1
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Srivastava R, Yow AP, Cheng J, Wong DWK, Tey HL. Three-dimensional graph-based skin layer segmentation in optical coherence tomography images for roughness estimation. Biomed Opt Express 2018; 9:3590-3606. [PMID: 30338142 PMCID: PMC6191621 DOI: 10.1364/boe.9.003590] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/10/2018] [Accepted: 05/16/2018] [Indexed: 06/01/2023]
Abstract
Automatic skin layer segmentation in optical coherence tomography (OCT) images is important for a topographic assessment of skin or skin disease detection. However, existing methods cannot deal with the problem of shadowing in OCT images due to the presence of hair, scales, etc. In this work, we propose a method to segment the topmost layer of the skin (or the skin surface) using 3D graphs with a novel cost function to deal with shadowing in OCT images. 3D graph cuts use context information across B-scans when segmenting the skin surface, which improves the segmentation as compared to segmenting each B-scan separately. The proposed method reduces the segmentation error by more than 20% as compared to the best performing related work. The method has been applied to roughness estimation and shows a high correlation with a manual assessment. Promising results demonstrate the usefulness of the proposed method for skin layer segmentation and roughness estimation in both normal OCT images and OCT images with shadowing.
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Affiliation(s)
- Ruchir Srivastava
- Institute for Infocomm Research, 1 Fusionopolis Way, No. 21-01 Connexis (South Tower), 138632,
Singapore
| | - Ai Ping Yow
- Institute for Infocomm Research, 1 Fusionopolis Way, No. 21-01 Connexis (South Tower), 138632,
Singapore
| | - Jun Cheng
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Industrial Technology, Chinese Academy of Sciences, 1219 Zhongguan West Road, Zhenhai District, Ningbo 315201,
China
| | - Damon W. K. Wong
- Institute for Infocomm Research, 1 Fusionopolis Way, No. 21-01 Connexis (South Tower), 138632,
Singapore
| | - Hong Liang Tey
- National Skin Center, 1 Mandalay Road, 308205,
Singapore
- Lee Kong Chian School of Medicine, Headquarters and Clinical Sciences Building, 11 Mandalay Road, 308232,
Singapore
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2
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Mekhail SP, Abudukeyoumu N, Ward J, Arbuthnott G, Chormaic SN. Fiber-bundle-basis sparse reconstruction for high resolution wide-field microendoscopy. Biomed Opt Express 2018; 9:1843-1851. [PMID: 29675323 PMCID: PMC5905928 DOI: 10.1364/boe.9.001843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/27/2018] [Accepted: 02/28/2018] [Indexed: 05/14/2023]
Abstract
In order to observe deep regions of the brain, we propose the use of a fiber bundle for microendoscopy. Fiber bundles allow for the excitation and collection of fluorescence as well as wide field imaging while remaining largely impervious to image distortions brought on by bending. Furthermore, their thin diameter, from 200-500 µm, means their impact on living tissue, though not absent, is minimal. Although wide field imaging with a bundle allows for a high temporal resolution since no scanning is involved, the largest criticism of bundle imaging is the drastically lowered spatial resolution. In this paper, we make use of sparsity in the object being imaged to up sample the low resolution images from the fiber bundle with compressive sensing. We take each image in a single shot by using a measurement basis dictated by the quasi-crystalline arrangement of the bundle's cores. We find that this technique allows us to increase the resolution of a typical image taken through a fiber bundle.
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Affiliation(s)
- Simon Peter Mekhail
- Light-Matter Interactions Unit, Okinawa Institute of Science and Technology Graduate University, Onna,
Japan
| | - Nilupaer Abudukeyoumu
- Brain Mechanisms for Behaviour Unit, Okinawa Institute of Science and Technology Graduate University, Onna,
Japan
| | - Jonathan Ward
- Light-Matter Interactions Unit, Okinawa Institute of Science and Technology Graduate University, Onna,
Japan
| | - Gordon Arbuthnott
- Brain Mechanisms for Behaviour Unit, Okinawa Institute of Science and Technology Graduate University, Onna,
Japan
| | - Síle Nic Chormaic
- Light-Matter Interactions Unit, Okinawa Institute of Science and Technology Graduate University, Onna,
Japan
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3
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Bozic I, Li X, Tao Y. Quantitative biometry of zebrafish retinal vasculature using optical coherence tomographic angiography. Biomed Opt Express 2018; 9:1244-1255. [PMID: 29541517 PMCID: PMC5846527 DOI: 10.1364/boe.9.001244] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/10/2018] [Accepted: 02/14/2018] [Indexed: 06/01/2023]
Abstract
The zebrafish is a robust model for studying human ophthalmic function and disease because of its fecundity, life-cycle, and similarities between its retinal structure and the human retina. Here, we demonstrate longitudinal in vivo imaging of retinal structure using optical coherence tomography (OCT) and noninvasive retinal vascular perfusion imaging using OCT angiography (OCT-A) in zebrafish. In addition, we present methods for retinal vascular segmentation and biometry to quantify vessel branch length, curvature, and angle. We further motivate retinal vascular biometry as a novel method for noninvasive zebrafish identification and demonstrated 99.9% accuracy for uniquely identifying eyes from a set of 200 longitudinal OCT/OCT-A volumes. The described methods enable the quantitative analysis of the vascular changes in zebrafish models of ophthalmic diseases and may broadly benefit large-scale zebrafish studies.
