1
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Chen G, Wang W, Li Y. Reducing noise in polarization-sensitive optical coherence tomography for high-quality local phase retardation imaging. APPLIED OPTICS 2024; 63:2822-2830. [PMID: 38856377 DOI: 10.1364/ao.515942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/17/2024] [Indexed: 06/11/2024]
Abstract
Local phase retardation (LPR) is increasingly recognized as a crucial biomarker for assessing disease progression. However, the presence of speckle noise significantly challenges its accuracy and polarization contrast. To address this challenge, we propose a signal-processing strategy aimed at reducing the impact of noise on LPR measurements. In this approach, the LPR is reconstructed by polar decomposition after averaging multiple Mueller matrices from different overlapping sub-spectra. To optimize measurement accuracy, we systematically combined and traversed different sub-spectral numbers and bandwidths. By examining the quarter-wave plate and glass slide, high-accuracy phase retardation measurements were successfully verified, and the maximum polarization contrast was improved by 23%. Moreover, experimental results from multi-tissue imaging vividly illustrate that the equivalent number of looks (ENL) and polarization contrast were improved by 18% and 19%, respectively. This outcome indicates that our proposed strategy can effectively reduce the noise spikes, enhancing tissue discrimination capabilities.
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2
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Zhu L, Makita S, Tamaoki J, Zhu Y, Mukherjee P, Lim Y, Kobayashi M, Yasuno Y. Polarization-artifact reduction and accuracy improvement of Jones-matrix polarization-sensitive optical coherence tomography by multi-focus-averaging based multiple scattering reduction. BIOMEDICAL OPTICS EXPRESS 2024; 15:256-276. [PMID: 38223182 PMCID: PMC10783893 DOI: 10.1364/boe.509763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/16/2024]
Abstract
Polarization-sensitive optical coherence tomography (PS-OCT) is a promising biomedical imaging tool for the differentiation of various tissue properties. However, the presence of multiple-scattering (MS) signals can degrade the quantitative polarization measurement accuracy. We demonstrate a method to reduce MS signals and increase the measurement accuracy of Jones matrix PS-OCT. This method suppresses MS signals by averaging multiple Jones matrix volumes measured using different focal positions. The MS signals are decorrelated among the volumes by focus position modulation and are thus reduced by averaging. However, the single scattering signals are kept consistent among the focus-modulated volumes by computational refocusing. We validated the proposed method using a scattering phantom and a postmortem medaka fish. The results showed reduced artifacts in birefringence and degree-of-polarization uniformity measurements, particularly in deeper regions in the samples. This method offers a practical solution to mitigate MS-induced artifacts in PS-OCT imaging and improves quantitative polarization measurement accuracy.
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Affiliation(s)
- Lida Zhu
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Shuichi Makita
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Junya Tamaoki
- Department of Molecular and Developmental
Biology, Institute of Medicine, University of
Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yiqiang Zhu
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Pradipta Mukherjee
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yiheng Lim
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Makoto Kobayashi
- Department of Molecular and Developmental
Biology, Institute of Medicine, University of
Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshiaki Yasuno
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
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3
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Chen G, Wang W, Li Y. Comparative study of OCTA algorithms with a high-sensitivity multi-contrast Jones matrix OCT system for human skin imaging. BIOMEDICAL OPTICS EXPRESS 2022; 13:4718-4736. [PMID: 36187265 PMCID: PMC9484425 DOI: 10.1364/boe.462941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/21/2022] [Accepted: 07/28/2022] [Indexed: 06/16/2023]
Abstract
The multi-contrast Jones matrix OCT (JMT) system can not only improve the tissue-specific contrast but also enhance the sensitivity of detecting flow, which is gaining increasing attention. However, for the JMT system, there is currently a lack of studies evaluating and guiding the selection of suitable angiography algorithms to map the most appealing quality of angiograms for clinical use. In this paper, by a homemade high-sensitivity multi-contrast JMT system based 200 kHz swept source, the performance of two complex-signal-based OCTA methods that are insensitive to phase instability and one amplitude-signal-based OCTA method are compared for in-vivo imaging of human skin qualitatively and quantitatively. Six metrics, including vascular connectivity, image contrast-to-noise ratio, image signal-to-noise ratio, vessel diameter index, blood vessel density, and processing time, are assessed. The results show that the vascular networks processed by all OCTA methods and the texture of skin could be visualized simultaneously and markedly. Additionally, the complex-signal-based OCTA methods successfully suppress phase instabilities and even outperform the amplitude-signal-based OCTA algorithm in some indicators. This paper has a certain guiding significance for selecting an appropriate angiography algorithm and expanding the application field with this system.
