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Jenne S, Zappe H. Simulation of light interaction with seedless grapes. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:57-63. [PMID: 35790007 DOI: 10.1002/jsfa.12111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/27/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Spectroscopic techniques are widely used for the non-destructive maturation and quality monitoring of different fruits. To develop new sensor devices for this purpose, knowing the optical properties of the agricultural sample is crucial for enabling the prediction of the interaction of the incident light with the fruit. RESULTS In the present study, the optical properties of three different seedless grape varieties (ARRA15, Tawny and Melody/Blagratwo) were determined from 400 to 1000 nm using a UV-visible/near-infrared spectrometer with an integrating sphere and subsequent calculation of the absorption and scattering coefficients and the anisotropy factor using the inverse adding doubling method. The results indicate that the optical properties of different grape varieties have significant differences, especially in the visible wavelength region, whereas these are less distinct in the near-infrared range. Independent of grape variety, the grape berry skin has a higher scattering coefficient and scattering occurs predominantly in the forward direction. Based on the optical properties of the grape berries, a three-dimensional grape berry model is generated within OpticStudio (Zemax, LLC) for the different varieties that can be used in optical illumination simulations. The bulk scattering inside the fruit is modeled by the Henyey-Greenstein distribution. A comparison of the simulated values for the total transmission and the specular reflection determined experimentally shows that realistic optical grape models can be created within OpticStudio. CONCLUSION Overall, the procedure for creating optical grape models presented here will be helpful for the development of optical applications used in pre- and post-harvest food quality monitoring. © 2022 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Sophie Jenne
- Department of Microsystems Engineering - IMTEK, Gisela and Erwin Sick Chair of Micro-Optics University of Freiburg, Freiburg, Germany
| | - Hans Zappe
- Department of Microsystems Engineering - IMTEK, Gisela and Erwin Sick Chair of Micro-Optics University of Freiburg, Freiburg, Germany
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2
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McMillan L, Bruce GD, Dholakia K. Meshless Monte Carlo radiation transfer method for curved geometries using signed distance functions. JOURNAL OF BIOMEDICAL OPTICS 2022; 27:JBO-210394SSRRR. [PMID: 35927789 PMCID: PMC9350858 DOI: 10.1117/1.jbo.27.8.083003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/20/2022] [Indexed: 05/18/2023]
Abstract
SIGNIFICANCE Monte Carlo radiation transfer (MCRT) is the gold standard for modeling light transport in turbid media. Typical MCRT models use voxels or meshes to approximate experimental geometry. A voxel-based geometry does not allow for the precise modeling of smooth curved surfaces, such as may be found in biological systems or food and drink packaging. Mesh-based geometry allows arbitrary complex shapes with smooth curved surfaces to be modeled. However, mesh-based models also suffer from issues such as the computational cost of generating meshes and inaccuracies in how meshes handle reflections and refractions. AIM We present our algorithm, which we term signedMCRT (sMCRT), a geometry-based method that uses signed distance functions (SDF) to represent the geometry of the model. SDFs are capable of modeling smooth curved surfaces precisely while also modeling complex geometries. APPROACH We show that using SDFs to represent the problem's geometry is more precise than voxel and mesh-based methods. RESULTS sMCRT is validated against theoretical expressions, and voxel and mesh-based MCRT codes. We show that sMCRT can precisely model arbitrary complex geometries such as microvascular vessel network using SDFs. In comparison with the current state-of-the-art in MCRT methods specifically for curved surfaces, sMCRT is more precise for cases where the geometry can be defined using combinations of shapes. CONCLUSIONS We believe that SDF-based MCRT models are a complementary method to voxel and mesh models in terms of being able to model complex geometries and accurately treat curved surfaces, with a focus on precise simulation of reflections and refractions. sMCRT is publicly available at https://github.com/lewisfish/signedMCRT.