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Affiliation(s)
- Ivan Bozic
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
- These authors contributed equally in this work
| | - Xiaoyue Li
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
- These authors contributed equally in this work
| | - Yuankai Tao
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
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4
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Byers RA, Fisher M, Brown NJ, Tozer GM, Matcher SJ. Vascular patterning of subcutaneous mouse fibrosarcomas expressing individual VEGF isoforms can be differentiated using angiographic optical coherence tomography. Biomed Opt Express 2017; 8:4551-4567. [PMID: 29082084 PMCID: PMC5654799 DOI: 10.1364/boe.8.004551] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/08/2017] [Accepted: 09/08/2017] [Indexed: 05/08/2023]
Abstract
Subcutaneously implanted experimental tumors in mice are commonly used in cancer research. Despite their superficial location, they remain a challenge to image non-invasively at sufficient spatial resolution for microvascular studies. Here we evaluate the capabilities of optical coherence tomography (OCT) angiography for imaging such tumors directly through the murine skin in-vivo. Data sets were collected from mouse tumors derived from fibrosarcoma cells genetically engineered to express only single splice variant isoforms of vascular endothelial growth factor A (VEGF); either VEGF120 or VEGF188 (fs120 and fs188 tumors respectively). Measured vessel diameter was found to be significantly (p<0.001) higher for fs120 tumors (60.7 ± 4.9μm) compared to fs188 tumors (45.0 ± 4.0μm). The fs120 tumors also displayed significantly higher vessel tortuosity, fractal dimension and density. The ability to differentiate between tumor types with OCT suggests that the visible abnormal vasculature is representative of the tumor microcirculation, providing a robust, non-invasive method for observing the longitudinal dynamics of the subcutaneous tumor microcirculation.
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Affiliation(s)
- Robert A. Byers
- Biophotonics Group, Kroto Research Institute, University of Sheffield, Sheffield, UK
| | - Matthew Fisher
- Department of Oncology & Metabolism, The Medical School, University of Sheffield, Sheffield, UK
| | - Nicola J. Brown
- Department of Oncology & Metabolism, The Medical School, University of Sheffield, Sheffield, UK
| | - Gillian M. Tozer
- Department of Oncology & Metabolism, The Medical School, University of Sheffield, Sheffield, UK
- GT and SM are Joint Senior Authors
| | - Stephen J. Matcher
- Biophotonics Group, Kroto Research Institute, University of Sheffield, Sheffield, UK
- GT and SM are Joint Senior Authors
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5
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Khansari MM, O'Neill W, Lim J, Shahidi M. Method for quantitative assessment of retinal vessel tortuosity in optical coherence tomography angiography applied to sickle cell retinopathy. Biomed Opt Express 2017; 8:3796-3806. [PMID: 28856050 PMCID: PMC5560841 DOI: 10.1364/boe.8.003796] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/10/2017] [Accepted: 07/16/2017] [Indexed: 05/05/2023]
Abstract
Tortuosity is an important geometric vessel parameter and among the first microvascular alterations observed in various retinopathies. In the current study, a quantitative vessel tortuosity index (VTI) based on a combination of local and global centerline features is presented. Performance of VTI and previously established tortuosity indices were compared against human observers' evaluation of tortuosity. An image-processing pipeline was developed for application of VTI in retinal vessels imaged by optical coherence tomography angiography (OCTA) in perifoveal (6 mm × 6 mm) and parafoveal (3 mm × 3 mm) regions centered on the fovea. Forty-one subjects (12 healthy control (NC) and 29 sickle cell retinopathy (SCR)) and 10 subjects (5 NC and 5 SCR) were imaged in the perifoveal and parafoveal regions, respectively. The relationship between VTI and age was examined in the perifoveal regions in NC subjects. VTI was measured from the OCTA images and compared between NC and SCR subjects using generalized least square regression with and without adjusting for age and race. VTI was found to correlate better than the 4 previous indices with performance of human observers. In the perifoveal region, a significant correlation was observed between VTI and age (r = -0.4, P<0.001, N = 12). VTI was higher in SCR than NC subjects in perifoveal and parafoveal regions (P≤0.001). The results demonstrate that the proposed method shows promise for detection of increased tortuosity in vessels due to retinal disorders.
