Abstract

We realized graphics processing unit (GPU) based real-time 4D (3D + time) signal processing and visualization on a regular Fourier-domain optical coherence tomography (FD-OCT) system with a nonlinear k-space spectrometer. An ultra-high speed linear spline interpolation (LSI) method for λ-to-k spectral re-sampling is implemented in the GPU architecture, which gives average interpolation speeds of >3,000,000 line/s for 1024-pixel OCT (1024-OCT) and >1,400,000 line/s for 2048-pixel OCT (2048-OCT). The complete FD-OCT signal processing including λ-to-k spectral re-sampling, fast Fourier transform (FFT) and post-FFT processing have all been implemented on a GPU. The maximum complete A-scan processing speeds are investigated to be 680,000 line/s for 1024-OCT and 320,000 line/s for 2048-OCT, which correspond to 1GByte processing bandwidth. In our experiment, a 2048-pixel CMOS camera running up to 70 kHz is used as an acquisition device. Therefore the actual imaging speed is camera- limited to 128,000 line/s for 1024-OCT or 70,000 line/s for 2048-OCT. 3D Data sets are continuously acquired in real time at 1024-OCT mode, immediately processed and visualized as high as 10 volumes/second (12,500 A-scans/volume) by either en face slice extraction or ray-casting based volume rendering from 3D texture mapped in graphics memory. For standard FD-OCT systems, a GPU is the only additional hardware needed to realize this improvement and no optical modification is needed. This technique is highly cost-effective and can be easily integrated into most ultrahigh speed FD-OCT systems to overcome the 3D data processing and visualization bottlenecks.

© 2010 OSA

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    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]
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    [CrossRef]
  17. NVIDIA, “NVIDIA CUDA Compute Unified Device Architecture Programming Guide Version 2.3.1,” (2009).
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    [CrossRef]
  22. D. Shreiner, M. Woo, J. Neider, and T. Davis, OpenGL Programming Guide, Sixth Edition (Addison-Wesley Professional, 2007), chap. 3.
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2010

K. Zhang, E. Katz, D. H. Kim, J. U. Kang, and I. K. Ilev, “Common-path optical coherence tomography guided fiber probe for spatially precise optical nerve stimulation,” Electron. Lett. 46(2), 118–120 (2010).
[CrossRef]

2009

J. Probst, P. Koch, and G. Huttmann, “Real-time 3D rendering of optical coherence tomography volumetric data,” Proc. SPIE 7372, 73720Q (2009).
[CrossRef]

K. Zhang, W. Wang, J. Han, and J. U. Kang, “A surface topology and motion compensation system for microsurgery guidance and intervention based on common-path optical coherence tomography,” IEEE Trans. Biomed. Eng. 56(9), 2318–2321 (2009).
[CrossRef] [PubMed]

Y. Watanabe and T. Itagaki, “Real-time display on Fourier domain optical coherence tomography system using a graphics processing unit,” J. Biomed. Opt. 14(6), 060506 (2009).
[CrossRef]

I. Grulkowski, M. Gora, M. Szkulmowski, I. Gorczynska, D. Szlag, S. Marcos, A. Kowalczyk, and M. Wojtkowski, “Anterior segment imaging with Spectral OCT system using a high-speed CMOS camera,” Opt. Express 17(6), 4842–4858 (2009), http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-17-6-4842 .
[CrossRef] [PubMed]

M. Gargesha, M. W. Jenkins, D. L. Wilson, and A. M. Rollins, “High temporal resolution OCT using image-based retrospective gating,” Opt. Express 17(13), 10786–10799 (2009), http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-17-13-10786 .
[CrossRef] [PubMed]

M. Gora, K. Karnowski, M. Szkulmowski, B. J. Kaluzny, R. Huber, A. Kowalczyk, and M. Wojtkowski, “Ultra high-speed swept source OCT imaging of the anterior segment of human eye at 200 kHz with adjustable imaging range,” Opt. Express 17(17), 14880–14894 (2009), http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-17-17-14880 .
[CrossRef] [PubMed]