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Affiliation(s)
- Guoqiang Chen
- Key Laboratory of Photoelectronic Imaging Technology and System of Ministry of Education of China, School of Optics and Photonics, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
| | - Wen’ai Wang
- Key Laboratory of Photoelectronic Imaging Technology and System of Ministry of Education of China, School of Optics and Photonics, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
- Institute of Engineering Medicine, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
| | - Yanqiu Li
- Key Laboratory of Photoelectronic Imaging Technology and System of Ministry of Education of China, School of Optics and Photonics, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
- Institute of Engineering Medicine, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
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4
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Mukherjee P, Fukuda S, Lukmanto D, Yamashita T, Okada K, Makita S, Abd El-Sadek I, Miyazawa A, Zhu L, Morishita R, Lichtenegger A, Oshika T, Yasuno Y. Label-free metabolic imaging of non-alcoholic-fatty-liver-disease (NAFLD) liver by volumetric dynamic optical coherence tomography. BIOMEDICAL OPTICS EXPRESS 2022; 13:4071-4086. [PMID: 35991915 PMCID: PMC9352293 DOI: 10.1364/boe.461433] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 05/30/2023]
Abstract
Label-free metabolic imaging of non-alcoholic fatty liver disease (NAFLD) mouse liver is demonstrated ex vivo by dynamic optical coherence tomography (OCT). The NAFLD mouse is a methionine choline-deficient (MCD)-diet model, and two mice fed the MCD diet for 1 and 2 weeks are involved in addition to a normal-diet mouse. The dynamic OCT is based on repeating raster scan and logarithmic intensity variance (LIV) analysis that enables volumetric metabolic imaging with a standard-speed (50,000 A-lines/s) OCT system. Metabolic domains associated with lipid droplet accumulation and inflammation are clearly visualized three-dimensionally. Particularly, the normal-diet liver exhibits highly metabolic vessel-like structures of peri-vascular hepatic zones. The 1-week MCD-diet liver shows ring-shaped highly metabolic structures formed with lipid droplets. The 2-week MCD-diet liver exhibits fragmented vessel-like structures associated with inflammation. These results imply that volumetric LIV imaging is useful for visualizing and assessing NAFLD abnormalities.
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Affiliation(s)
- Pradipta Mukherjee
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Shinichi Fukuda
- Department of Ophthalmology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Department of Advanced Vision Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Donny Lukmanto
- Department of Advanced Vision Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Toshiharu Yamashita
- Laboratory of Regenerative Medicine and Stem Cell Biology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kosuke Okada
- Division of Medical Sciences, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Shuichi Makita
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Ibrahim Abd El-Sadek
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Department of Physics, Faculty of Science, Damietta University, 34517 New Damietta City, Damietta, Egypt
| | | | - Lida Zhu
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Rion Morishita
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Antonia Lichtenegger
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Austria
| | - Tetsuro Oshika
- Department of Ophthalmology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshiaki Yasuno
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
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5
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Cannon TM, Uribe-Patarroyo N, Villiger M, Bouma BE. Measuring collagen injury depth for burn severity determination using polarization sensitive optical coherence tomography. Sci Rep 2022; 12:10479. [PMID: 35729262 PMCID: PMC9213509 DOI: 10.1038/s41598-022-14326-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/06/2022] [Indexed: 12/19/2022] Open
Abstract
Determining the optimal treatment course for a dermatologic burn wound requires knowledge of the wound’s severity, as quantified by the depth of thermal damage. In current clinical practice, burn depth is inferred based exclusively on superficial visual assessment, a method which is subject to substantial error rates in the classification of partial thickness (second degree) burns. Here, we present methods for direct, quantitative determination of the depth extent of injury to the dermal collagen matrix using polarization-sensitive optical coherence tomography (PS-OCT). By visualizing the depth-dependence of the degree of polarization of light in the tissue, rather than cumulative retardation, we enable direct and volumetric assessment of local collagen status. We further augment our PS-OCT measurements by visualizing adnexal structures such as hair follicles to relay overall dermal viability in the wounded region. Our methods, which we have validated ex vivo with matched histology, offer an information-rich tool for precise interrogation of burn wound severity and healing potential in both research and clinical settings.