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Affiliation(s)
- Maziyar M Khansari
- Department of Bioengineering, University of Illinois at Chicago, IL, USA
| | - William O'Neill
- Department of Bioengineering, University of Illinois at Chicago, IL, USA
| | - Jennifer Lim
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, IL, USA
| | - Mahnaz Shahidi
- Department of Ophthalmology, University of Southern California, CA, USA
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6
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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. Biomed Opt 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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Park KS, Kim DU, Lee J, Kim GH, Chang KS. Simultaneous multicolor imaging of wide-field epi-fluorescence microscopy with four-bucket detection. Biomed Opt Express 2016; 7:2285-2294. [PMID: 27375944 PMCID: PMC4918582 DOI: 10.1364/boe.7.002285] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/29/2016] [Accepted: 05/10/2016] [Indexed: 06/06/2023]
Abstract
We demonstrate simultaneous imaging of multiple fluorophores using wide-field epi-fluorescence microscopy with a monochrome camera. The intensities of the three lasers are modulated by a sinusoidal waveform in order to excite each fluorophore with the same modulation frequency and a different time-delay. Then, the modulated fluorescence emissions are simultaneously detected by a camera operating at four times the excitation frequency. We show that two different fluorescence beads having crosstalk can be clearly separated using digital processing based on the phase information. In addition, multiple organelles within multi-stained single cells are shown with the phase mapping method, demonstrating an improved dynamic range and contrast compared to the conventional fluorescence image. These findings suggest that wide-field epi-fluorescence microscopy with four-bucket detection could be utilized for high-contrast multicolor imaging applications such as drug delivery and fluorescence in situ hybridization.
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8
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Dragoi IC, Stanciu SG, Hristu R, Coanda HG, Tranca DE, Popescu M, Coltuc D. Embedding complementary imaging data in laser scanning microscopy micrographs by reversible watermarking. Biomed Opt Express 2016; 7:1127-1137. [PMID: 27446641 PMCID: PMC4933558 DOI: 10.1364/boe.7.001127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/05/2016] [Accepted: 02/05/2016] [Indexed: 06/06/2023]
Abstract
Complementary laser scanning microscopy micrographs are considered as pairs consisting in a master image (MI) and a slave image (SI), the latter with potential for facilitating the interpretation of the MI. We propose a strategy based on reversible watermarking for embedding a lossy compressed version of the SI into the MI. The use of reversible watermarking ensures the exact recovery of the host image. By storing and/or transmitting the watermarked MI in a single file, the information contained in both images that constitute the pair is made available to a potential end-user, which simplifies data association and transfer. Examples are presented using support images collected by two complementary techniques, confocal scanning laser microscopy and transmission laser scanning microscopy, on Hematoxylin and Eosin stained tissue fragments. A strategy for minimizing the watermarking distortions of the MI, while preserving the content of the SI, is discussed in detail.
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Affiliation(s)
- Ioan-Catalin Dragoi
- Electrical Engineering Department, Valahia University of Targoviste, Bd. Carol I, nr. 2, Targoviste, Romania
| | - Stefan G Stanciu
- Center for Microscopy-Microanalysis and Information Processing, University Politehnica of Bucharest, 313 Splaiul Independentei Bvd., Bucharest, Romania;
| | - Radu Hristu
- Center for Microscopy-Microanalysis and Information Processing, University Politehnica of Bucharest, 313 Splaiul Independentei Bvd., Bucharest, Romania
| | - Henri-George Coanda
- Electrical Engineering Department, Valahia University of Targoviste, Bd. Carol I, nr. 2, Targoviste, Romania
| | - Denis E Tranca
- Center for Microscopy-Microanalysis and Information Processing, University Politehnica of Bucharest, 313 Splaiul Independentei Bvd., Bucharest, Romania
| | - Marius Popescu
- Center for Microscopy-Microanalysis and Information Processing, University Politehnica of Bucharest, 313 Splaiul Independentei Bvd., Bucharest, Romania; Department of Plastic Surgery and Reconstructive Microsurgery, Clinical Emergency Hospital of Bucharest, 8 Calea Floreasca St., Bucharest, Romania
| | - Dinu Coltuc
- Electrical Engineering Department, Valahia University of Targoviste, Bd. Carol I, nr. 2, Targoviste, Romania;
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9
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Guerra-Rosas E, Álvarez-Borrego J. Methodology for diagnosing of skin cancer on images of dermatologic spots by spectral analysis. Biomed Opt Express 2015; 6:3876-91. [PMID: 26504638 PMCID: PMC4605047 DOI: 10.1364/boe.6.003876] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/21/2015] [Accepted: 08/24/2015] [Indexed: 05/21/2023]
Abstract
In this paper a new methodology for the diagnosing of skin cancer on images of dermatologic spots using image processing is presented. Currently skin cancer is one of the most frequent diseases in humans. This methodology is based on Fourier spectral analysis by using filters such as the classic, inverse and k-law nonlinear. The sample images were obtained by a medical specialist and a new spectral technique is developed to obtain a quantitative measurement of the complex pattern found in cancerous skin spots. Finally a spectral index is calculated to obtain a range of spectral indices defined for skin cancer. Our results show a confidence level of 95.4%.