G. Liu, J. Zhang, L. Yu, T. Xie, and Z. Chen, “Real-time polarization-sensitive optical coherence tomography data processing with parallel computing,” Appl. Opt. 48(32), 6365–6370 (2009).
[CrossRef] [PubMed]

2008

2007

Z. Hu and A. M. Rollins, “Fourier domain optical coherence tomography with a linear-in-wavenumber spectrometer,” Opt. Lett. 32(24), 3525–3527 (2007).
[CrossRef] [PubMed]

U. Sharma and U. Jin, “Common-path optical coherence tomography with side-viewing bare fiber probe for endoscopic OCT,” Rev. Sci. Instrum. 78, 113102 (2007).
[CrossRef] [PubMed]

2006

2005

U. Sharma, N. M. Fried, and J. U. Kang, “All-fiber common optical coherence tomography: sensitivity optimization and system analysis,” IEEE J. Sel. Top. Quantum Electron. 11(4), 799–805 (2005).
[CrossRef]

2003

2000

1988

M. Levoy, “Display of surfaces from volume data,” IEEE Comput. Graph. Appl. 8(3), 29–37 (1988).
[CrossRef]

Adler, D. C.

Aguirre, A. D.

Belabas, N.

Biedermann, B. R.

Cable, A.

Chen, Y.

Chen, Z.

Dorrer, C.

Efimov, I. R.

Eigenwillig, C. M.

Fried, N. M.

U. Sharma, N. M. Fried, and J. U. Kang, “All-fiber common optical coherence tomography: sensitivity optimization and system analysis,” IEEE J. Sel. Top. Quantum Electron. 11(4), 799–805 (2005).
[CrossRef]

Fujimoto, J. G.

Gargesha, M.

Gora, M.

Gorczynska, I.

Grulkowski, I.

Han, J.

K. Zhang, W. Wang, J. Han, and J. U. Kang, “A surface topology and motion compensation system for microsurgery guidance and intervention based on common-path optical coherence tomography,” IEEE Trans. Biomed. Eng. 56(9), 2318–2321 (2009).
[CrossRef] [PubMed]

Hartl, I.

Hsiung, P.

Hu, Z.

Huber, R.

Huttmann, G.

J. Probst, P. Koch, and G. Huttmann, “Real-time 3D rendering of optical coherence tomography volumetric data,” Proc. SPIE 7372, 73720Q (2009).
[CrossRef]

Ilev, I. K.

K. Zhang, E. Katz, D. H. Kim, J. U. Kang, and I. K. Ilev, “Common-path optical coherence tomography guided fiber probe for spatially precise optical nerve stimulation,” Electron. Lett. 46(2), 118–120 (2010).
[CrossRef]

Itagaki, T.

Y. Watanabe and T. Itagaki, “Real-time display on Fourier domain optical coherence tomography system using a graphics processing unit,” J. Biomed. Opt. 14(6), 060506 (2009).
[CrossRef]

Jenkins, M. W.

Jiang, J.

Jin, U.

U. Sharma and U. Jin, “Common-path optical coherence tomography with side-viewing bare fiber probe for endoscopic OCT,” Rev. Sci. Instrum. 78, 113102 (2007).
[CrossRef] [PubMed]

Joffre, M.

Kaluzny, B. J.

Kang, J. U.

K. Zhang, E. Katz, D. H. Kim, J. U. Kang, and I. K. Ilev, “Common-path optical coherence tomography guided fiber probe for spatially precise optical nerve stimulation,” Electron. Lett. 46(2), 118–120 (2010).
[CrossRef]

K. Zhang, W. Wang, J. Han, and J. U. Kang, “A surface topology and motion compensation system for microsurgery guidance and intervention based on common-path optical coherence tomography,” IEEE Trans. Biomed. Eng. 56(9), 2318–2321 (2009).
[CrossRef] [PubMed]

U. Sharma, N. M. Fried, and J. U. Kang, “All-fiber common optical coherence tomography: sensitivity optimization and system analysis,” IEEE J. Sel. Top. Quantum Electron. 11(4), 799–805 (2005).
[CrossRef]

Karnowski, K.