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Affiliation(s)
- Taylor M Cannon
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA. .,Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
| | - Néstor Uribe-Patarroyo
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Martin Villiger
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Brett E Bouma
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.,Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, 02114, USA
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6
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Zhu L, Makita S, Oida D, Miyazawa A, Oikawa K, Mukherjee P, Lichtenegger A, Distel M, Yasuno Y. Computational refocusing of Jones matrix polarization-sensitive optical coherence tomography and investigation of defocus-induced polarization artifacts. BIOMEDICAL OPTICS EXPRESS 2022; 13:2975-2994. [PMID: 35774308 PMCID: PMC9203103 DOI: 10.1364/boe.454975] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/13/2022] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
Here we demonstrate a long-depth-of-focus imaging method using polarization sensitive optical coherence tomography (PS-OCT). This method involves a combination of Fresnel-diffraction-model-based phase sensitive computational refocusing and Jones-matrix based PS-OCT (JM-OCT). JM-OCT measures four complex OCT images corresponding to four polarization channels. These OCT images are computationally refocused as preserving the mutual phase consistency. This method is validated using a static phantom, postmortem zebrafish, and ex vivo porcine muscle samples. All the samples demonstrated successful computationally-refocused birefringence and degree-of-polarization-uniformity (DOPU) images. We found that defocusing induces polarization artifacts, i.e., incorrectly high birefringence values and low DOPU values, which are substantially mitigated by computational refocusing.
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Affiliation(s)
- Lida Zhu
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Shuichi Makita
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Daisuke Oida
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Arata Miyazawa
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Sky technology Inc., Tsukuba, Ibaraki, Japan
| | - Kensuke Oikawa
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Pradipta Mukherjee
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Antonia Lichtenegger
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Martin Distel
- Innovative Cancer Models, St. Anna Children’s Cancer Research Institute, Vienna, Austria
| | - Yoshiaki Yasuno
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
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7
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Li Q, Yu Y, Ding Z, Zhu F, Li Y, Tao K, Hua P, Lai T, Kuang H, Liu T. Analysis and reduction of noise-induced depolarization in catheter based polarization sensitive optical coherence tomography. OPTICS EXPRESS 2022; 30:11130-11149. [PMID: 35473063 DOI: 10.1364/oe.453116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
In catheter based polarization sensitive optical coherence tomography (PS-OCT), a optical fiber with a rapid rotation in the catheter can cause low signal-to-noise ratio (SNR), polarization state instability, phase change of PS-OCT signals and then heavy noise-induced depolarization, which has a strong impact on the phase retardation measurement of the sample. In this paper, we analyze the noise-induced depolarization and find that the effect of depolarization can be reduced by polar decomposition after incoherent averaging in the Mueller matrix averaging (MMA) method. Namely, MMA can reduce impact of noise on phase retardation mapping. We present a Monte Carlo method based on PS-OCT to numerically describe noise-induced depolarization effect and contrast phase retardation imaging results by MMA and Jones matrix averaging (JMA) methods. The peak signal to noise ratio (PSNR) of simulated images processed by MMA is higher than about 8.9 dB than that processed by JMA. We also implement experiments of multiple biological tissues using the catheter based PS-OCT system. From the simulation and experimental results, we find the polarization contrasts processed by the MMA are better than those by JMA, especially at areas with high depolarization, because the MMA can reduce effect of noise-induced depolarization on the phase retardation measurement.
