Overview: This software suite contains methods to simulate diffuse optical imaging (DOI) systems and optimize DOI systems.

Software description: DOI is an emerging imaging modality where near-infrared light is used to determine the localized optical properties of a tissue. However, the high amount of scatter in the biological tissue with near-infrared light complicates the task of computing these properties. Thus, there is an important need for computational methods to accomplish DOI. This software package contains a set of such methods:

a. Methods to simulate photon transport: The software implements a novel Neumann-series approach to model photon transport in optical medium. The approach overcomes many issues suffered by the traditional diffusion-approximation-based methods. Two versions of this approach are present in the package:

  • Uniform medium: The approach is implemented for media that has constant optical coefficients throughout. The implementation is for non-GPU-based systems.
  • Non-uniform medium: This approach  with non-uniform optical coefficients: This approach is for GPU-based systems and can provide up to two orders of magnitude speedup compared to state-of-the-art non-GPU based systems.

b. Methods to optimize DOI systems: Next, software is provided to optimize DOI systems on the task of detecting a tumor with a high-absorption coefficient within the tissue. For this purpose, a new Fisher-information-based mathematical observer is implemented in conjunction with the Neumann-series approach. This observer does not require any reconstruction of the image.

Download: The software package is available for download at this link.

References: The following manuscripts describe the methods developed in this package. Please refer to the relevant manuscript when using the software:

Modeling photon propagation in uniform medium: A. K. Jha, M. A. Kupinski, T. Masumura, E. Clarkson, A. A. Maslov, H. H. Barrett, “Simulating photon transport in uniform media using the radiative transport equation: A study using the Neumann-series approach”, J. Opt. Soc. Amer. A, 29(8), 1741-1757, 2012. (Top 10 downloaded articles in Aug. 2012 edition) (link)

Modeling photon propagation in non-uniform medium: A. K. Jha, M. A. Kupinski, H. H. Barrett, E. Clarkson, J. H. Hartman, “A three-dimensional Neumann-series approach to model light transport in non-uniform media”, J. Opt. Soc. Amer. A, 29(8), 1885-99, 2012 (link)

Optimizing DOI systems: A. K. Jha, E. Clarkson, M. A. Kupinski, “An ideal-observer framework to investigate signal detectability in diffuse optical imaging”, Biomed. Opt. Express, 4(10), 2107-23, 2013 (link)

Creators: Authors listed on the article above. The work was done at the lab of Dr. Matthew Kupinski at University of Arizona when Abhinav Jha was a student in that lab.