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Affiliation(s)
- Lewis McMillan
- University of St Andrews, SUPA School of Physics and Astronomy, St Andrews, Scotland
- Address all correspondence to Lewis McMillan,
| | - Graham D. Bruce
- University of St Andrews, SUPA School of Physics and Astronomy, St Andrews, Scotland
| | - Kishan Dholakia
- University of St Andrews, SUPA School of Physics and Astronomy, St Andrews, Scotland
- Yonsei University, College of Science, Department of Physics, Seoul, South Korea
- The University of Adelaide, School of Biological Sciences, Adelaide, South Australia, Australia
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3
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Vera DA, García HA, Victoria Waks Serra M, Baez GR, Iriarte DI, Pomarico JA. A Monte Carlo study of near infrared light propagation in the human head with lesions-a time-resolved approach. Biomed Phys Eng Express 2022; 8. [PMID: 35235912 DOI: 10.1088/2057-1976/ac59f3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/01/2022] [Indexed: 11/11/2022]
Abstract
Several clinical conditions leading to traumatic brain injury can cause hematomas or edemas inside the cerebral tissue. If these are not properly treated in time, they are prone to produce long-term neurological disabilities, or even death. Low-cost, portable and easy-to-handle devices are desired for continuous monitoring of these conditions and Near Infrared Spectroscopy (NIRS) techniques represent an appropriate choice. In this work, we use Time-Resolved (TR) Monte Carlo simulations to present a study of NIR light propagation over a digital MRI phantom. Healthy and injured (hematoma/edema) situations are considered. TR Diffuse Reflectance simulations for different lesion volumes and interoptode distances are performed in the frontal area and the left parietal area. Results show that mean partial pathlengths, photon measurement density functions and time dependent contrasts are sensitive to the presence of lesions, allowing their detection mainly for intermediate optodes separations, which proves that these metrics represent robust means of diagnose and monitoring. Conventional Continuous Wave (CW) contrasts are also presented as a particular case of the time dependent ones, but they result less sensitive to the lesions, and have higher associated uncertainties.
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Affiliation(s)
- Demián A Vera
- Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires (CIFICEN, UNCPBA-CICPBA - CONICET) Pinto 399, B7000GHG-Tandil, Buenos Aires, Argentina
| | - Héctor A García
- Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires (CIFICEN, UNCPBA-CICPBA - CONICET) Pinto 399, B7000GHG-Tandil, Buenos Aires, Argentina
| | - Ma Victoria Waks Serra
- Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires (CIFICEN, UNCPBA-CICPBA - CONICET) Pinto 399, B7000GHG-Tandil, Buenos Aires, Argentina
| | - Guido R Baez
- Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires (CIFICEN, UNCPBA-CICPBA - CONICET) Pinto 399, B7000GHG-Tandil, Buenos Aires, Argentina
| | - Daniela I Iriarte
- Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires (CIFICEN, UNCPBA-CICPBA - CONICET) Pinto 399, B7000GHG-Tandil, Buenos Aires, Argentina
| | - Juan A Pomarico
- Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires (CIFICEN, UNCPBA-CICPBA - CONICET) Pinto 399, B7000GHG-Tandil, Buenos Aires, Argentina
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4
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Fang Q, Yan S. MCX Cloud-a modern, scalable, high-performance and in-browser Monte Carlo simulation platform with cloud computing. JOURNAL OF BIOMEDICAL OPTICS 2022; 27:JBO-210206SSR. [PMID: 34989198 PMCID: PMC8728956 DOI: 10.1117/1.jbo.27.8.083008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 11/17/2021] [Indexed: 05/06/2023]
Abstract
SIGNIFICANCE Despite the ample progress made toward faster and more accurate Monte Carlo (MC) simulation tools over the past decade, the limited usability and accessibility of these advanced modeling tools remain key barriers to widespread use among the broad user community. AIM An open-source, high-performance, web-based MC simulator that builds upon modern cloud computing architectures is highly desirable to deliver state-of-the-art MC simulations and hardware acceleration to general users without the need for special hardware installation and optimization. APPROACH We have developed a configuration-free, in-browser 3D MC simulation platform-Monte Carlo eXtreme (MCX) Cloud-built upon an array of robust and modern technologies, including a Docker Swarm-based cloud-computing backend and a web-based graphical user interface (GUI) that supports in-browser 3D visualization, asynchronous data communication, and automatic data validation via JavaScript Object Notation (JSON) schemas. RESULTS The front-end of the MCX Cloud platform offers an intuitive simulation design, fast 3D data rendering, and convenient simulation sharing. The Docker Swarm container orchestration backend is highly scalable and can support high-demand GPU MC simulations using MCX over a dynamically expandable virtual cluster. CONCLUSION MCX Cloud makes fast, scalable, and feature-rich MC simulations readily available to all biophotonics researchers without overhead. It is fully open-source and can be freely accessed at http://mcx.space/cloud.