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8
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Seesan T, Abd El-Sadek I, Mukherjee P, Zhu L, Oikawa K, Miyazawa A, Shen LTW, Matsusaka S, Buranasiri P, Makita S, Yasuno Y. Deep convolutional neural network-based scatterer density and resolution estimators in optical coherence tomography. BIOMEDICAL OPTICS EXPRESS 2022; 13:168-183. [PMID: 35154862 PMCID: PMC8803045 DOI: 10.1364/boe.443343] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/03/2021] [Accepted: 11/25/2021] [Indexed: 05/02/2023]
Abstract
We present deep convolutional neural network (DCNN)-based estimators of the tissue scatterer density (SD), lateral and axial resolutions, signal-to-noise ratio (SNR), and effective number of scatterers (ENS, the number of scatterers within a resolution volume). The estimators analyze the speckle pattern of an optical coherence tomography (OCT) image in estimating these parameters. The DCNN is trained by a large number (1,280,000) of image patches that are fully numerically generated in OCT imaging simulation. Numerical and experimental validations were performed. The numerical validation shows good estimation accuracy as the root mean square errors were 0.23%, 3.65%, 3.58%, 3.79%, and 6.15% for SD, lateral and axial resolutions, SNR, and ENS, respectively. The experimental validation using scattering phantoms (Intralipid emulsion) shows reasonable estimations. Namely, the estimated SDs were proportional to the Intralipid concentrations, and the average estimation errors of lateral and axial resolutions were 1.36% and 0.68%, respectively. The scatterer density estimator was also applied to an in vitro tumor cell spheroid, and a reduction in the scatterer density during cell necrosis was found.
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Affiliation(s)
- Thitiya Seesan
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Department of Physics, School of Science, King Mongkut’s Institute of Technology Ladkrabang, Ladkrabang, Bangkok, Thailand
| | - Ibrahim Abd El-Sadek
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Department of Physics, Faculty of Science, Damietta University, New Damietta City, Damietta, Egypt
| | - Pradipta Mukherjee
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Lida Zhu
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kensuke Oikawa
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Arata Miyazawa
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Sky Technology Inc., Tsukuba, Ibaraki, Japan
| | - Larina Tzu-Wei Shen
- Clinical Research and Regional Innovation, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Satoshi Matsusaka
- Clinical Research and Regional Innovation, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Prathan Buranasiri
- Department of Physics, School of Science, King Mongkut’s Institute of Technology Ladkrabang, Ladkrabang, Bangkok, Thailand
| | - Shuichi Makita
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshiaki Yasuno
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, Japan
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9
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Label-free functional and structural imaging of liver microvascular complex in mice by Jones matrix optical coherence tomography. Sci Rep 2021; 11:20054. [PMID: 34625574 PMCID: PMC8501041 DOI: 10.1038/s41598-021-98909-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/16/2021] [Indexed: 12/21/2022] Open
Abstract
We demonstrate label-free imaging of the functional and structural properties of microvascular complex in mice liver. The imaging was performed by a custom-built Jones-matrix based polarization sensitive optical coherence tomography (JM-OCT), which is capable of measuring tissue's attenuation coefficient, birefringence, and tiny tissue dynamics. Two longitudinal studies comprising a healthy liver and an early fibrotic liver model were performed. In the healthy liver, we observed distinctive high dynamics beneath the vessel at the initial time point (0 h) and reappearance of high dynamics at 32-h time point. In the early fibrotic liver model, we observed high dynamics signal that reveals a clear network vascular structure by volume rendering. Longitudinal time-course imaging showed that these high dynamics signals faded and decreased over time.
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10
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Baumann B, Harper DJ, Eugui P, Gesperger J, Lichtenegger A, Merkle CW, Augustin M, Woehrer A. Improved accuracy of quantitative birefringence imaging by polarization sensitive OCT with simple noise correction and its application to neuroimaging. JOURNAL OF BIOPHOTONICS 2021; 14:e202000323. [PMID: 33332741 DOI: 10.1002/jbio.202000323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 05/25/2023]
Abstract
Polarization-sensitive optical coherence tomography (PS-OCT) enables three-dimensional imaging of biological tissues based on the inherent contrast provided by scattering and polarization properties. In fibrous tissue such as the white matter of the brain, PS-OCT allows quantitative mapping of tissue birefringence. For the popular PS-OCT layout using a single circular input state, birefringence measurements are based on a straight-forward evaluation of phase retardation data. However, the accuracy of these measurements strongly depends on the signal-to-noise ratio (SNR) and is prone to mapping artifacts when the SNR is low. Here we present a simple yet effective approach for improving the accuracy of PS-OCT phase retardation and birefringence measurements. By performing a noise bias correction of the detected OCT signal amplitudes, the impact of the noise floor on retardation measurements can be markedly reduced. We present simulation data to illustrate the influence of the noise bias correction on phase retardation measurements and support our analysis with real-world PS-OCT image data.
