriabova, T.

Y. K. Park, C. A. Best, K. Badizadegan, R. R. Dasari, M. S. Feld, T. Kuriabova, M. L. Henle, A. J. Levine, and G. Popescu, “Measurement of red blood cell mechanics during morphological changes,” Proc. Natl. Acad. Sci. U.S.A. 107(15), 6731–6736 (2010).
[CrossRef] [PubMed]

Levine, A. J.

Y. K. Park, C. A. Best, K. Badizadegan, R. R. Dasari, M. S. Feld, T. Kuriabova, M. L. Henle, A. J. Levine, and G. Popescu, “Measurement of red blood cell mechanics during morphological changes,” Proc. Natl. Acad. Sci. U.S.A. 107(15), 6731–6736 (2010).
[CrossRef] [PubMed]

Lykotrafitis, G.

Y. K. Park, M. Diez-Silva, G. Popescu, G. Lykotrafitis, W. Choi, M. S. Feld, and S. Suresh, “Refractive index maps and membrane dynamics of human red blood cells parasitized by Plasmodium falciparum,” Proc. Natl. Acad. Sci. U.S.A. 105(37), 13730–13735 (2008).
[CrossRef] [PubMed]

Nguyen, F.

H. F. Ding, Z. Wang, F. Nguyen, S. A. Boppart, and G. Popescu, “Fourier transform light scattering of inhomogeneous and dynamic structures,” Phys. Rev. Lett. 101(23), 238102 (2008).
[CrossRef] [PubMed]

Park, Y. K.

Y. K. Park, C. A. Best, K. Badizadegan, R. R. Dasari, M. S. Feld, T. Kuriabova, M. L. Henle, A. J. Levine, and G. Popescu, “Measurement of red blood cell mechanics during morphological changes,” Proc. Natl. Acad. Sci. U.S.A. 107(15), 6731–6736 (2010).
[CrossRef] [PubMed]

Y. K. Park, M. Diez-Silva, G. Popescu, G. Lykotrafitis, W. Choi, M. S. Feld, and S. Suresh, “Refractive index maps and membrane dynamics of human red blood cells parasitized by Plasmodium falciparum,” Proc. Natl. Acad. Sci. U.S.A. 105(37), 13730–13735 (2008).
[CrossRef] [PubMed]

Popescu, G.

Y. K. Park, C. A. Best, K. Badizadegan, R. R. Dasari, M. S. Feld, T. Kuriabova, M. L. Henle, A. J. Levine, and G. Popescu, “Measurement of red blood cell mechanics during morphological changes,” Proc. Natl. Acad. Sci. U.S.A. 107(15), 6731–6736 (2010).
[CrossRef] [PubMed]

Y. K. Park, M. Diez-Silva, G. Popescu, G. Lykotrafitis, W. Choi, M. S. Feld, and S. Suresh, “Refractive index maps and membrane dynamics of human red blood cells parasitized by Plasmodium falciparum,” Proc. Natl. Acad. Sci. U.S.A. 105(37), 13730–13735 (2008).
[CrossRef] [PubMed]

H. F. Ding, Z. Wang, F. Nguyen, S. A. Boppart, and G. Popescu, “Fourier transform light scattering of inhomogeneous and dynamic structures,” Phys. Rev. Lett. 101(23), 238102 (2008).
[CrossRef] [PubMed]

G. Popescu, T. Ikeda, R. R. Dasari, and M. S. Feld, “Diffraction phase microscopy for quantifying cell structure and dynamics,” Opt. Lett. 31(6), 775–777 (2006).
[CrossRef] [PubMed]

T. Ikeda, G. Popescu, R. R. Dasari, and M. S. Feld, “Hilbert phase microscopy for investigating fast dynamics in transparent systems,” Opt. Lett. 30(10), 1165–1167 (2005).
[CrossRef] [PubMed]

G. Popescu, L. P. Deflores, J. C. Vaughan, K. Badizadegan, H. Iwai, R. R. Dasari, and M. S. Feld, “Fourier phase microscopy for investigation of biological structures and dynamics,” Opt. Lett. 29(21), 2503–2505 (2004).
[CrossRef] [PubMed]

Suresh, S.

Y. K. Park, M. Diez-Silva, G. Popescu, G. Lykotrafitis, W. Choi, M. S. Feld, and S. Suresh, “Refractive index maps and membrane dynamics of human red blood cells parasitized by Plasmodium falciparum,” Proc. Natl. Acad. Sci. U.S.A. 105(37), 13730–13735 (2008).
[CrossRef] [PubMed]

Vaughan, J. C.

Wang, Z.