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Affiliation(s)
- Qianqian Fang
- Northeastern University, Department of Bioengineering, Boston, Massachusetts, United States
- Northeastern University, Department of Electrical and Computer Engineering, Boston, Massachusetts, United States
- Address all correspondence to Qianqian Fang,
| | - Shijie Yan
- Northeastern University, Department of Electrical and Computer Engineering, Boston, Massachusetts, United States
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5
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Alanazi RS, Laref A. Monte Carlo simulations of photodynamic therapy in human blood model. Lasers Med Sci 2021; 37:1515-1529. [PMID: 34453656 DOI: 10.1007/s10103-021-03383-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/19/2021] [Indexed: 11/26/2022]
Abstract
This study aims to simulate a therapeutic plan for a normal human blood model under various patho-physiological conditions, such as the development of leukemia/blood diseases, by means of Monte Carlo multilayered simulation. The photosensitizing compound selectively accumulates in the target cells. A superficial treatment of a blood sample was performed at different ratios of oxygen saturation ([Formula: see text]) under the concentration ([Formula: see text] = 30 µM) effect of merocyanine 540 (MC540) in the blood irradiation. This was done under the application of visible light of wavelength ~ [Formula: see text] at an exposure time ~ 60 s. The dose of photodynamic therapy (PDT) was evaluated for the biological damage, leading to necrosis and blood damage during the treatment. In addition, the effect of PDT treatment response in the blood is related to hemoglobin oxygen saturation, resulting in an excellent relationship between the changes caused by the treatment in the blood at a peculiar oxygen saturation rate (for the highest response: [Formula: see text] 50%) and a light dose (LD) of 3.83 [Formula: see text] above the minimal toxicity of normal tissues. The photodynamic dose is related to the depth of necrosis and the time of treatment for the achievement of the LD delivery at the PDT of blood.
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Affiliation(s)
- R S Alanazi
- Department of Physics and Astronomy, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
- Department of Biomedical Technology, College of Applied Medical Sciences, King Saud University, P.O. Box 10219, Riyadh, Saudi Arabia
| | - A Laref
- Department of Physics and Astronomy, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
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Dumont AP, Fang Q, Patil CA. A computationally efficient Monte-Carlo model for biomedical Raman spectroscopy. JOURNAL OF BIOPHOTONICS 2021; 14:e202000377. [PMID: 33733621 PMCID: PMC10069992 DOI: 10.1002/jbio.202000377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 05/29/2023]
Abstract
Monte Carlo (MC) modeling is a valuable tool to gain fundamental understanding of light-tissue interactions, provide guidance and assessment to optical instrument designs, and help analyze experimental data. It has been a major challenge to efficiently extend MC towards modeling of bulk-tissue Raman spectroscopy (RS) due to the wide spectral range, relatively sharp spectral features, and presence of background autofluorescence. Here, we report a computationally efficient MC approach for RS by adapting the massively-parallel Monte Carlo eXtreme (MCX) simulator. Simulation efficiency is achieved through "isoweight," a novel approach that combines the statistical generation of Raman scattered and Fluorescence emission with a lookup-table-based technique well-suited for parallelization. The MC model uses a graphics processor to produce dense Raman and fluorescence spectra over a range of 800 - 2000 cm-1 with an approximately 100× increase in speed over prior RS Monte Carlo methods. The simulated RS signals are compared against experimentally collected spectra from gelatin phantoms, showing a strong correlation.