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Affiliation(s)
- Esperanza Guerra-Rosas
- Departamento de Investigación en Física, Universidad de Sonora (UNISON), Luis Encinas y Rosales S/N, Col. Centro, Hermosillo, Sonora, C.P. 83000, Mexico ;
| | - Josué Álvarez-Borrego
- Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), División de Física Aplicada, Departamento de Óptica, Carretera Ensenada-Tijuana No. 3918, Fraccionamiento Zona Playitas, Ensenada, Baja California, C.P. 22860, Mexico ;
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10
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Kumar A, Kamali T, Platzer R, Unterhuber A, Drexler W, Leitgeb RA. Anisotropic aberration correction using region of interest based digital adaptive optics in Fourier domain OCT. Biomed Opt Express 2015; 6:1124-34. [PMID: 25908999 PMCID: PMC4399654 DOI: 10.1364/boe.6.001124] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 02/25/2015] [Accepted: 02/25/2015] [Indexed: 05/22/2023]
Abstract
In this paper a numerical technique is presented to compensate for anisotropic optical aberrations, which are usually present across the lateral field of view in the out of focus regions, in high resolution optical coherence tomography and microscopy (OCT/OCM) setups. The recorded enface image field at different depths in the tomogram is digitally divided into smaller sub-regions or the regions of interest (ROIs), processed individually using subaperture based digital adaptive optics (DAO), and finally stitched together to yield a final image with a uniform diffraction limited resolution across the entire field of view (FOV). Using this method, a sub-micron lateral resolution is achieved over a depth range of 218 [Formula: see text]for a nano-particle phantom sample imaged using a fiber based point scanning spectral domain (SD) OCM system with a limited depth of focus (DOF) of ~7 [Formula: see text]at a numerical aperture (NA) of 0.6. Thus, an increase in DOF by ~30x is demonstrated in this case. The application of this method is also shown in ex vivo mouse adipose tissue.
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Affiliation(s)
- Abhishek Kumar
- Center of Medical Physics and Biomedical Engineering, Medical University of Vienna,
Austria
- Christian Doppler Laboratory for Laser Development and their Application to Medicine and Biology, Waehringer Guertel 18-20 A-1090 Vienna,
Austria
| | - Tschackad Kamali
- Center of Medical Physics and Biomedical Engineering, Medical University of Vienna,
Austria
| | - René Platzer
- Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Lazarettgasse 19 A-1090 Vienna,
Austria
| | - Angelika Unterhuber
- Center of Medical Physics and Biomedical Engineering, Medical University of Vienna,
Austria
| | - Wolfgang Drexler
- Center of Medical Physics and Biomedical Engineering, Medical University of Vienna,
Austria
- Christian Doppler Laboratory for Laser Development and their Application to Medicine and Biology, Waehringer Guertel 18-20 A-1090 Vienna,
Austria
| | - Rainer A. Leitgeb
- Center of Medical Physics and Biomedical Engineering, Medical University of Vienna,
Austria
- Christian Doppler Laboratory for Laser Development and their Application to Medicine and Biology, Waehringer Guertel 18-20 A-1090 Vienna,
Austria
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11
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Liu X, Kirby M, Zhao F. Motion analysis and removal in intensity variation based OCT angiography. Biomed Opt Express 2014; 5:3833-47. [PMID: 25426314 PMCID: PMC4242021 DOI: 10.1364/boe.5.003833] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 05/18/2023]
Abstract
In this work, we investigated how bulk motion degraded the quality of optical coherence tomography (OCT) angiography that was obtained through calculating interframe signal variation, i.e., interframe signal variation based optical coherence angiography (isvOCA). We demonstrated theoretically and experimentally that the spatial average of isvOCA signal had an explicit functional dependency on bulk motion. Our result suggested that the bulk motion could lead to an increased background in angiography image. Based on our motion analysis, we proposed to reduce image artifact induced by transient bulk motion in isvOCA through adaptive thresholding. The motion artifact reduced angiography was demonstrated in a 1.3μm spectral domain OCT system. We implemented signal processing using graphic processing unit for real-time imaging and conducted in vivo microvasculature imaging on human skin. Our results clearly showed that the adaptive thresholding method was highly effective in the motion artifact removal for OCT angiography.
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Affiliation(s)
- Xuan Liu
- Department of Electrical and Computer Engineering, New Jersey Institute of Technology, 323 Dr Martin Luther King Jr Blvd, Newark, NJ USA
| | - Mitchell Kirby
- Department of Biomedical Engineering, Michigan Technological University, 1400 Townsend Dr., Houghton, MI USA
| | - Feng Zhao
- Department of Biomedical Engineering, Michigan Technological University, 1400 Townsend Dr., Houghton, MI USA
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12
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Dsouza R, Subhash H, Neuhaus K, Hogan J, Wilson C, Leahy M. Dermascope guided multiple reference optical coherence tomography. Biomed Opt Express 2014; 5:2870-82. [PMID: 25401004 PMCID: PMC4230876 DOI: 10.1364/boe.5.002870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/20/2014] [Accepted: 07/28/2014] [Indexed: 05/03/2023]
Abstract
In this paper, we report the feasibility of integrating a novel low cost optical coherence tomography (OCT) system with a dermascope for point-of-care applications. The proposed OCT system is based on an enhanced time-domain optical coherence tomographic system, called multiple reference OCT (MR-OCT), which uses a single miniature voice coil actuator and a partial mirror for extending the axial scan range. The system can simultaneously register both the superficial dermascope image and the depth-resolved OCT sub-surface information by an interactive beam steering method. A practitioner is able to obtain the depth resolved information of the point of interest by simply using the mouse cursor. The proposed approach of combining a dermascope with a low cost OCT provides a unique powerful optical imaging modality for a range of dermatological applications. Hand-held dermascopic OCT devices would also enable point of care and remote health monitoring.
