Open source software for electric field Monte Carlo simulation of coherent backscattering in biological media containing birefringence

Radosevich, Andrew J.; Rogers, Jeremy D.; Capoglu, Ilker; Mutyal, Nikhil N.; Pradhan, Prabhakar; Backman, Vadim

doi:10.1117/1.jbo.17.11.115001

Cited by 26 publications

(23 citation statements)

References 50 publications

(78 reference statements)

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“…[26][27][28][29] More recently, publications from our group detail the application of EBS to biological tissue characterization. These publications include an open source Monte Carlo program, 30 detailed description of the bench-top instrument used to measure biological tissue, 7 description of the measurement of the spatial reflectance profile using EBS, 11 description of an inverse method to extract optical properties, 31 and development of a miniaturized probe-based LEBS instrument to characterize tissue in vivo.…”

Section: Enhanced Backscattering Theorymentioning

confidence: 99%

Ultrastructural alterations in field carcinogenesis measured by enhanced backscattering spectroscopy

Radosevich¹,

Mutyal²,

Yi³

et al. 2013

J. Biomed. Opt

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Abstract. Optical characterization of biological tissue in field carcinogenesis offers a method with which to study the mechanisms behind early cancer development and the potential to perform clinical diagnosis. Previously, lowcoherence enhanced backscattering spectroscopy (LEBS) has demonstrated the ability to discriminate between normal and diseased organs based on measurements of histologically normal-appearing tissue in the field of colorectal (CRC) and pancreatic (PC) cancers. Here, we implement the more comprehensive enhanced backscattering (EBS) spectroscopy to better understand the structural and optical changes which lead to the previous findings. EBS provides high-resolution measurement of the spatial reflectance profile Pðr s Þ between 30 microns and 2.7 mm, where information about nanoscale mass density fluctuations in the mucosa can be quantified. A demonstration of the length-scales at which Pðr s Þ is optimally altered in CRC and PC field carcinogenesis is given and subsequently these changes are related to the tissue's structural composition. Three main conclusions are made. First, the most significant changes in Pðr s Þ occur at short length-scales corresponding to the superficial mucosal layer. Second, these changes are predominantly attributable to a reduction in the presence of subdiffractional structures. Third, similar trends are seen for both cancer types, suggesting a common progression of structural alterations in each. © The Authors.Published by SPIE under a Creative Commons Attribution 3.0 Unported License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI.

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Section: Enhanced Backscattering Theorymentioning

confidence: 99%

Ultrastructural alterations in field carcinogenesis measured by enhanced backscattering spectroscopy

Radosevich¹,

Mutyal²,

Yi³

et al. 2013

J. Biomed. Opt

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“…[7][8][9] Under these assumptions, we conducted a series of Monte Carlo simulations for a total of over 1 million processor-hours using an open-source code previously described in Ref. 35. We subsequently smoothed and compressed this vast dataset from ∼6 gigabytes down to ∼70 megabytes for easier portability and improved loading speed.…”

Section: Discussionmentioning

confidence: 99%

“…35 We next detail the implementation of three algorithms, which allow us to (1) smooth and compress a large library of Monte Carlo simulated pðr; λÞ results, (2) quickly and accurately generate pðr; λÞ using the prerun library of simulations, and (3) invert pðr; λÞ measurements to determine a particular specimen's physical properties. Each of the three algorithms are written in MATLAB and are posted on our laboratory website.…”

Section: Methodsmentioning

confidence: 99%

“…In-depth details of the Monte Carlo algorithm and software used to accurately simulate enhanced backscattering spectroscopy (EBS) are discussed in another publication. 35 The code for this software is open source and can be downloaded on our laboratory website. 25 Below, we summarize the relevant simulation parameters.…”

Section: Monte Carlo Simulation and Pðr S ; Z Max þ Library Populationmentioning

confidence: 99%

See 1 more Smart Citation

Subdiffusion reflectance spectroscopy to measure tissue ultrastructure and microvasculature: model and inverse algorithm

Radosevich¹,

Eshein²,

Nguyen³

et al. 2015

J. Biomed. Opt

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Abstract. Reflectance measurements acquired from within the subdiffusion regime (i.e., lengthscales smaller than a transport mean free path) retain much of the original information about the shape of the scattering phase function. Given this sensitivity, many models of subdiffusion regime light propagation have focused on parametrizing the optical signal through various optical and empirical parameters. We argue, however, that a more useful and universal way to characterize such measurements is to focus instead on the fundamental physical properties, which give rise to the optical signal. This work presents the methodologies that used to model and extract tissue ultrastructural and microvascular properties from spatially resolved subdiffusion reflectance spectroscopy measurements. We demonstrate this approach using ex-vivo rat tissue samples measured by enhanced backscattering spectroscopy. © The Authors. Published by SPIE under a Creative Commons Attribution 3.0 Unported License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI.

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“…14 The amplitude scattering matrix for CBS has been computed with the electric field MC, 15 and by using the Jones N-matrix formalism, the implementation of birefringent properties of the medium has been performed. 16 MC approach has been extended and extensively used for imitation of 2D images of human skin obtained by Optical Coherence Tomography (OCT). [17][18][19] In the current report we present further development of the unified MC approach 20 for modeling of vector light beam propagation and scattering in a complex multiple scattering medium.…”

Section: Introductionmentioning

confidence: 99%

Propagation and scattering of vector light beam in turbid scattering medium

et al. 2014

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Due to its high sensitivity to subtle alterations in medium morphology the vector light beams have recently gained much attention in the area of photonics. This leads to development of a new non-invasive optical technique for tissue diagnostics. Conceptual design of the particular experimental systems requires careful selection of various technical parameters, including beam structure, polarization, coherence, wavelength of incident optical radiation, as well as an estimation of how the spatial and temporal structural alterations in biological tissues can be distinguished by variations of these parameters. Therefore, an accurate realistic description of vector light beams propagation within tissue-like media is required. To simulate and mimic the propagation of vector light beams within the turbid scattering media the stochastic Monte Carlo (MC) technique has been used. In current report we present the developed MC model and the results of simulation of different vector light beams propagation in turbid tissue-like scattering media. The developed MC model takes into account the coherent properties of light, the influence of reflection and refraction at the medium boundary, helicity flip of vortexes and their mutual interference. Finally, similar to the concept of higher order Poincaré sphere (HOPS), to link the spatial distribution of the intensity of the backscattered vector light beam and its state of polarization on the medium surface we introduced the color-coded HOPS.

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Open source software for electric field Monte Carlo simulation of coherent backscattering in biological media containing birefringence

Cited by 26 publications

References 50 publications

Ultrastructural alterations in field carcinogenesis measured by enhanced backscattering spectroscopy

Ultrastructural alterations in field carcinogenesis measured by enhanced backscattering spectroscopy

Subdiffusion reflectance spectroscopy to measure tissue ultrastructure and microvasculature: model and inverse algorithm

Propagation and scattering of vector light beam in turbid scattering medium

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