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Affiliation(s)
- Alexander P. Dumont
- Department of Bioengineering, Temple University, Philadelphia, Pennsylvania, USA
| | - Qianqian Fang
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA
| | - Chetan A. Patil
- Department of Bioengineering, Temple University, Philadelphia, Pennsylvania, USA
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7
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Jia H, Chen B, Li D, Jin Y. Strategy of boundary discretization in numerical simulation of laser propagation in skin tissue with vascular lesions. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:2455-2472. [PMID: 33892555 DOI: 10.3934/mbe.2021125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Understanding light propagation in skin tissues with complex blood vessels can help improve clinical efficacy in the laser treatment of cutaneous vascular lesions. The voxel-based Monte Carlo (VMC) algorithm with simple blood vessel geometry is commonly used in studying the law of light propagation in tissues. However, unavoidable errors are expected in VMC because of the zigzag polygonal interface. A tetrahedron-based Monte Carlo with extended boundary condition (TMCE) solver is developed to discretize complex tissue boundaries accurately. Tetrahedra are generated along the interface, resulting in a polyhedron approximation to match the real interface. A comparison between TMCE and VMC shows neglected differences in the overall distribution of energy deposition of different models, but poor adaptability of the curved tissue interface in VMC leads to a higher energy deposition error than TMCE in a mostly deposited region in blood vessels. Replacing the real blood vessel with a cylinder-shaped vessel shows an error lower than that caused by VMC. Statistical significance analysis of energy deposition by TMCE shows that mean curvature has stronger relationship with energy deposition than the Gaussian curvature, which indicates the importance of this geometric parameter in predicting photon behavior in vascular lesions.
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Affiliation(s)
- Hao Jia
- State-Province Joint Engineering Lab of Fluid Transmission System Technology, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Bin Chen
- State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Dong Li
- State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yuzhen Jin
- State-Province Joint Engineering Lab of Fluid Transmission System Technology, Zhejiang Sci-Tech University, Hangzhou 310018, China
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8
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Yuan Y, Yan S, Fang Q. Light transport modeling in highly complex tissues using the implicit mesh-based Monte Carlo algorithm. BIOMEDICAL OPTICS EXPRESS 2021; 12:147-161. [PMID: 33520382 PMCID: PMC7818958 DOI: 10.1364/boe.411898] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/22/2020] [Accepted: 11/25/2020] [Indexed: 05/16/2023]
Abstract
The mesh-based Monte Carlo (MMC) technique has grown tremendously since its initial publication nearly a decade ago. It is now recognized as one of the most accurate Monte Carlo (MC) methods, providing accurate reference solutions for the development of novel biophotonics techniques. In this work, we aim to further advance MMC to address a major challenge in biophotonics modeling, i.e. light transport within highly complex tissues, such as dense microvascular networks, porous media and multi-scale tissue structures. Although the current MMC framework is capable of simulating light propagation in such media given its generality, the run-time and memory usage grow rapidly with increasing media complexity and size. This greatly limits our capability to explore complex and multi-scale tissue structures. Here, we propose a highly efficient implicit mesh-based Monte Carlo (iMMC) method that incorporates both mesh- and shape-based tissue representations to create highly complex yet memory-efficient light transport simulations. We demonstrate that iMMC is capable of providing accurate solutions for dense vessel networks and porous tissues while reducing memory usage by greater than a hundred- or even thousand-fold. In a sample network of microvasculature, the reduced shape complexity results in nearly 3x speed acceleration. The proposed algorithm is now available in our open-source MMC software at http://mcx.space/#mmc.
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Affiliation(s)
- Yaoshen Yuan
- Department of Electrical and Computer Engineering, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Shijie Yan
- Department of Electrical and Computer Engineering, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Qianqian Fang
- Department of Bioengineering, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
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9
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Yan S, Fang Q. Hybrid mesh and voxel based Monte Carlo algorithm for accurate and efficient photon transport modeling in complex bio-tissues. BIOMEDICAL OPTICS EXPRESS 2020; 11:6262-6270. [PMID: 33282488 PMCID: PMC7687934 DOI: 10.1364/boe.409468] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/01/2020] [Accepted: 10/01/2020] [Indexed: 05/23/2023]
Abstract
Over the past decade, an increasing body of evidence has suggested that three-dimensional (3-D) Monte Carlo (MC) light transport simulations are affected by the inherent limitations and errors of voxel-based domain boundaries. In this work, we specifically address this challenge using a hybrid MC algorithm, namely split-voxel MC or SVMC, that combines both mesh and voxel domain information to greatly improve MC simulation accuracy while remaining highly flexible and efficient in parallel hardware, such as graphics processing units (GPU). We achieve this by applying a marching-cubes algorithm to a pre-segmented domain to extract and encode sub-voxel information of curved surfaces, which is then used to inform ray-tracing computation within boundary voxels. This preservation of curved boundaries in a voxel data structure demonstrates significantly improved accuracy in several benchmarks, including a human brain atlas. The accuracy of the SVMC algorithm is comparable to that of mesh-based MC (MMC), but runs 2x-6x faster and requires only a lightweight preprocessing step. The proposed algorithm has been implemented in our open-source software and is freely available at http://mcx.space.