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Affiliation(s)
- Roshan Dsouza
- Tissue Optics and Microcirculation Imaging Group, School of Physics, National University of Ireland, Galway, Ireland
| | - Hrebesh Subhash
- Tissue Optics and Microcirculation Imaging Group, School of Physics, National University of Ireland, Galway, Ireland
| | - Kai Neuhaus
- Tissue Optics and Microcirculation Imaging Group, School of Physics, National University of Ireland, Galway, Ireland
| | - Josh Hogan
- Compact Imaging, Inc., 897 Independence Ave., Suite 5B, Mountain View, CA 94043 USA
| | - Carol Wilson
- Compact Imaging, Inc., 897 Independence Ave., Suite 5B, Mountain View, CA 94043 USA
| | - Martin Leahy
- Tissue Optics and Microcirculation Imaging Group, School of Physics, National University of Ireland, Galway, Ireland
- Royal College of Surgeons (RCSI), Dublin, Ireland
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13
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Liao YH, Kuo WC, Chou SY, Tsai CS, Lin GL, Tsai MR, Shih YT, Lee GG, Sun CK. Quantitative analysis of intrinsic skin aging in dermal papillae by in vivo harmonic generation microscopy. Biomed Opt Express 2014; 5:3266-79. [PMID: 25401037 PMCID: PMC4230862 DOI: 10.1364/boe.5.003266] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/25/2014] [Accepted: 08/08/2014] [Indexed: 05/20/2023]
Abstract
Chronological skin aging is associated with flattening of the dermal-epidermal junction (DEJ), but to date no quantitative analysis focusing on the aging changes in the dermal papillae (DP) has been performed. The aim of the study is to determine the architectural changes and the collagen density related to chronological aging in the dermal papilla zone (DPZ) by in vivo harmonic generation microscopy (HGM) with a sub-femtoliter spatial resolution. We recruited 48 Asian subjects and obtained in vivo images on the sun-protected volar forearm. Six parameters were defined to quantify 3D morphological changes of the DPZ, which we analyzed both manually and computationally to study their correlation with age. The depth of DPZ, the average height of isolated DP, and the 3D interdigitation index decreased with age, while DP number density, DP volume, and the collagen density in DP remained constant over time. In vivo high-resolution HGM technology has uncovered chronological aging-related variations in DP, and sheds light on real-time quantitative skin fragility assessment and disease diagnostics based on collagen density and morphology.
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Affiliation(s)
- Yi-Hua Liao
- Department of Dermatology, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei 10002, Taiwan
- Molecular Imaging Center, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Cheng Kuo
- Department of Electrical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Sin-Yo Chou
- Department of Electrical Engineering, National Taiwan University, Taipei 10617, Taiwan
- Graduate Institute of Photonics and Optoelectronics, National Taiwan University, Taipei 10617, Taiwan
| | - Cheng-Shiun Tsai
- Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Guan-Liang Lin
- Department of Electrical Engineering, National Taiwan University, Taipei 10617, Taiwan
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Ming-Rung Tsai
- Molecular Imaging Center, National Taiwan University, Taipei 10617, Taiwan
| | - Yuan-Ta Shih
- Molecular Imaging Center, National Taiwan University, Taipei 10617, Taiwan
| | - Gwo-Giun Lee
- Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Chi-Kuang Sun
- Molecular Imaging Center, National Taiwan University, Taipei 10617, Taiwan
- Department of Electrical Engineering, National Taiwan University, Taipei 10617, Taiwan
- Graduate Institute of Photonics and Optoelectronics, National Taiwan University, Taipei 10617, Taiwan
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
- Research Center for Applied Sciences and Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
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14
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Martens MA, Boesmans W, Vanden Berghe P. Calcium imaging at kHz frame rates resolves millisecond timing in neuronal circuits and varicosities. Biomed Opt Express 2014; 5:2648-2661. [PMID: 25136492 PMCID: PMC4132995 DOI: 10.1364/boe.5.002648] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/10/2014] [Accepted: 07/11/2014] [Indexed: 06/03/2023]
Abstract
We have configured a widefield fast imaging system that allows imaging at 1000 frames per second (512x512 pixels). The system was extended with custom processing tools including a time correlation method to facilitate the analysis of static subcellular compartments (e.g. neuronal varicosities) with enhanced contrast, as well as a dynamic intensity processing (DIP) algorithm that aids in data size reduction and fast visualization and interpretation of timing and directionality in neuronal circuits. This system, together with our custom developed processing tools enables efficient detection of fast physiological events, such as action potential dependent calcium steps. We show, using a specific blocker of nerve communication, that with this setup it is possible to discriminate between a pre and post synaptic event in an all optical way.
