1
|
Hayakawa CK, Malenfant L, Ranasinghesagara J, Cuccia DJ, Spanier J, Venugopalan V. MCCL: an open-source software application for Monte Carlo simulations of radiative transport. JOURNAL OF BIOMEDICAL OPTICS 2022; 27:JBO-210348SSTR. [PMID: 35415991 PMCID: PMC9005200 DOI: 10.1117/1.jbo.27.8.083005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
The Monte Carlo Command Line application (MCCL) is an open-source software package that provides Monte Carlo simulations of radiative transport through heterogeneous turbid media. MCCL is available on GitHub through our virtualphotonics.org website, is actively supported, and carries extensive documentation. Here, we describe the main technical capabilities, the overall software architecture, and the operational details of MCCL.
Collapse
Affiliation(s)
- Carole K. Hayakawa
- University of California at Irvine, Department of Chemical and Biomolecular Engineering, Irvine, California, United States
- University of California at Irvine, Beckman Laser Institute, Irvine, California, United States
| | - Lisa Malenfant
- University of California at Irvine, Beckman Laser Institute, Irvine, California, United States
| | - Janaka Ranasinghesagara
- University of California at Irvine, Department of Chemical and Biomolecular Engineering, Irvine, California, United States
- University of California at Irvine, Beckman Laser Institute, Irvine, California, United States
| | | | - Jerome Spanier
- University of California at Irvine, Beckman Laser Institute, Irvine, California, United States
| | - Vasan Venugopalan
- University of California at Irvine, Department of Chemical and Biomolecular Engineering, Irvine, California, United States
- University of California at Irvine, Beckman Laser Institute, Irvine, California, United States
| |
Collapse
|
2
|
Swami MK, Gupta PK. Optical Spectroscopy for Biomedical Diagnosis. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES INDIA SECTION A-PHYSICAL SCIENCES 2018. [DOI: 10.1007/s40010-018-0519-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
3
|
Nguyen J, Hayakawa CK, Mourant JR, Venugopalan V, Spanier J. Development of perturbation Monte Carlo methods for polarized light transport in a discrete particle scattering model. BIOMEDICAL OPTICS EXPRESS 2016; 7:2051-2066. [PMID: 27231642 PMCID: PMC4871102 DOI: 10.1364/boe.7.002051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/13/2016] [Accepted: 04/15/2016] [Indexed: 06/05/2023]
Abstract
We present a polarization-sensitive, transport-rigorous perturbation Monte Carlo (pMC) method to model the impact of optical property changes on reflectance measurements within a discrete particle scattering model. The model consists of three log-normally distributed populations of Mie scatterers that approximate biologically relevant cervical tissue properties. Our method provides reflectance estimates for perturbations across wavelength and/or scattering model parameters. We test our pMC model performance by perturbing across number densities and mean particle radii, and compare pMC reflectance estimates with those obtained from conventional Monte Carlo simulations. These tests allow us to explore different factors that control pMC performance and to evaluate the gains in computational efficiency that our pMC method provides.
