Abstract

We present a 3D implementation of the UCL imaging package for absorption and scatter reconstruction from time-resolved data (TOAST), embedded in the SCIRun interactive simulation and visualization package developed at the University of Utah. SCIRun is a scientific programming environment that allows the interactive construction, debugging, and steering of large-scale scientific computations. While the capabilities of SCIRun’s interactive approach are not yet fully exploited in the current TOAST implementation, an immediate benefit of the combined TOAST/SCIRun package is the availability of optimized parallel finite element forward solvers, and the use of SCIRun’s existing 3D visualisation tools. A reconstruction of a segmented 3D head model is used as an example for demonstrating the capability of TOAST/SCIRun of simulating anatomically shaped meshes.

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References

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  1. S. R. Arridge, M. Schweiger and D. T. Delpy, "Iterative reconstruction of near-infrared absorption images," In Inverse Problems in Scattering and Imaging, M. A. Fiddy, ed., Proc. SPIE 1767, 372{383 (1992).
    [CrossRef]
  2. M. Schweiger, S. R. Arridge and D. T. Delpy, "Application of the finite-element method for the forward and inverse models in optical tomography," J. Math. Imag. Vision 3, 263-283 (1993).
    [CrossRef]
  3. K. D. Paulsen and H. Jiang, "Spatially-varying optical property reconstruction using a finite element diffusion equation approximation," Med. Phys. 22, 691-701 (1995).
    [CrossRef] [PubMed]
  4. B. W. Pogue, M. S. Patterson, H. Jiang and K. D. Paulsen, "Initial assessment of a simple system for frequency domain diffuse optical tomography," Phys. Med. Biol. 40, 1709-1729 (1995).
    [CrossRef] [PubMed]
  5. R. Model, M. Orlt, M. Walzel and R. Hunlich, "Reconstruction algorithm for near-infrared imaging in turbid media by means of time-domain data," Appl. Opt. 14, 313-324 (1997).
  6. S. R. Arridge, "Optical tomography in medical imaging," Inverse Problems 15, R1-R53 (1999).
    [CrossRef]
  7. J. C. Hebden, S. R. Arridge and D. T. Delpy, "Optical imaging in medicine: I. Experimental techniques," Phys. Med. Biol. 42, 825-840 (1997).
    [CrossRef] [PubMed]
  8. S. R. Arridge and J. C. Hebden, "Optical imaging in medicine: II. Modelling and reconstruction," Phys. Med. Biol. 42, 841-853 (1997).
    [CrossRef] [PubMed]
  9. H. Jiang, K. D. Paulsen, U. L. Osterberg, B. W. Pogue and M. S. Patterson, "Simultaneous reconstruction of absorption and scattering profiles in turbid media from near-infrared frequency- domain data," Opt. Lett. 20, 2128-2130 (1995).
    [CrossRef] [PubMed]
  10. S. R. Arridge and M. Schweiger, "Sensitivity to prior knowledge in optical tomographic reconstruction," In Optical Tomography, Photon Migration, and Spectroscopy of Tissue and Model Media: Theory, Human Studies, and Instrumentation, B. Chance and R. R. Alfano, eds., Proc SPIE 2389, 378-388 (1995).
    [CrossRef]
  11. J. C. Hebden, F. E. W. Schmidt, M. E. Fry, M. Schweiger, E. C. Hillman, D. T. Delpy and S. R. Arridge, "Simultaneous reconstruction of absorption and scattering images by multichannel measurement of purely temporal data," Opt. Lett. 24 (1999).
  12. M. Schweiger and S. R. Arridge, "The UCL optical tomography software system (TOAST)" http://www.medphys.ucl.ac.uk/toast/index.htm
  13. M. Schweiger and S. R. Arridge, "Comparison of 2D and 3D reconstruction algorithms in optical tomography," Appl. Opt. 37, 7419-7428 (1998).
    [CrossRef]
  14. S. G. Parker, D. M. Weinstein and C. R. Johnson, "The SCIRun computational steering software system," In Modern Software Tools in Scientific Computing, edited by E. Arge, A. M. Bruaset and H. P. Langtangen, 1-40 (Birkhauser Press, 1997).
  15. S. G. Parker and C. R. Johnson, "SCIRun: A scientific programming environment for computational steering," Supercomputing `95 (1995) http://www.supercomp.org/sc95/proceedings/499 SPAR/SC95.HTM
  16. J. Vetter and K. Schwan, "Models for computational steering," in: Proceedings of the Third International Conference on Configurable Distributed Systems (1996).
  17. S. G. Parker, M. Miller, C. D. Hansen and C. R. Johnson, "An integrated problem solving environment: The SCIRun computational steering system," In Proceedings of the 31st Hawaii International Conference on System Sciences (HICSS-31) (IEEE Computer Society Press, 1998).
  18. T. A. McCormick, T. A. DeFanti and M. D. Brown, "Visualisation in scientific computing," Computer Graphics 21, v-ix, 1-14, A1-E8 (1987).
  19. S. R. Arridge and M. Schweiger, "Photon measurement density functions. Part 2: Finite element calculations." Appl. Opt. 34, 8026-8037, (1995).
    [CrossRef] [PubMed]
  20. M. Schweiger and S. R. Arridge, "Optimal data types in Optical Tomography," In Information Processing in Medical Imaging, edited by J. Duncan and G. Gindi, 71-84 (Springer, New York, 1997).
    [CrossRef]

Other (20)

S. R. Arridge, M. Schweiger and D. T. Delpy, "Iterative reconstruction of near-infrared absorption images," In Inverse Problems in Scattering and Imaging, M. A. Fiddy, ed., Proc. SPIE 1767, 372{383 (1992).
[CrossRef]

M. Schweiger, S. R. Arridge and D. T. Delpy, "Application of the finite-element method for the forward and inverse models in optical tomography," J. Math. Imag. Vision 3, 263-283 (1993).
[CrossRef]

K. D. Paulsen and H. Jiang, "Spatially-varying optical property reconstruction using a finite element diffusion equation approximation," Med. Phys. 22, 691-701 (1995).
[CrossRef] [PubMed]

B. W. Pogue, M. S. Patterson, H. Jiang and K. D. Paulsen, "Initial assessment of a simple system for frequency domain diffuse optical tomography," Phys. Med. Biol. 40, 1709-1729 (1995).
[CrossRef] [PubMed]

R. Model, M. Orlt, M. Walzel and R. Hunlich, "Reconstruction algorithm for near-infrared imaging in turbid media by means of time-domain data," Appl. Opt. 14, 313-324 (1997).