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Affiliation(s)
- Michiel A. Martens
- Laboratory for Enteric Neuroscience (LENS),TARGID, University of Leuven, O&N 1 Herestraat 49-box 701, Leuven 3000, Belgium
| | - Werend Boesmans
- Laboratory for Enteric Neuroscience (LENS),TARGID, University of Leuven, O&N 1 Herestraat 49-box 701, Leuven 3000, Belgium
| | - Pieter Vanden Berghe
- Laboratory for Enteric Neuroscience (LENS),TARGID, University of Leuven, O&N 1 Herestraat 49-box 701, Leuven 3000, Belgium
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15
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Minetti C, Podgorski T, Coupier G, Dubois F. Fully automated digital holographic processing for monitoring the dynamics of a vesicle suspension under shear flow. Biomed Opt Express 2014; 5:1554-68. [PMID: 24877015 PMCID: PMC4026899 DOI: 10.1364/boe.5.001554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 05/16/2023]
Abstract
We investigate the dynamics of a vesicle suspension under shear flow between plates using DHM with a spatially reduced coherent source. Holograms are grabbed at a frequency of 24 frames/sec. The distribution of the vesicle suspension is obtained after numerical processing of the digital holograms sequence resulting in a 4D distribution. Obtaining this distribution is not straightforward and requires special processing to automate the analysis. We present an original method that fully automates the analysis and provides distributions that are further analyzed to extract physical properties of the fluid. Details of the numerical implementation, as well as sample experimental results are presented.
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Affiliation(s)
- Christophe Minetti
- Service de Chimie-Physique EP, Université libre de Bruxelles, 50 Avenue F. Roosevelt, CP16/62, B-1050 Brussels, Belgium
| | - Thomas Podgorski
- Laboratoire Interdisciplinaire de Physique, CNRS-UMR 5588, Université Grenoble I, B.P. 87, 38402 Saint Martin d’Hères Cedex, France
| | - Gwennou Coupier
- Laboratoire Interdisciplinaire de Physique, CNRS-UMR 5588, Université Grenoble I, B.P. 87, 38402 Saint Martin d’Hères Cedex, France
| | - Frank Dubois
- Service de Chimie-Physique EP, Université libre de Bruxelles, 50 Avenue F. Roosevelt, CP16/62, B-1050 Brussels, Belgium
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16
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Nadler Z, Wang B, Wollstein G, Nevins JE, Ishikawa H, Bilonick R, Kagemann L, Sigal IA, Ferguson RD, Patel A, Hammer DX, Schuman JS. Repeatability of in vivo 3D lamina cribrosa microarchitecture using adaptive optics spectral domain optical coherence tomography. Biomed Opt Express 2014; 5:1114-23. [PMID: 24761293 PMCID: PMC3986004 DOI: 10.1364/boe.5.001114] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 02/04/2014] [Accepted: 02/21/2014] [Indexed: 05/05/2023]
Abstract
We demonstrate the repeatability of lamina cribrosa (LC) microarchitecture for in vivo 3D optical coherence tomography (OCT) scans of healthy, glaucoma suspects, and glaucomatous eyes. Eyes underwent two scans using a prototype adaptive optics spectral domain OCT (AO-SDOCT) device from which LC microarchitecture was semi-automatically segmented. LC segmentations were used to quantify pore and beam structure through several global microarchitecture parameters. Repeatability of LC microarchitecture was assessed qualitatively and quantitatively by calculating parameter imprecision. For all but one parameters (pore volume) measurement imprecision was <4.7% of the mean value, indicating good measurement reproducibility. Imprecision ranged between 27.3% and 54.5% of the population standard deviation for each parameter, while there was not a significant effect on imprecision due to disease status, indicating utility in testing for LC structural trends.
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Affiliation(s)
- Zach Nadler
- UPMC Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Bo Wang
- UPMC Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Gadi Wollstein
- UPMC Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jessica E. Nevins
- UPMC Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Hiroshi Ishikawa
- UPMC Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Richard Bilonick
- UPMC Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Larry Kagemann
- UPMC Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ian A. Sigal
- UPMC Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Ankit Patel
- Physical Science Inc., Andover, Massachusetts, USA
| | - Daniel X. Hammer
- Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Joel S. Schuman
- UPMC Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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17
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Antony BJ, Abràmoff MD, Harper MM, Jeong W, Sohn EH, Kwon YH, Kardon R, Garvin MK. A combined machine-learning and graph-based framework for the segmentation of retinal surfaces in SD-OCT volumes. Biomed Opt Express 2013; 4:2712-28. [PMID: 24409375 PMCID: PMC3862166 DOI: 10.1364/boe.4.002712] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/24/2013] [Accepted: 10/27/2013] [Indexed: 05/19/2023]
Abstract
Optical coherence tomography is routinely used clinically for the detection and management of ocular diseases as well as in research where the studies may involve animals. This routine use requires that the developed automated segmentation methods not only be accurate and reliable, but also be adaptable to meet new requirements. We have previously proposed the use of a graph-theoretic approach for the automated 3-D segmentation of multiple retinal surfaces in volumetric human SD-OCT scans. The method ensures the global optimality of the set of surfaces with respect to a cost function. Cost functions have thus far been typically designed by hand by domain experts. This difficult and time-consuming task significantly impacts the adaptability of these methods to new models. Here, we describe a framework for the automated machine-learning based design of the cost function utilized by this graph-theoretic method. The impact of the learned components on the final segmentation accuracy are statistically assessed in order to tailor the method to specific applications. This adaptability is demonstrated by utilizing the method to segment seven, ten and five retinal surfaces from SD-OCT scans obtained from humans, mice and canines, respectively. The overall unsigned border position errors observed when using the recommended configuration of the graph-theoretic method was 6.45 ± 1.87 μm, 3.35 ± 0.62 μm and 9.75 ± 3.18 μm for the human, mouse and canine set of images, respectively.