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Affiliation(s)
- Shijie Yan
- Department of Electrical and Computer Engineering, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Qianqian Fang
- Department of Bioengineering, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
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10
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Tran AP, Jacques SL. Modeling voxel-based Monte Carlo light transport with curved and oblique boundary surfaces. JOURNAL OF BIOMEDICAL OPTICS 2020; 25:1-13. [PMID: 32100491 PMCID: PMC7040455 DOI: 10.1117/1.jbo.25.2.025001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 01/31/2020] [Indexed: 05/06/2023]
Abstract
SIGNIFICANCE Monte Carlo (MC) light transport simulations are most often performed in regularly spaced three-dimensional voxels, a type of data representation that naturally struggles to represent boundary surfaces with curvature and oblique angles. Not accounting properly for such boundaries with an index of refractivity, mismatches can lead to important inaccuracies, not only in the calculated angles of reflection and transmission but also in the amount of light that transmits through or reflects from these mismatched boundary surfaces. AIM A new MC light transport algorithm is introduced to deal with curvature and oblique angles of incidence when simulated photons encounter mismatched boundary surfaces. APPROACH The core of the proposed algorithm applies the efficient preprocessing step of calculating a gradient map of the mismatched boundaries, a smoothing step on this calculated 3D vector field to remove surface roughness due to discretization and an interpolation scheme to improve the handling of curvature. RESULTS Through simulations of light hitting the side of a sphere and going through a lens, the agreement of this approach with analytical solutions is shown to be strong. CONCLUSIONS The MC method introduced here has the advantage of requiring only slight implementation changes from the current state-of-the-art to accurately simulate mismatched boundaries and readily exploit the acceleration of general-purpose graphics processing units. A code implementation, mcxyzn, is made available and maintained at https://omlc.org/software/mc/mcxyzn/.
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Affiliation(s)
- Anh Phong Tran
- Northeastern University, Department of Chemical Engineering, Boston, Massachusetts, United States
| | - Steven L. Jacques
- University of Washington, Department of Bioengineering, Seattle, Washington, United States
- Address all correspondence to Steven L. Jacques, E-mail:
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Fung KLB, Samim M, Gribble A, Barzda V, Vitkin IA. Monte Carlo simulation of polarization-sensitive second-harmonic generation and propagation in biological tissue. JOURNAL OF BIOPHOTONICS 2018; 11:e201800036. [PMID: 29971932 DOI: 10.1002/jbio.201800036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/01/2018] [Indexed: 06/08/2023]
Abstract
Polarization-sensitive second harmonic generation (p-SHG) is a nonlinear optical microscopy technique that has shown great promise in biomedicine, such as in detecting changes in the collagen ultrastructure of the tumor microenvironment. However, the complex nature of light-tissue interactions and the heterogeneity of biological samples pose challenges in creating an analytical and experimental quantification platform for tissue characterization via p-SHG. We present a Monte Carlo (MC) p-SHG simulation model based on double Stokes-Mueller polarimetry for the investigation of nonlinear light-tissue interaction. The MC model predictions are compared with experimental measurements of second-order nonlinear susceptibility component ratio and degree of polarization (DOP) in rat-tail collagen. The observed trends in the behavior of these parameters as a function of tissue thickness, as well as the overall extent of agreement between MC and experimental results, are discussed. High sensitivities of the susceptibility ratio and DOP are observed for the varying tissue thickness on the incoming fundamental light propagation pathway.