Collapse
Affiliation(s)
- Jennifer Nguyen
- Department of Biomedical Engineering, 3120 Natural Sciences II, University of California, Irvine, CA 92697-2715,
USA
- Laser Microbeam and Medical Program, Beckman Laser Institute, University of California, Irvine Irvine, California 92697,
USA
| | - Carole K. Hayakawa
- Laser Microbeam and Medical Program, Beckman Laser Institute, University of California, Irvine Irvine, California 92697,
USA
- Department of Chemical Engineering and Materials Science, 916 Engineering Tower, University of California, Irvine, CA 92697-2575,
USA
| | - Judith R. Mourant
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545,
USA
| | - Vasan Venugopalan
- Department of Biomedical Engineering, 3120 Natural Sciences II, University of California, Irvine, CA 92697-2715,
USA
- Laser Microbeam and Medical Program, Beckman Laser Institute, University of California, Irvine Irvine, California 92697,
USA
- Department of Chemical Engineering and Materials Science, 916 Engineering Tower, University of California, Irvine, CA 92697-2575,
USA
| | - Jerome Spanier
- Laser Microbeam and Medical Program, Beckman Laser Institute, University of California, Irvine Irvine, California 92697,
USA
| |
Collapse
|
4
|
Chen C, Lu JQ, Li K, Zhao S, Brock RS, Hu XH. Numerical study of reflectance imaging using a parallel Monte Carlo method. Med Phys 2016; 34:2939-48. [PMID: 17822002 DOI: 10.1118/1.2745241] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Reflectance imaging of biological tissues with visible and near-infrared light has the significant potential to provide a noninvasive and safe imaging modality for diagnosis of dysplastic and malignant lesions in the superficial tissue layers. The difficulty in the extraction of optical and structural parameters lies in the lack of efficient methods for accurate modeling of light scattering in biological tissues of turbid nature. We present a parallel Monte Carlo method for accurate and efficient modeling of reflectance images from turbid tissue phantoms. A parallel Monte Carlo code has been developed with the message passing interface and evaluated on a computing cluster with 16 processing elements. The code was validated against the solutions of the radiative transfer equation on the bidirectional reflection and transmission functions. With this code we investigated numerically the dependence of reflectance image on the imaging system and phantom parameters. The contrasts of reflectance images were found to be nearly independent of the numerical aperture (NA) of the imaging camera despite the fact that reflectance depends on the NA. This enables efficient simulations of the reflectance images using an NA at 1.00. Using heterogeneous tissue phantoms with an embedded region simulating a lesion, we investigated the correlation between the reflectance image profile or contrast and the phantom parameters. It has been shown that the image contrast approaches 0 when the single-scattering albedos of the two regions in the heterogeneous phantoms become matched. Furthermore, a zone of detection has been demonstrated for determination of the thickness of the embedded region and optical parameters from the reflectance image profile and contrast. Therefore, the utility of the reflectance imaging method with visible and near-infrared light has been firmly established. We conclude from these results that the optical parameters of the embedded region can be determined inversely from reflectance images acquired with full-field illumination at multiple incident angles or multiple wavelengths.
Collapse
Affiliation(s)
- Cheng Chen
- Department of Physics, East Carolina University, Greenville, North Carolina 27858, USA
| | | | | | | | | | | |
Collapse
|
5
|
Shaw CB, Yalavarthy PK. Incoherence-based optimal selection of independent measurements in diffuse optical tomography. JOURNAL OF BIOMEDICAL OPTICS 2014; 19:36017. [PMID: 24658778 DOI: 10.1117/1.jbo.19.3.036017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 02/20/2014] [Indexed: 06/03/2023]
Abstract
An optimal measurement selection strategy based on incoherence among rows (corresponding to measurements) of the sensitivity (or weight) matrix for the near infrared diffuse optical tomography is proposed. As incoherence among the measurements can be seen as providing maximum independent information into the estimation of optical properties, this provides high level of optimization required for knowing the independency of a particular measurement on its counterparts. The proposed method was compared with the recently established data-resolution matrix-based approach for optimal choice of independent measurements and shown, using simulated and experimental gelatin phantom data sets, to be superior as it does not require an optimal regularization parameter for providing the same information.
Collapse
|
6
|
Nguyen J, Hayakawa CK, Mourant JR, Spanier J. Perturbation Monte Carlo methods for tissue structure alterations. BIOMEDICAL OPTICS EXPRESS 2013; 4:1946-1963. [PMID: 24156056 PMCID: PMC3799658 DOI: 10.1364/boe.4.001946] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 08/02/2013] [Accepted: 08/08/2013] [Indexed: 05/29/2023]
Abstract
This paper describes an extension of the perturbation Monte Carlo method to model light transport when the phase function is arbitrarily perturbed. Current perturbation Monte Carlo methods allow perturbation of both the scattering and absorption coefficients, however, the phase function can not be varied. The more complex method we develop and test here is not limited in this way. We derive a rigorous perturbation Monte Carlo extension that can be applied to a large family of important biomedical light transport problems and demonstrate its greater computational efficiency compared with using conventional Monte Carlo simulations to produce forward transport problem solutions. The gains of the perturbation method occur because only a single baseline Monte Carlo simulation is needed to obtain forward solutions to other closely related problems whose input is described by perturbing one or more parameters from the input of the baseline problem. The new perturbation Monte Carlo methods are tested using tissue light scattering parameters relevant to epithelia where many tumors originate. The tissue model has parameters for the number density and average size of three classes of scatterers; whole nuclei, organelles such as lysosomes and mitochondria, and small particles such as ribosomes or large protein complexes. When these parameters or the wavelength is varied the scattering coefficient and the phase function vary. Perturbation calculations give accurate results over variations of ∼15-25% of the scattering parameters.
