## Optical tomography using the SCIRun problem solving environment: Preliminary results for three-dimensional geometries and parallel processing

Optics Express, Vol. 4, Issue 8, pp. 263-269 (1999)

http://dx.doi.org/10.1364/OE.4.000263

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### 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.

© Optical Society of America

## 1. Introduction

*viz*. to treat the problem as the minimization of an objective function representing the sum-squared difference between measured and modeled data [1–5

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]

*F*is a function giving modelled data of type

^{M}*M*,

*y*is measured data of this type, and

^{M}*G*is a functional representing prior knowledge. For recent detailed reviews of Optical Tomography see [6–8

6. S. R. Arridge, “Optical tomography in medical imaging,” Inverse Problems **15**, R1–R53 (1999). [CrossRef]

*μ*,

_{a}*μ*′

_{s}) are represented in the basis of simple locally supported functions on a mesh. Successful reconstructions have been performed with this approach from simulated and simple phantom data [9–11

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]

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

*y*, which includes for example Laplace transforms and temporal moments (variance, skew, etc.) Most reported results with FEM have been limited to two-dimensional problems, due to the high computational cost of 3D reconstructions and the limited availability of 3D mesh generation and visualization software. Recently we showed 3D reconstructions from simulated data of a cylindrical test case with small embedded absorption inhomogeneities [13

^{M}13. M. Schweiger and S. R. Arridge, “Comparison of 2D and 3D reconstruction algorithms in optical tomography,” Appl. Opt. **37**, 7419–7428 (1998). [CrossRef]

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

## 2. The SCIRun programming environment

*computational steering*problem solving environment [16] that allows the interactive construction, debugging, and steering of large-scale scientific computations [14, 17]. A scientific application is constructed by connecting computational elements (modules) to form a program (network). This program may contain several computational elements as well as several visualization elements, all of which work together in orchestrating a solution to a scientific problem. SCIRun has been designed to allow the interactive modification of geometric inputs and computational parameters, so that the results of these changes provide immediate feedback to the investigator [18].

- TOASTReadMesh: Read a mesh from an input stream and provide it on an output port.
- TOASTReadData: Read data from an input stream and provide it on an output port.
- TOASTReadQM: Read a QM (source/detector) specification file.
- TOASTGenData: Given mesh and QM description, generate data on the fly.
- TOASTAddNoise: Add a specified amount of noise to a data set.
- TOASTDataArray: Combine a series of data sets to a single composite data array which can be passed to the reconstruction module.
- TOAST: The main reconstruction module. This accepts a mesh, QM specification and data array, and provides absorption and scatter reconstruction images on the output ports. Images are emitted for each iteration, so the progress of the reconstruction can be controlled during the program run.
- TOASTResetParam: Reset the
*μ*and_{a}*μ*parameter values stored in the mesh to an initial guess prior to reconstruction._{s}

*connections*in the network diagram.

## 3. 3D reconstructions in a head model

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]

*Photon Measurement Density Function*(PMDF) [19

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

## 4. Conclusions

## References and links

1. | S. R. Arridge, M. Schweiger, and D. T. Delpy, “Iterative reconstruction of near-infrared absorption images,” In |

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. | K. D. Paulsen and H. Jiang, “Spatially-varying optical property reconstruction using a finite element diffusion equation approximation,” Med. Phys. |

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. |

5. | R. Model, M. Orlt, M. Walzel, and R. Hünlich, “Reconstruction algorithm for near-infrared imaging in turbid media by means of time-domain data,” Appl. Opt. |

6. | S. R. Arridge, “Optical tomography in medical imaging,” Inverse Problems |

7. | J. C. Hebden, S. R. Arridge, and D. T. Delpy, “Optical imaging in medicine: I. Experimental techniques,” Phys. Med. Biol. |

8. | S. R. Arridge and J. C. Hebden, “Optical imaging in medicine: II. Modelling and reconstruction,” Phys. Med. Biol. |

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. |

10. | S. R. Arridge and M. Schweiger, “Sensitivity to prior knowledge in optical tomographic reconstruction,” In |

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. |

14. | S. G. Parker, D. M. Weinstein, and C. R. Johnson, “The SCIRun computational steering software system,” In |

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 |

18. | T. A. McCormick, T. A. DeFanti, and M. D. Brown, “Visualisation in scientific computing,” Computer Graphics |

19. | S. R. Arridge and M. Schweiger. “Photon measurement density functions. Part 2: Finite element calculations.” Appl. Opt. |

20. | M. Schweiger and S. R. Arridge, “Optimal data types in Optical Tomography”, In |

**OCIS Codes**

(100.6890) Image processing : Three-dimensional image processing

(100.6950) Image processing : Tomographic image processing

(170.3010) Medical optics and biotechnology : Image reconstruction techniques

**ToC Category:**

Focus Issue: Biomedical diffuse optical tomography

**History**

Original Manuscript: March 2, 1999

Published: April 12, 1999

**Citation**

Martin Schweiger, Leonid Zhukov, Simon Arridge, and Christopher Johnson, "Optical tomography using the SCIRun problem solving environment: Preliminary results for three-dimensional geometries and parallel processing," Opt. Express **4**, 263-269 (1999)

http://www.opticsinfobase.org/oe/abstract.cfm?URI=oe-4-8-263

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### References

- 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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