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Affiliation(s)
- Bhavna J. Antony
- Dept. of Electrical and Computer Engineering, The University of Iowa, Iowa City, IA,
USA
| | - Michael D. Abràmoff
- Dept. of Electrical and Computer Engineering, The University of Iowa, Iowa City, IA,
USA
- Dept. of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA,
USA
- Iowa City VA Healthcare System, Iowa City, IA,
USA
- Dept. of Biomedical Engineering, The University of Iowa, Iowa City, IA,
USA
- The Stephen A. Wynn Institute for Vision Research, Iowa City, IA,
USA
| | - Matthew M. Harper
- Dept. of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA,
USA
- Iowa City VA Healthcare System, Iowa City, IA,
USA
| | - Woojin Jeong
- Dept. of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA,
USA
- Department of Ophthalmology, Dong-A University, College of Medicine and Medical Research Center, Busan,
South Korea
| | - Elliott H. Sohn
- Dept. of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA,
USA
- The Stephen A. Wynn Institute for Vision Research, Iowa City, IA,
USA
| | - Young H. Kwon
- Dept. of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA,
USA
| | - Randy Kardon
- Dept. of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA,
USA
- Iowa City VA Healthcare System, Iowa City, IA,
USA
| | - Mona K. Garvin
- Dept. of Electrical and Computer Engineering, The University of Iowa, Iowa City, IA,
USA
- Iowa City VA Healthcare System, Iowa City, IA,
USA
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18
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Mattison SP, Shelton RL, Maxson RT, Applegate BE. Continuous real-time photoacoustic demodulation via field programmable gate array for dynamic imaging of zebrafish cardiac cycle. Biomed Opt Express 2013; 4:1451-63. [PMID: 24010007 PMCID: PMC3756580 DOI: 10.1364/boe.4.001451] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/22/2013] [Accepted: 07/23/2013] [Indexed: 05/18/2023]
Abstract
A four dimensional data set of the cardiac cycle of a zebrafish embryo was acquired using postacquisition synchronization of real time photoacoustic b-scans. Utilizing an off-axis photoacoustic microscopy (OA-PAM) setup, we have expanded upon our previous work with OA-PAM to develop a system that can sustain 100 kHz line rates while demodulating the bipolar photoacoustic signal in real-time. Real-time processing was accomplished by quadrature demodulation on a Field Programmable Gate Array (FPGA) in line with the signal digitizer. Simulated data acquisition verified the system is capable of real-time processing up to a line rate of 1 MHz. Galvanometer-scanning of the excitation laser inside the focus of the ultrasonic transducer enables real data acquisition of a 200 by 200 by 200 pixel, volumetric data set across a 2 millimeter field of view at a rate of 2.5 Hz.
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19
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Nadler Z, Wang B, Wollstein G, Nevins JE, Ishikawa H, Kagemann L, Sigal IA, Ferguson RD, Hammer DX, Grulkowski I, Liu JJ, Kraus MF, Lu CD, Hornegger J, Fujimoto JG, Schuman JS. Automated lamina cribrosa microstructural segmentation in optical coherence tomography scans of healthy and glaucomatous eyes. Biomed Opt Express 2013; 4:2596-608. [PMID: 24298418 PMCID: PMC3829553 DOI: 10.1364/boe.4.002596] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/17/2013] [Accepted: 10/17/2013] [Indexed: 05/05/2023]
Abstract
We demonstrate an automated segmentation method for in-vivo 3D optical coherence tomography (OCT) imaging of the lamina cribrosa (LC). Manual segmentations of coronal slices of the LC were used as a gold standard in parameter selection and evaluation of the automated technique. The method was validated using two prototype OCT devices; each had a subject cohort including both healthy and glaucomatous eyes. Automated segmentation of in-vivo 3D LC OCT microstructure performed comparably to manual segmentation and is useful for investigative research and in clinical quantification of the LC.