Katz, E.

K. Zhang, E. Katz, D. H. Kim, J. U. Kang, and I. K. Ilev, “Common-path optical coherence tomography guided fiber probe for spatially precise optical nerve stimulation,” Electron. Lett. 46(2), 118–120 (2010).
[CrossRef]

Kim, D. H.

K. Zhang, E. Katz, D. H. Kim, J. U. Kang, and I. K. Ilev, “Common-path optical coherence tomography guided fiber probe for spatially precise optical nerve stimulation,” Electron. Lett. 46(2), 118–120 (2010).
[CrossRef]

Ko, T. H.

Koch, P.

J. Probst, P. Koch, and G. Huttmann, “Real-time 3D rendering of optical coherence tomography volumetric data,” Proc. SPIE 7372, 73720Q (2009).
[CrossRef]

Kowalczyk, A.

Levoy, M.

M. Levoy, “Display of surfaces from volume data,” IEEE Comput. Graph. Appl. 8(3), 29–37 (1988).
[CrossRef]

Likforman, J.

Liu, G.

Marcos, S.

Nikolski, V. P.

Palte, G.

Potsaid, B.

Probst, J.

J. Probst, P. Koch, and G. Huttmann, “Real-time 3D rendering of optical coherence tomography volumetric data,” Proc. SPIE 7372, 73720Q (2009).
[CrossRef]

Rollins, A. M.

Rothenberg, F.

Roy, D.

Sharma, U.

U. Sharma and U. Jin, “Common-path optical coherence tomography with side-viewing bare fiber probe for endoscopic OCT,” Rev. Sci. Instrum. 78, 113102 (2007).
[CrossRef] [PubMed]

U. Sharma, N. M. Fried, and J. U. Kang, “All-fiber common optical coherence tomography: sensitivity optimization and system analysis,” IEEE J. Sel. Top. Quantum Electron. 11(4), 799–805 (2005).
[CrossRef]

Srinivasan, V. J.

Szkulmowski, M.

Szlag, D.

Wang, W.

K. Zhang, W. Wang, J. Han, and J. U. Kang, “A surface topology and motion compensation system for microsurgery guidance and intervention based on common-path optical coherence tomography,” IEEE Trans. Biomed. Eng. 56(9), 2318–2321 (2009).
[CrossRef] [PubMed]

Watanabe, M.

Watanabe, Y.

Y. Watanabe and T. Itagaki, “Real-time display on Fourier domain optical coherence tomography system using a graphics processing unit,” J. Biomed. Opt. 14(6), 060506 (2009).
[CrossRef]

Wieser, W.

Wilson, D. L.

Wojtkowski, M.

Xie, T.

Yu, L.

Zhang, J.

Zhang, K.

K. Zhang, E. Katz, D. H. Kim, J. U. Kang, and I. K. Ilev, “Common-path optical coherence tomography guided fiber probe for spatially precise optical nerve stimulation,” Electron. Lett. 46(2), 118–120 (2010).
[CrossRef]

K. Zhang, W. Wang, J. Han, and J. U. Kang, “A surface topology and motion compensation system for microsurgery guidance and intervention based on common-path optical coherence tomography,” IEEE Trans. Biomed. Eng. 56(9), 2318–2321 (2009).
[CrossRef] [PubMed]

Appl. Opt.

Electron. Lett.

K. Zhang, E. Katz, D. H. Kim, J. U. Kang, and I. K. Ilev, “Common-path optical coherence tomography guided fiber probe for spatially precise optical nerve stimulation,” Electron. Lett. 46(2), 118–120 (2010).
[CrossRef]

IEEE Comput. Graph. Appl.

M. Levoy, “Display of surfaces from volume data,” IEEE Comput. Graph. Appl. 8(3), 29–37 (1988).
[CrossRef]

IEEE J. Sel. Top. Quantum Electron.