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Affiliation(s)
- Bernhard Baumann
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Danielle J Harper
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Pablo Eugui
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Johanna Gesperger
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Antonia Lichtenegger
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Conrad W Merkle
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Marco Augustin
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Adelheid Woehrer
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
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11
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Keahey PA, Bouma BE, Villiger M. Automated noise estimation in polarization-sensitive optical coherence tomography. OPTICS LETTERS 2020; 45:2748-2751. [PMID: 32412457 PMCID: PMC7506521 DOI: 10.1364/ol.390334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/07/2020] [Indexed: 05/19/2023]
Abstract
Advanced signal reconstruction in polarization-sensitive optical coherence tomography (OCT) frequently relies on an accurate determination of the signal noise floor. However, current methods for evaluating the noise floor are often impractical and subjective. Here we present a method using the degree of polarization uniformity and known speckle intensity statistics to model and estimate the OCT noise floor automatically. We establish the working principle of our method with a series of phantom experiments and demonstrate the robustness of our noise estimation method across different imaging systems and applications in vivo.
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Affiliation(s)
- P. A. Keahey
- Wellman Center for Photomedicine, Massachusetts General Hospital, 50 Blossom St., Boston, Massachusetts 02114, USA
- Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA
- Corresponding author:
| | - B. E. Bouma
- Wellman Center for Photomedicine, Massachusetts General Hospital, 50 Blossom St., Boston, Massachusetts 02114, USA
- Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - M. Villiger
- Wellman Center for Photomedicine, Massachusetts General Hospital, 50 Blossom St., Boston, Massachusetts 02114, USA
- Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA
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12
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Azuma S, Makita S, Kasaragod D, Sugiyama S, Miura M, Yasuno Y. Clinical multi-functional OCT for retinal imaging. BIOMEDICAL OPTICS EXPRESS 2019; 10:5724-5743. [PMID: 31799043 PMCID: PMC6865108 DOI: 10.1364/boe.10.005724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 05/09/2023]
Abstract
A compact clinical prototype multi-functional optical coherence tomography (OCT) device for the posterior human eye has been developed. This compact Jones-matrix OCT (JM-OCT) device integrates all components into a single package. Multiple image functions, i.e., scattering intensity, OCT angiography, and the degree of polarization uniformity, are obtained. The device has the capability for measuring local birefringence. Multi-functional imaging of several eyes with age-related macular degeneration is demonstrated. The compact JM-OCT device will be useful for the in vivo non-invasive investigation of abnormal tissues.
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Affiliation(s)
- Shinnosuke Azuma
- Computational Optics Group, University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8573, Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki 305–8531, Japan
| | - Shuichi Makita
- Computational Optics Group, University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8573, Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki 305–8531, Japan
| | - Deepa Kasaragod
- Computational Optics Group, University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8573, Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki 305–8531, Japan
| | | | - Masahiro Miura
- Tokyo Medical University Ibaraki Medical Center, 3–20–1 Chuo, Ami, Ibaraki 300–0395, Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki 305–8531, Japan
| | - Yoshiaki Yasuno
- Computational Optics Group, University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8573, Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki 305–8531, Japan
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13
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Miyazawa A, Makita S, Li E, Yamazaki K, Kobayashi M, Sakai S, Yasuno Y. Polarization-sensitive optical coherence elastography. BIOMEDICAL OPTICS EXPRESS 2019; 10:5162-5181. [PMID: 31646039 PMCID: PMC6788587 DOI: 10.1364/boe.10.005162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 05/05/2023]
Abstract
Polarization-sensitive optical coherence elastography (PS-OCE) is developed for improved tissue discrimination. It integrates Jones matrix-based PS-optical coherence tomography (PS-OCT) with compression OCE. The method simultaneously measures the OCT intensity, attenuation coefficient, birefringence, and microstructural deformation (MSD) induced by tissue compression. Ex vivo porcine aorta and esophagus tissues were investigated by PS-OCE and histological imaging. The tissue properties measured by PS-OCE are shown as cross-sectional images and a three-dimensional (3-D) depth-trajectory plot. In this trajectory plot, the average attenuation coefficient, birefringence, and MSD were computed at each depth, and the trajectory in the depth direction was plotted in a 3-D feature space of these three properties. The tissue boundaries in a histological image corresponded with the depth-trajectory inflection points. Histogram analysis and t-distributed stochastic neighbour embedding (t-SNE) visualization of the three tissue properties indicated that the PS-OCE measurements provide sufficient information to discriminate porcine esophagus tissues.