H. F. Ding, Z. Wang, F. Nguyen, S. A. Boppart, and G. Popescu, “Fourier transform light scattering of inhomogeneous and dynamic structures,” Phys. Rev. Lett. 101(23), 238102 (2008).
[CrossRef] [PubMed]

Opt. Lett.

Phys. Rev. Lett.

H. F. Ding, Z. Wang, F. Nguyen, S. A. Boppart, and G. Popescu, “Fourier transform light scattering of inhomogeneous and dynamic structures,” Phys. Rev. Lett. 101(23), 238102 (2008).
[CrossRef] [PubMed]

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

Y. K. Park, C. A. Best, K. Badizadegan, R. R. Dasari, M. S. Feld, T. Kuriabova, M. L. Henle, A. J. Levine, and G. Popescu, “Measurement of red blood cell mechanics during morphological changes,” Proc. Natl. Acad. Sci. U.S.A. 107(15), 6731–6736 (2010).
[CrossRef] [PubMed]

Y. K. Park, M. Diez-Silva, G. Popescu, G. Lykotrafitis, W. Choi, M. S. Feld, and S. Suresh, “Refractive index maps and membrane dynamics of human red blood cells parasitized by Plasmodium falciparum,” Proc. Natl. Acad. Sci. U.S.A. 105(37), 13730–13735 (2008).
[CrossRef] [PubMed]

Other

D. Kirk and W.-m. Hwu, Programming Massively Parallel Processors Hands-on With CUDA (Morgan Kaufmann, Burlington, MA, 2010).

P. A. Karasev, D. P. Campbell, and M. A. Richards, “Obtaining a 35x speedup in 2d phase unwrapping using commodity graphics processors,” in 2007 IEEE Radar Conference (IEEE, 2007), pp. 574–578.

P. Mistry, S. Braganza, D. Kaeli, and M. Leeser, Accelerating Phase Unwrapping and Affine Transformations for Optical Quadrature Microscopy Using CUDA (ACM, Washington, D.C., 2009), pp. 28–37.

NVIDIA, NVIDIA CUFFT Library.

NVIDIA, NVIDIA CUDA Programming Guide 3.2 (2010).

G. Popescu, in Methods in Cell Biology, B. P. Jena, ed. (Academic Press, San Diego, 2008), pp. 87–115.

C. Depeursinge, “Digital holography applied to microscopy,” in Digital Holography and Three-Dimensional Display, T.-C. Poon, ed. (Springer, 2006), p. 98.

D. C. Ghiglia and M. D. Pritt, Two-Dimensional Phase Unwrapping: Theory, Algorithms, and Software (Wiley, New York, 1998).

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Figures (8)

Fig. 1
Fig. 1

Diffraction phase microscope: VPS virtual point source, RL relay lens, G grating, IP image plane, SF spatial filter, L1-2 lenses, CCD charged coupled device.

Fig. 2
Fig. 2

Phase reconstruction in QPI system

Fig. 3
Fig. 3

Interferogram of a red blood cell (a) and its power spectrum (b)

Fig. 4
Fig. 4

Flow chart of unwrapping algorithm

Fig. 5
Fig. 5

Phase unwrapping of red blood cell image

Fig. 6
Fig. 6

CUDA GPU architecture

Fig. 7
Fig. 7

Detecting residues in 2D arrays

Fig. 8
Fig. 8

Residue identification flow chart.

Tables (2)

Tables Icon

Table 1 CUDA implementation versus C based sequential implementation

Tables Icon

Table 2 Structure of bit flag array elements

Equations (7)

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

I ( x , y ) = | U i ( x , y ) | 2 + | U r | 2 + 2 | U r | | U i ( x , y ) | cos [ Δ k x + ϕ ( x , y ) ] .
sin [ Δ k x + ϕ ( x , y ) ] = P cos [ Δ k x ' + ϕ ( x ' , y ) ] x x ' d x ,
ϕ ( x , y ) + Δ k x = arg [ cos ( Δ k x + ϕ ) , sin ( Δ k x + ϕ ) ] .
ψ ( i ) = φ ( i ) + 2 π k ( i ) ,
φ ( r ) d r = 2 π q ,
q = k = 1 4 Δ k
Δ 1 = W { ψ ( i , j + 1 ) ψ ( i , j ) } Δ 2 = W { ψ ( i + 1 , j + 1 ) ψ ( i , j + 1 ) } Δ 3 = W { ψ ( i + 1 , j ) ψ ( i + 1 , j + 1 ) } Δ 4 = W { ψ ( i , j ) ψ ( i + 1 , j ) }

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