U. Sharma, N. M. Fried, and J. U. Kang, “All-fiber common optical coherence tomography: sensitivity optimization and system analysis,” IEEE J. Sel. Top. Quantum Electron. 11(4), 799–805 (2005).
[CrossRef]

IEEE Trans. Biomed. Eng.

K. Zhang, W. Wang, J. Han, and J. U. Kang, “A surface topology and motion compensation system for microsurgery guidance and intervention based on common-path optical coherence tomography,” IEEE Trans. Biomed. Eng. 56(9), 2318–2321 (2009).
[CrossRef] [PubMed]

J. Biomed. Opt.

Y. Watanabe and T. Itagaki, “Real-time display on Fourier domain optical coherence tomography system using a graphics processing unit,” J. Biomed. Opt. 14(6), 060506 (2009).
[CrossRef]

J. Opt. Soc. Am. B

Opt. Express

M. W. Jenkins, F. Rothenberg, D. Roy, V. P. Nikolski, Z. Hu, M. Watanabe, D. L. Wilson, I. R. Efimov, and A. M. Rollins, “4D embryonic cardiography using gated optical coherence tomography,” Opt. Express 14(2), 736–748 (2006), http://www.opticsinfobase.org/oe/abstract.cfm?URI=OPEX-14-2-736 .
[CrossRef] [PubMed]

M. Gargesha, M. W. Jenkins, A. M. Rollins, and D. L. Wilson, “Denoising and 4D visualization of OCT images,” Opt. Express 16(16), 12313–12333 (2008), http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-16-16-12313 .
[CrossRef] [PubMed]

B. Potsaid, I. Gorczynska, V. J. Srinivasan, Y. Chen, J. Jiang, A. Cable, and J. G. Fujimoto, “Ultrahigh speed spectral / Fourier domain OCT ophthalmic imaging at 70,000 to 312,500 axial scans per second,” Opt. Express 16(19), 15149–15169 (2008), http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-16-19-15149 .
[CrossRef] [PubMed]

I. Grulkowski, M. Gora, M. Szkulmowski, I. Gorczynska, D. Szlag, S. Marcos, A. Kowalczyk, and M. Wojtkowski, “Anterior segment imaging with Spectral OCT system using a high-speed CMOS camera,” Opt. Express 17(6), 4842–4858 (2009), http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-17-6-4842 .
[CrossRef] [PubMed]

M. Gargesha, M. W. Jenkins, D. L. Wilson, and A. M. Rollins, “High temporal resolution OCT using image-based retrospective gating,” Opt. Express 17(13), 10786–10799 (2009), http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-17-13-10786 .
[CrossRef] [PubMed]

M. Gora, K. Karnowski, M. Szkulmowski, B. J. Kaluzny, R. Huber, A. Kowalczyk, and M. Wojtkowski, “Ultra high-speed swept source OCT imaging of the anterior segment of human eye at 200 kHz with adjustable imaging range,” Opt. Express 17(17), 14880–14894 (2009), http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-17-17-14880 .
[CrossRef] [PubMed]

Opt. Lett.

Proc. SPIE

J. Probst, P. Koch, and G. Huttmann, “Real-time 3D rendering of optical coherence tomography volumetric data,” Proc. SPIE 7372, 73720Q (2009).
[CrossRef]

Rev. Sci. Instrum.

U. Sharma and U. Jin, “Common-path optical coherence tomography with side-viewing bare fiber probe for endoscopic OCT,” Rev. Sci. Instrum. 78, 113102 (2007).
[CrossRef] [PubMed]

Other

D. Shreiner, M. Woo, J. Neider, and T. Davis, OpenGL Programming Guide, Sixth Edition (Addison-Wesley Professional, 2007), chap. 3.

NVIDIA, “NVIDIA CUDA Compute Unified Device Architecture Programming Guide Version 2.3.1,” (2009).

NVIDIA, “NVIDIA CUDA CUFFT Library Version 2.3,” (2009).