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Affiliation(s)
- Arata Miyazawa
- Computational Optics Group, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8573, Japan
| | - Shuichi Makita
- Computational Optics Group, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8573, Japan
| | - En Li
- Computational Optics Group, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8573, Japan
| | - Kohei Yamazaki
- Biological Science Research, Kao Corporation, 5-3-28, Kotobukicho, Odawara, Kanagawa, 250-0002, Japan
| | - Masaki Kobayashi
- Biological Science Research, Kao Corporation, 5-3-28, Kotobukicho, Odawara, Kanagawa, 250-0002, Japan
| | - Shingo Sakai
- Skin Care Product Research, Kao Corporation, 5-3-28, Kotobukicho, Odawara, Kanagawa, 250-0002, Japan
| | - Yoshiaki Yasuno
- Computational Optics Group, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8573, Japan
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14
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Azuma S, Makita S, Miyazawa A, Ikuno Y, Miura M, Yasuno Y. Pixel-wise segmentation of severely pathologic retinal pigment epithelium and choroidal stroma using multi-contrast Jones matrix optical coherence tomography. BIOMEDICAL OPTICS EXPRESS 2018; 9:2955-2973. [PMID: 29984078 PMCID: PMC6033570 DOI: 10.1364/boe.9.002955] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 05/04/2023]
Abstract
Tissue segmentation of retinal optical coherence tomography (OCT) is widely used in ophthalmic diagnosis. However, its performance in severe pathologic cases is still insufficient. We propose a pixel-wise segmentation method that uses the multi-contrast measurement capability of Jones matrix OCT (JM-OCT). This method is applicable to both normal and pathologic retinal pigment epithelium (RPE) and choroidal stroma. In this method, "features," which are sensitive to specific tissues of interest, are synthesized by combining the multi-contrast images of JM-OCT, including attenuation coefficient, degree-of-polarization-uniformity, and OCT angiography. The tissue segmentation is done by simple thresholding of the feature. Compared with conventional segmentation methods for pathologic maculae, the proposed method is less computationally intensive. The segmentation method was validated by applying it to images from normal and severely pathologic cases. The segmentation results enabled the development of several types of en face visualizations, including melano-layer thickness maps, RPE elevation maps, choroidal thickness maps, and choroidal stromal attenuation coefficient maps. These facilitate close examination of macular pathology. The melano-layer thickness map is very similar to a near infrared fundus autofluorescence image, so the map can be used to identify the source of a hyper-autofluorescent signal.