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Affiliation(s)
- K L Barry Fung
- Division of Engineering Science, University of Toronto, Toronto, Ontario, Canada
| | - Masood Samim
- Division of Biophysics and Bioimaging, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Adam Gribble
- Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Virginijus Barzda
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - I Alex Vitkin
- Division of Biophysics and Bioimaging, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
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Duy PK, Chun S, Chung H. Characterization of Raman Scattering in Solid Samples with Different Particle Sizes and Elucidation on the Trends of Particle Size-Dependent Intensity Variations in Relation to Changes in the Sizes of Laser Illumination and Detection Area. Anal Chem 2017; 89:11937-11943. [DOI: 10.1021/acs.analchem.7b01400] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pham K. Duy
- Department of Chemistry and
Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Seulah Chun
- Department of Chemistry and
Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Hoeil Chung
- Department of Chemistry and
Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Republic of Korea
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13
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Malektaji S, Lima IT, Escobar I MR, Sherif SS. Massively parallel simulator of optical coherence tomography of inhomogeneous turbid media. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2017; 150:97-105. [PMID: 28859833 DOI: 10.1016/j.cmpb.2017.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 07/31/2017] [Accepted: 08/07/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND AND OBJECTIVE An accurate and practical simulator for Optical Coherence Tomography (OCT) could be an important tool to study the underlying physical phenomena in OCT such as multiple light scattering. Recently, many researchers have investigated simulation of OCT of turbid media, e.g., tissue, using Monte Carlo methods. The main drawback of these earlier simulators is the long computational time required to produce accurate results. We developed a massively parallel simulator of OCT of inhomogeneous turbid media that obtains both Class I diffusive reflectivity, due to ballistic and quasi-ballistic scattered photons, and Class II diffusive reflectivity due to multiply scattered photons. METHODS This Monte Carlo-based simulator is implemented on graphic processing units (GPUs), using the Compute Unified Device Architecture (CUDA) platform and programming model, to exploit the parallel nature of propagation of photons in tissue. It models an arbitrary shaped sample medium as a tetrahedron-based mesh and uses an advanced importance sampling scheme. RESULTS This new simulator speeds up simulations of OCT of inhomogeneous turbid media by about two orders of magnitude. To demonstrate this result, we have compared the computation times of our new parallel simulator and its serial counterpart using two samples of inhomogeneous turbid media. We have shown that our parallel implementation reduced simulation time of OCT of the first sample medium from 407 min to 92 min by using a single GPU card, to 12 min by using 8 GPU cards and to 7 min by using 16 GPU cards. For the second sample medium, the OCT simulation time was reduced from 209 h to 35.6 h by using a single GPU card, and to 4.65 h by using 8 GPU cards, and to only 2 h by using 16 GPU cards. Therefore our new parallel simulator is considerably more practical to use than its central processing unit (CPU)-based counterpart. CONCLUSIONS Our new parallel OCT simulator could be a practical tool to study the different physical phenomena underlying OCT, or to design OCT systems with improved performance.
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Affiliation(s)
- Siavash Malektaji
- University of Manitoba, Department of Electrical and Computer Engineering, 75A Chancellor's Circle, Winnipeg, Manitoba R3T 5V6, Canada
| | - Ivan T Lima
- North Dakota State University, Department of Electrical and Computer Engineering, 1411 Centennial Boulevard, Fargo, ND 58108-6050, USA
| | - Mauricio R Escobar I
- University of Manitoba, Department of Electrical and Computer Engineering, 75A Chancellor's Circle, Winnipeg, Manitoba R3T 5V6, Canada
| | - Sherif S Sherif
- University of Manitoba, Department of Electrical and Computer Engineering, 75A Chancellor's Circle, Winnipeg, Manitoba R3T 5V6, Canada.
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Periyasamy V, Pramanik M. Advances in Monte Carlo Simulation for Light Propagation in Tissue. IEEE Rev Biomed Eng 2017; 10:122-135. [PMID: 28816674 DOI: 10.1109/rbme.2017.2739801] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Monte Carlo (MC) simulation for light propagation in tissue is the gold standard for studying the light propagation in biological tissue and has been used for years. Interaction of photons with a medium is simulated based on its optical properties. New simulation geometries, tissue-light interaction methods, and recording techniques recently have been designed. Applications, such as whole mouse body simulations for fluorescence imaging, eye modeling for blood vessel imaging, skin modeling for terahertz imaging, and human head modeling for sinus imaging, have emerged. Here, we review the technical advances and recent applications of MC simulation.