J. Kruger, and R. Westermann, “Acceleration techniques for GPU-based volume rendering,” in Proceedings of the 14th IEEE Visualization Conference (VIS’03) (IEEE Computer Society, Washington, DC, 2003), pp. 287–292.

A. Kaufman, and K. Mueller, “Overview of Volume Rendering,” in The Visualization Handbook, C. Johnson and C. Hansen, ed. (Academic Press, 2005).

Supplementary Material (5)

» Media 1: AVI (3663 KB)     
» Media 2: AVI (3928 KB)     
» Media 3: AVI (3845 KB)     
» Media 4: AVI (3480 KB)     
» Media 5: AVI (3919 KB)     

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Figures (11)

Fig. 1
Fig. 1

System configuration; CMOS, CMOS line scan camera; L, spectrometer lens; G, reflective grating; C1, C2, achromatic collimators; C, 50:50 broadband fiber coupler; CL, camera link cable; COMP, host computer; GPU, graphics processing unit; PCIE-X16, PCI Express x16 2.0 interface; MON, Monitor; GVS, galvanometer mirror pairs; R1, R2, relay lens; SL, scanning lens; RG, reference glass; SP, Sample.

Fig. 2
Fig. 2

CPU-GPU hybrid system architecture.

Fig. 3
Fig. 3

Flowchart of parallelized LSI. Blue blocks: memory for pre-stored data; yellow blocks: memory for real-timely refreshed data.

Fig. 4
Fig. 4

(a) Schematic of ray-casting CPU-GPU hybrid architecture; (b) flowchart of interactive volume rendering by GPU.

Fig. 5
Fig. 5

(a) GPU processing time versus one-batch A-scan number; (b) GPU processing line rate versus one-batch A-scan number.

Fig. 6
Fig. 6

System sensitivity roll-off: (a) 1024-OCT; (b) 2048-OCT.

Fig. 7
Fig. 7

B-scan images of an infrared sensing card: (a) 1024-OCT, 10,000 A-scan/frame, 12.8 frame/s; (b) 2048-OCT, 10,000 A-scan/frame, 7.0 frame/s. The scale bars represent 250µm in both dimensions.

Fig. 8
Fig. 8

En face slices reconstructed from real-timely acquired and processed volumetric data, the scale bar represents 100µm for all images: (a) 250 × 160 × 512 voxels; (b) from the same volume as (a) but 25 µm deeper; (c) 250 × 80 × 512 voxels; (d) from the same volume as (c) but 25 µm deeper; (e) 125 × 80 × 512 voxels; (f) from the same volume as (e) but 25 µm deeper.

Fig. 9
Fig. 9

(a) (Media 1) The dynamic 3D OCT movie of a piece of sugar-shell coated chocolate; (b) sugar-shell top truncated by the X-Y plane, inner structure visible; (c) a five-layer phantom.

Fig. 10
Fig. 10

In vivo real-time 3D imaging of a human finger tip. (a) (Media 2) Skin and fingernail connection; (b) (Media 3) Fingerprint, side-view with “L” volume rendering frame; (c) (Media 4) Fingerprint, top-view.

Fig. 11
Fig. 11

(Media 5) Multiple 2D frames real-time rendering from the same 3D data set with different model view matrix.

Equations (5)

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

S ' [ j ] = S [ i ] + S [ i + 1 ] S [ i ] k [ i + 1 ] k [ i ] ( k ' [ j ] k [ i ] ) ,
k [ i ] < k ' [ j ] < k [ i + 1 ] .
S ' [ j ] = S [ E [ j ] ] + S [ E [ j ] + 1 ] S [ E [ j ] ] k [ E [ j ] + 1 ] k [ E [ j ] ] ( k ' [ j ] k [ E [ j ] ] ) .
C ( λ ) o u t ( u j ) = C ( λ ) i n ( u j ) ( 1 α ( x i ) ) + C ( λ ) ( x i ) * α ( x i ) ,
α o u t ( u j ) = α i n ( u j ) * ( 1 α ( x i ) ) + α ( x i ) ,

Metrics