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Affiliation(s)
- Shinnosuke Azuma
- Computational Optics Group, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573,
Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki 305-8531,
Japan
| | - Shuichi Makita
- Computational Optics Group, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573,
Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki 305-8531,
Japan
| | - Arata Miyazawa
- Computational Optics Group, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573,
Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki 305-8531,
Japan
| | - Yasushi Ikuno
- Ikuno Eye Center, 2-9-10-3F Juso-Higashi, Yodogawa-Ku, Osaka 532-0023,
Japan
| | - Masahiro Miura
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki 305-8531,
Japan
- Tokyo Medical University Ibaraki Medical Center, 3-20-1 Chuo, Ami, Ibaraki 300-0395,
Japan
| | - Yoshiaki Yasuno
- Computational Optics Group, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573,
Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki 305-8531,
Japan
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15
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Kasaragod D, Makita S, Hong YJ, Yasuno Y. Machine-learning based segmentation of the optic nerve head using multi-contrast Jones matrix optical coherence tomography with semi-automatic training dataset generation. BIOMEDICAL OPTICS EXPRESS 2018; 9:3220-3243. [PMID: 29984095 PMCID: PMC6033556 DOI: 10.1364/boe.9.003220] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/08/2018] [Accepted: 06/08/2018] [Indexed: 05/18/2023]
Abstract
A pixel-by-pixel tissue classification framework using multiple contrasts obtained by Jones matrix optical coherence tomography (JM-OCT) is demonstrated. The JM-OCT is an extension of OCT that provides OCT, OCT angiography, birefringence tomography, degree-of-polarization uniformity tomography, and attenuation coefficient tomography, simultaneously. The classification framework consists of feature engineering, k-means clustering that generates a training dataset, training of a tissue classifier using the generated training dataset, and tissue classification by the trained classifier. The feature engineering process generates synthetic features from the primary optical contrasts obtained by JM-OCT. The tissue classification is performed in the feature space of the engineered features. We applied this framework to the in vivo analysis of optic nerve heads of posterior eyes. This classified each JM-OCT pixel into prelamina, lamina cribrosa (lamina beam), and retrolamina tissues. The lamina beam segmentation results were further utilized for birefringence and attenuation coefficient analysis of lamina beam.
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Affiliation(s)
- Deepa Kasaragod
- Computational Optics Group, University of Tsukuba, Tsukuba,
Japan
| | - Shuichi Makita
- Computational Optics Group, University of Tsukuba, Tsukuba,
Japan
| | - Young-Joo Hong
- Computational Optics Group, University of Tsukuba, Tsukuba,
Japan
| | - Yoshiaki Yasuno
- Computational Optics Group, University of Tsukuba, Tsukuba,
Japan
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16
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Comparison of intensity, phase retardation, and local birefringence images for filtering blebs using polarization-sensitive optical coherence tomography. Sci Rep 2018; 8:7519. [PMID: 29760407 PMCID: PMC5951885 DOI: 10.1038/s41598-018-25884-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 05/01/2018] [Indexed: 11/17/2022] Open
Abstract
Polarization-sensitive optical coherence tomography (PS-OCT) allows the recording of depth-resolved polarimetric measurements. It has been reported that phase retardation and local birefringence images can noninvasively detect fibrotic area in blebs after glaucoma surgery. Evaluation of scar fibrosis in blebs is important not only for predicting bleb function, but also for planning revision trabeculectomy. Herein, we characterize the intensity, phase retardation, and local birefringence images of blebs using PS-OCT. A total of 85 blebs from 85 patients who had undergone trabeculectomy were examined. Both phase retardation and local birefringence images detected fibrotic changes in blebs after glaucoma surgery. Phase retardation images detected slight fibrotic change during the early stage after surgery, whereas local birefringence images showed localized fibrotic tissue. There are two main patterns of local birefringence image changes in blebs: plate-like birefringence changes and diffuse changes. The area of plate-like birefringence change was significantly larger in poorly functioning blebs and is thus correlated with bleb function. These data suggest that the plate-like fibrotic change evaluation by PS-OCT may be useful not only for noninvasive evaluation of fibrotic scar tissue in blebs, but also for developing strategies for revision trabeculectomy.
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17
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Miyazawa A, Hong YJ, Makita S, Kasaragod D, Yasuno Y. Generation and optimization of superpixels as image processing kernels for Jones matrix optical coherence tomography. BIOMEDICAL OPTICS EXPRESS 2017; 8:4396-4418. [PMID: 29082073 PMCID: PMC5654788 DOI: 10.1364/boe.8.004396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 08/31/2017] [Accepted: 09/01/2017] [Indexed: 05/05/2023]
Abstract
Jones matrix-based polarization sensitive optical coherence tomography (JM-OCT) simultaneously measures optical intensity, birefringence, degree of polarization uniformity, and OCT angiography. The statistics of the optical features in a local region, such as the local mean of the OCT intensity, are frequently used for image processing and the quantitative analysis of JM-OCT. Conventionally, local statistics have been computed with fixed-size rectangular kernels. However, this results in a trade-off between image sharpness and statistical accuracy. We introduce a superpixel method to JM-OCT for generating the flexible kernels of local statistics. A superpixel is a cluster of image pixels that is formed by the pixels' spatial and signal value proximities. An algorithm for superpixel generation specialized for JM-OCT and its optimization methods are presented in this paper. The spatial proximity is in two-dimensional cross-sectional space and the signal values are the four optical features. Hence, the superpixel method is a six-dimensional clustering technique for JM-OCT pixels. The performance of the JM-OCT superpixels and its optimization methods are evaluated in detail using JM-OCT datasets of posterior eyes. The superpixels were found to well preserve tissue structures, such as layer structures, sclera, vessels, and retinal pigment epithelium. And hence, they are more suitable for local statistics kernels than conventional uniform rectangular kernels.