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Sivasubramanian K, Periyasamy V, Wen KK, Pramanik M. Optimizing light delivery through fiber bundle in photoacoustic imaging with clinical ultrasound system: Monte Carlo simulation and experimental validation. JOURNAL OF BIOMEDICAL OPTICS 2017; 22:41008. [PMID: 27997016 DOI: 10.1117/1.jbo.22.4.041008] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 11/28/2016] [Indexed: 05/04/2023]
Abstract
Translating photoacoustic (PA) imaging into clinical setup is a challenge. We report an integrated PA and ultrasound imaging system by combining the light delivery to the tissue with the ultrasound probe. First, Monte Carlo simulations were run to study the variation in absorbance within tissue for different angles of illumination, fiber-to-probe distance (FPD), and fiber-to-tissue distance (FTD). This is followed by simulation for different depths of the embedded sphere (object of interest). Several probe holders were designed for different light launching angles. Phantoms were developed to mimic a sentinel lymph node imaging scenario. It was observed that, for shallower imaging depths, the variation in signal-to-noise ratio (SNR) values could be as high as 100% depending on the angle of illumination at a fixed FPD and FTD. Results confirm that different light illumination angles are required for different imaging depths to get the highest SNR PA images. The results also validate that one can use Monte Carlo simulation as a tool to optimize the probe holder design depending on the imaging needs. This eliminates a trial-and-error approach generally used for designing a probe holder.
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Affiliation(s)
- Kathyayini Sivasubramanian
- Nanyang Technological University, School of Chemical and Biomedical Engineering, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Vijitha Periyasamy
- Nanyang Technological University, School of Chemical and Biomedical Engineering, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Kew Kok Wen
- Nanyang Technological University, School of Chemical and Biomedical Engineering, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Manojit Pramanik
- Nanyang Technological University, School of Chemical and Biomedical Engineering, 62 Nanyang Drive, Singapore 637459, Singapore
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16
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Hochuli R, Powell S, Arridge S, Cox B. Quantitative photoacoustic tomography using forward and adjoint Monte Carlo models of radiance. JOURNAL OF BIOMEDICAL OPTICS 2016; 21:126004. [PMID: 27918801 DOI: 10.1117/1.jbo.21.12.126004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/07/2016] [Indexed: 05/06/2023]
Abstract
Forward and adjoint Monte Carlo (MC) models of radiance are proposed for use in model-based quantitative photoacoustic tomography. A two-dimensional (2-D) radiance MC model using a harmonic angular basis is introduced and validated against analytic solutions for the radiance in heterogeneous media. A gradient-based optimization scheme is then used to recover 2-D absorption and scattering coefficients distributions from simulated photoacoustic measurements. It is shown that the functional gradients, which are a challenge to compute efficiently using MC models, can be calculated directly from the coefficients of the harmonic angular basis used in the forward and adjoint models. This work establishes a framework for transport-based quantitative photoacoustic tomography that can fully exploit emerging highly parallel computing architectures.
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Affiliation(s)
- Roman Hochuli
- University College London, Department of Medical Physics and Biomedical Engineering, Malet Place, WC1E 6BT London, United Kingdom
| | - Samuel Powell
- University College London, Department of Medical Physics and Biomedical Engineering, Malet Place, WC1E 6BT London, United Kingdom
| | - Simon Arridge
- University College London, Department of Computer Science, Malet Place, WC1E 6BT London, United Kingdom
| | - Ben Cox
- University College London, Department of Medical Physics and Biomedical Engineering, Malet Place, WC1E 6BT London, United Kingdom
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17
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Periyasamy V, Pramanik M. Importance sampling-based Monte Carlo simulation of time-domain optical coherence tomography with embedded objects. APPLIED OPTICS 2016; 55:2921-9. [PMID: 27139855 DOI: 10.1364/ao.55.002921] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Monte Carlo simulation for light propagation in biological tissue is widely used to study light-tissue interaction. Simulation for optical coherence tomography (OCT) studies requires handling of embedded objects of various shapes. In this work, time-domain OCT simulations for multilayered tissue with embedded objects (such as sphere, cylinder, ellipsoid, and cuboid) was done. Improved importance sampling (IS) was implemented for the proposed OCT simulation for faster speed. At first, IS was validated against standard and angular biased Monte Carlo methods for OCT. Both class I and class II photons were in agreement in all the three methods. However, the IS method had more than tenfold improvement in terms of simulation time. Next, B-scan images were obtained for four types of embedded objects. All the four shapes are clearly visible from the B-scan OCT images. With the improved IS B-scan OCT images of embedded objects can be obtained with reasonable simulation time using a standard desktop computer. User-friendly, C-based, Monte Carlo simulation for tissue layers with embedded objects for OCT (MCEO-OCT) will be very useful for time-domain OCT simulations in many biological applications.