S. R. Arridge, "Optical tomography in medical imaging," Inverse Problems 15, R1-R53 (1999).
[CrossRef]

J. C. Hebden, S. R. Arridge and D. T. Delpy, "Optical imaging in medicine: I. Experimental techniques," Phys. Med. Biol. 42, 825-840 (1997).
[CrossRef] [PubMed]

S. R. Arridge and J. C. Hebden, "Optical imaging in medicine: II. Modelling and reconstruction," Phys. Med. Biol. 42, 841-853 (1997).
[CrossRef] [PubMed]

H. Jiang, K. D. Paulsen, U. L. Osterberg, B. W. Pogue and M. S. Patterson, "Simultaneous reconstruction of absorption and scattering profiles in turbid media from near-infrared frequency- domain data," Opt. Lett. 20, 2128-2130 (1995).
[CrossRef] [PubMed]

S. R. Arridge and M. Schweiger, "Sensitivity to prior knowledge in optical tomographic reconstruction," In Optical Tomography, Photon Migration, and Spectroscopy of Tissue and Model Media: Theory, Human Studies, and Instrumentation, B. Chance and R. R. Alfano, eds., Proc SPIE 2389, 378-388 (1995).
[CrossRef]

J. C. Hebden, F. E. W. Schmidt, M. E. Fry, M. Schweiger, E. C. Hillman, D. T. Delpy and S. R. Arridge, "Simultaneous reconstruction of absorption and scattering images by multichannel measurement of purely temporal data," Opt. Lett. 24 (1999).

M. Schweiger and S. R. Arridge, "The UCL optical tomography software system (TOAST)" http://www.medphys.ucl.ac.uk/toast/index.htm

M. Schweiger and S. R. Arridge, "Comparison of 2D and 3D reconstruction algorithms in optical tomography," Appl. Opt. 37, 7419-7428 (1998).
[CrossRef]

S. G. Parker, D. M. Weinstein and C. R. Johnson, "The SCIRun computational steering software system," In Modern Software Tools in Scientific Computing, edited by E. Arge, A. M. Bruaset and H. P. Langtangen, 1-40 (Birkhauser Press, 1997).

S. G. Parker and C. R. Johnson, "SCIRun: A scientific programming environment for computational steering," Supercomputing `95 (1995) http://www.supercomp.org/sc95/proceedings/499 SPAR/SC95.HTM

J. Vetter and K. Schwan, "Models for computational steering," in: Proceedings of the Third International Conference on Configurable Distributed Systems (1996).

S. G. Parker, M. Miller, C. D. Hansen and C. R. Johnson, "An integrated problem solving environment: The SCIRun computational steering system," In Proceedings of the 31st Hawaii International Conference on System Sciences (HICSS-31) (IEEE Computer Society Press, 1998).

T. A. McCormick, T. A. DeFanti and M. D. Brown, "Visualisation in scientific computing," Computer Graphics 21, v-ix, 1-14, A1-E8 (1987).

S. R. Arridge and M. Schweiger, "Photon measurement density functions. Part 2: Finite element calculations." Appl. Opt. 34, 8026-8037, (1995).
[CrossRef] [PubMed]

M. Schweiger and S. R. Arridge, "Optimal data types in Optical Tomography," In Information Processing in Medical Imaging, edited by J. Duncan and G. Gindi, 71-84 (Springer, New York, 1997).
[CrossRef]

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Figures (6)

Figure 1.
Figure 1.

SCIRun data flow example for loading and visualization of reconstruction results as scalar fields

Figure 2.
Figure 2.

User interface for the TOAST module.

Figure 3.
Figure 3.

Left: high-resolution head mesh (98142 nodes, 452243 elements) used for forward data calculation; right: cross section of a low-resolution mesh showing the 4 regions opex-4-8-263-i001, opex-4-8-263-i002, opex-4-8-263-i003 and opex-4-8-263-i004.

Figure 4.
Figure 4.

Timings for forward data generation of intensity (left) and skew data (right). Tested platforms are: SGI Onyx VTX (1-8 processors) and dual Pentium-II 450 (1 and 2 processors). Each bar is divided into setup and system matrix assembly time (bottom) and conjugate gradient solver time (top).

Figure 5.
Figure 5.

Isosurfaces of PMDF for skew data. Green: absorption PMDF (isosurface value -2), blue: diffusion PMDF (isosurface value -0.23).

Figure 6.
Figure 6.

Simultaneous (μa ,μs ) reconstruction of inhomogeneities from known background parameters using skew and Laplace(s=0.005) data. Isosurfaces denote: opex-4-8-263-i005 (value 0.025),opex-4-8-263-i006(value 1.5), opex-4-8-263-i007 (left image, value 0.0126) and opex-4-8-263-i008 (right image, value 1.5).

Equations (1)

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( μ ̂ a , μ ̂ s ) = arg min μ a , μ s [ y M F M ( μ a , μ s ) + G ( μ a , μ s ) ]

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