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18
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Chan AC, Hong YJ, Makita S, Miura M, Yasuno Y. Noise-bias and polarization-artifact corrected optical coherence tomography by maximum a-posteriori intensity estimation. BIOMEDICAL OPTICS EXPRESS 2017; 8:2069-2087. [PMID: 28736656 PMCID: PMC5516815 DOI: 10.1364/boe.8.002069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 05/05/2023]
Abstract
We propose using maximum a-posteriori (MAP) estimation to improve the image signal-to-noise ratio (SNR) in polarization diversity (PD) optical coherence tomography. PD-detection removes polarization artifacts, which are common when imaging highly birefringent tissue or when using a flexible fiber catheter. However, dividing the probe power to two polarization detection channels inevitably reduces the SNR. Applying MAP estimation to PD-OCT allows for the removal of polarization artifacts while maintaining and improving image SNR. The effectiveness of the MAP-PD method is evaluated by comparing it with MAP-non-PD, intensity averaged PD, and intensity averaged non-PD methods. Evaluation was conducted in vivo with human eyes. The MAP-PD method is found to be optimal, demonstrating high SNR and artifact suppression, especially for highly birefringent tissue, such as the peripapillary sclera. The MAP-PD based attenuation coefficient image also shows better differentiation of attenuation levels than non-MAP attenuation images.
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Affiliation(s)
- Aaron C. Chan
- Computational Optics Group, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8573,
Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki,
Japan
| | - Young-Joo Hong
- Computational Optics Group, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8573,
Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki,
Japan
| | - Shuichi Makita
- Computational Optics Group, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8573,
Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki,
Japan
| | - Masahiro Miura
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki,
Japan
- Department of Ophthalmology, Tokyo Medical University Ibaraki Medical Center, 3-20-1 Chuo, Ami, Ibaraki,
Japan
| | - Yoshiaki Yasuno
- Computational Optics Group, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8573,
Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki,
Japan
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19
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Li E, Makita S, Hong YJ, Kasaragod D, Yasuno Y. Three-dimensional multi-contrast imaging of in vivo human skin by Jones matrix optical coherence tomography. BIOMEDICAL OPTICS EXPRESS 2017; 8:1290-1305. [PMID: 28663829 PMCID: PMC5480544 DOI: 10.1364/boe.8.001290] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 05/18/2023]
Abstract
A custom made dermatological Jones matrix optical coherence tomography (JM-OCT) is presented. It uses a passive-polarization-delay component based swept-source JM-OCT configuration, but is specially designed for in vivo human skin measurement. The center wavelength of its probe beam is 1310 nm and the A-line rate is 49.6 kHz. The JM-OCT is capable of simultaneously providing birefringence (local retardation) tomography, degree-of-polarization-uniformity tomography, complex-correlation-based optical coherence angiography, and conventional scattering OCT. To evaluate the performance of this JM-OCT, we measured in vivo human skin at several locations. Using the four kinds of OCT contrasts, the morphological characteristics and optical properties of different skin types were visualized.
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Affiliation(s)
- En Li
- Computational Optics Group, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8573,
Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki,
Japan
| | - Shuichi Makita
- Computational Optics Group, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8573,
Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki,
Japan
| | - Young-Joo Hong
- Computational Optics Group, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8573,
Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki,
Japan
| | - Deepa Kasaragod
- Computational Optics Group, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8573,
Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki,
Japan
| | - Yoshiaki Yasuno
- Computational Optics Group, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8573,
Japan
- Computational Optics and Ophthalmology Group, Tsukuba, Ibaraki,
Japan
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