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18
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Shin Y, Kwon HS. Mesh-based Monte Carlo method for fibre-optic optogenetic neural stimulation with direct photon flux recording strategy. Phys Med Biol 2016; 61:2265-82. [DOI: 10.1088/0031-9155/61/6/2265] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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19
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Yang D, Chen X, Cao X, Wang J, Liang J, Tian J. Performance investigation of SP3 and diffusion approximation for three-dimensional whole-body optical imaging of small animals. Med Biol Eng Comput 2015; 53:805-14. [PMID: 25850985 DOI: 10.1007/s11517-015-1293-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 03/26/2015] [Indexed: 01/31/2023]
Abstract
The third-order simplified harmonic spherical approximation (SP3) and diffusion approximation (DA) equations have been widely used in the three-dimensional (3D) whole-body optical imaging of small animals. With different types of tissues, which were classified by the ratio of µ s'/µ ɑ, the two equations have their own application scopes. However, the classification criterion was blurring and unreasonable, and the scope has not been systematically investigated until now. In this study, a new criterion for classifying tissues was established based on the absolute value of absorption and reduced scattering coefficients. Using the newly defined classification criterion, the performance and applicability of the SP3 and DA equations were evaluated with a series of investigation experiments. Extensive investigation results showed that the SP3 equation exhibited a better performance and wider applicability than the DA one in most of the observed cases, especially in tissues of low-scattering-low-absorption and low-scattering-high-absorption range. For the case of tissues with the high-scattering-low-absorption properties, a similar performance was observed for both the SP3 and the DA equations, in which case the DA was the preferred option for 3D whole-body optical imaging. Results of this study would provide significant reference for the study of hybrid light transport models.
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Affiliation(s)
- Defu Yang
- Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, 710071, Shaanxi, China
| | - Xueli Chen
- Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, 710071, Shaanxi, China.
| | - Xu Cao
- Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, 710071, Shaanxi, China
| | - Jing Wang
- Department of Nuclear Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China
| | - Jimin Liang
- Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, 710071, Shaanxi, China
| | - Jie Tian
- Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, 710071, Shaanxi, China
- Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
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20
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Majaron B, Milanič M, Premru J. Monte Carlo simulation of radiation transport in human skin with rigorous treatment of curved tissue boundaries. JOURNAL OF BIOMEDICAL OPTICS 2015; 20:015002. [PMID: 25604544 DOI: 10.1117/1.jbo.20.1.015002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 12/17/2014] [Indexed: 05/09/2023]
Abstract
In three-dimensional (3-D) modeling of light transport in heterogeneous biological structures using the Monte Carlo (MC) approach, space is commonly discretized into optically homogeneous voxels by a rectangular spatial grid. Any round or oblique boundaries between neighboring tissues thus become serrated, which raises legitimate concerns about the realism of modeling results with regard to reflection and refraction of light on such boundaries. We analyze the related effects by systematic comparison with an augmented 3-D MC code, in which analytically defined tissue boundaries are treated in a rigorous manner. At specific locations within our test geometries, energy deposition predicted by the two models can vary by 10%. Even highly relevant integral quantities, such as linear density of the energy absorbed by modeled blood vessels, differ by up to 30%. Most notably, the values predicted by the customary model vary strongly and quite erratically with the spatial discretization step and upon minor repositioning of the computational grid. Meanwhile, the augmented model shows no such unphysical behavior. Artifacts of the former approach do not converge toward zero with ever finer spatial discretization, confirming that it suffers from inherent deficiencies due to inaccurate treatment of reflection and refraction at round tissue boundaries.
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