Collapse
Affiliation(s)
- Jennifer Nguyen
- Department of Biomedical Engineering, 3120 Natural Sciences II, University of California, Irvine, CA 92697-2715,
USA
| | - Carole K. Hayakawa
- Department of Chemical Engineering and Materials Science, 916 Engineering Tower, University of California, Irvine, CA 92697-2575,
USA
| | - Judith R. Mourant
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545,
USA
| | - Jerome Spanier
- Department of Surgery, Beckman Laser Institute and Medical Clinic, 1002 Health Sciences Rd., E., University of California, Irvine, CA 92612,
USA
| |
Collapse
|
7
|
Seo I, You JS, Hayakawa CK, Venugopalan V. Perturbation and differential Monte Carlo methods for measurement of optical properties in a layered epithelial tissue model. JOURNAL OF BIOMEDICAL OPTICS 2007; 12:014030. [PMID: 17343505 DOI: 10.1117/1.2697735] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The use of perturbation and differential Monte Carlo (pMC/dMC) methods in conjunction with nonlinear optimization algorithms were proposed recently as a means to solve inverse photon migration problems in regionwise heterogeneous turbid media. We demonstrate the application of pMC/dMC methods for the recovery of optical properties in a two-layer extended epithelial tissue model from experimental measurements of spatially resolved diffuse reflectance. The results demonstrate that pMC/dMC methods provide a rapid and accurate approach to solve two-region inverse photon migration problems in the transport regime, that is, on spatial scales smaller than a transport mean free path and in media where optical scattering need not dominate absorption. The pMC/dMC approach is found to be effective over a broad range of absorption (50 to 400%) and scattering (70 to 130%) perturbations. The recovery of optical properties from spatially resolved diffuse reflectance measurements is examined for different sets of source-detector separation. These results provide some guidance for the design of compact fiber-based probes to determine and isolate optical properties from both epithelial and stromal layers of superficial tissues.
Collapse
Affiliation(s)
- InSeok Seo
- University of California, Irvine, Department of Chemical Engineering and Materials Science, Irvine, California 92697, USA
| | | | | | | |
Collapse
|
8
|
Gebhart SC, Lin WC, Mahadevan-Jansen A. In vitro determination of normal and neoplastic human brain tissue optical properties using inverse adding-doubling. Phys Med Biol 2006; 51:2011-27. [PMID: 16585842 DOI: 10.1088/0031-9155/51/8/004] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
To complement a project towards the development of real-time optical biopsy for brain tissue discrimination and surgical resection guidance, the optical properties of various brain tissues were measured in vitro and correlated to features within clinical diffuse reflectance tissue spectra measured in vivo. Reflectance and transmission spectra of in vitro brain tissue samples were measured with a single-integrating-sphere spectrometer for wavelengths 400-1300 nm and converted to absorption and reduced scattering spectra using an inverse adding-doubling technique. Optical property spectra were classified as deriving from white matter, grey matter or glioma tissue according to histopathologic diagnosis, and mean absorption and reduced scattering spectra were calculated for the three tissue categories. Absolute reduced scattering and absorption values and their relative differences between histopathological groups agreed with previously reported results with the exception that absorption coefficients were often overestimated, most likely due to biologic variability or unaccounted light loss during reflectance/transmission measurement. Absorption spectra for the three tissue classes were dominated by haemoglobin absorption below 600 nm and water absorption above 900 nm and generally determined the shape of corresponding clinical diffuse reflectance spectra. Reduced scattering spectral shapes followed the power curve predicted by the Rayleigh limit of Mie scattering theory. While tissue absorption governed the shape of clinical diffuse reflectance spectra, reduced scattering determined their relative emission intensities between the three tissue categories.
Collapse
Affiliation(s)
- S C Gebhart
- Department of Biomedical Engineering, Vanderbilt University, Box 1631, Station B, Nashville, TN 37235-1631, USA
| | | | | |
Collapse
|