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Affiliation(s)
- Zach Nadler
- UPMC Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Bo Wang
- UPMC Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Gadi Wollstein
- UPMC Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jessica E. Nevins
- UPMC Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Hiroshi Ishikawa
- UPMC Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Larry Kagemann
- UPMC Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ian A. Sigal
- UPMC Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Daniel X. Hammer
- Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Ireneusz Grulkowski
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jonathan J. Liu
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Martin F. Kraus
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Pattern Recognition Lab and School of Advanced Optical Technologies (SAOT), University of Erlangen-Nuremberg, Nuremberg, Germany
| | - Chen D. Lu
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Joachim Hornegger
- Pattern Recognition Lab and School of Advanced Optical Technologies (SAOT), University of Erlangen-Nuremberg, Nuremberg, Germany
| | - James G. Fujimoto
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Joel S. Schuman
- UPMC Eye Center, Eye and Ear Institute, Ophthalmology and Visual Science Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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20
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Huang Y, Liu X, Song C, Kang JU. Motion-compensated hand-held common-path Fourier-domain optical coherence tomography probe for image-guided intervention. Biomed Opt Express 2012; 3:3105-18. [PMID: 23243562 PMCID: PMC3521294 DOI: 10.1364/boe.3.003105] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/25/2012] [Accepted: 10/29/2012] [Indexed: 05/04/2023]
Abstract
A motion-compensated, hand-held, common-path, Fourier-domain optical coherence tomography imaging probe has been developed for image-guided intervention during microsurgery. A hand-held prototype instrument was achieved by integrating an imaging fiber probe inside a stainless steel needle and attached to the ceramic shaft of a piezoelectric motor housed in an aluminum handle. The fiber probe obtains A-scan images. The distance information was extracted from the A-scans to track the sample surface distance and a fixed distance was maintained by a feedback motor control which effectively compensated hand tremor and target movements in the axial direction. Real-time data acquisition, processing, motion compensation, and image visualization and saving were implemented on a custom CPU-GPU hybrid architecture. We performed 10× zero padding to the raw spectrum to obtain 0.16 µm position accuracy with a compensation rate of 460 Hz. The root-mean-square error of hand-held distance variation from target position was measured to be 2.93 µm. We used a cross-correlation maximization-based shift correction algorithm for topology correction. To validate the system, we performed free-hand OCT M-scan imaging using various samples.
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21
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Huang Y, Liu X, Kang JU. Real-time 3D and 4D Fourier domain Doppler optical coherence tomography based on dual graphics processing units. Biomed Opt Express 2012; 3:2162-74. [PMID: 23024910 PMCID: PMC3447558 DOI: 10.1364/boe.3.002162] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 08/15/2012] [Accepted: 08/16/2012] [Indexed: 05/04/2023]
Abstract
We present real-time 3D (2D cross-sectional image plus time) and 4D (3D volume plus time) phase-resolved Doppler OCT (PRDOCT) imaging based on configuration of dual graphics processing units (GPU). A GPU-accelerated phase-resolving processing algorithm was developed and implemented. We combined a structural image intensity-based thresholding mask and average window method to improve the signal-to-noise ratio of the Doppler phase image. A 2D simultaneous display of the structure and Doppler flow images was presented at a frame rate of 70 fps with an image size of 1000 × 1024 (X × Z) pixels. A 3D volume rendering of tissue structure and flow images-each with a size of 512 × 512 pixels-was presented 64.9 milliseconds after every volume scanning cycle with a volume size of 500 × 256 × 512 (X × Y × Z) voxels, with an acquisition time window of only 3.7 seconds. To the best of our knowledge, this is the first time that an online, simultaneous structure and Doppler flow volume visualization has been achieved. Maximum system processing speed was measured to be 249,000 A-scans per second with each A-scan size of 2048 pixels.
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22
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Liew YM, McLaughlin RA, Wood FM, Sampson DD. Motion correction of in vivo three-dimensional optical coherence tomography of human skin using a fiducial marker. Biomed Opt Express 2012; 3:1774-86. [PMID: 22876343 PMCID: PMC3409698 DOI: 10.1364/boe.3.001774] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 06/21/2012] [Accepted: 06/26/2012] [Indexed: 05/04/2023]
Abstract
This paper presents a novel method based on a fiducial marker for correction of motion artifacts in 3D, in vivo, optical coherence tomography (OCT) scans of human skin and skin scars. The efficacy of this method was compared against a standard cross-correlation intensity-based registration method. With a fiducial marker adhered to the skin, OCT scans were acquired using two imaging protocols: direct imaging from air into tissue; and imaging through ultrasound gel into tissue, which minimized the refractive index mismatch at the tissue surface. The registration methods were assessed with data from both imaging protocols and showed reduced distortion of skin features due to motion. The fiducial-based method was found to be more accurate and robust, with an average RMS error below 20 µm and success rate above 90%. In contrast, the intensity-based method had an average RMS error ranging from 36 to 45 µm, and a success rate from 50% to 86%. The intensity-based algorithm was found to be particularly confounded by corrugations in the skin. By contrast, tissue features did not affect the fiducial-based method, as the motion correction was based on delineation of the flat fiducial marker. The average computation time for the fiducial-based algorithm was approximately 21 times less than for the intensity-based algorithm.
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Affiliation(s)
- Yih Miin Liew
- Optical+Biomedical Engineering Laboratory, School of Electrical, Electronic & Computer Engineering, The University of Western Australia, M018, 35 Stirling Highway, Crawley WA 6009, Australia
| | - Robert A. McLaughlin
- Optical+Biomedical Engineering Laboratory, School of Electrical, Electronic & Computer Engineering, The University of Western Australia, M018, 35 Stirling Highway, Crawley WA 6009, Australia
| | - Fiona M. Wood
- Burns Service of Western Australia, Royal Perth Hospital (RPH), Wellington Street, Perth WA 6000, Australia
- Burn Injury Research Unit, School of Surgery, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
| | - David D. Sampson
- Optical+Biomedical Engineering Laboratory, School of Electrical, Electronic & Computer Engineering, The University of Western Australia, M018, 35 Stirling Highway, Crawley WA 6009, Australia
- Centre for Microscopy, Characterisation & Analysis, The University of Western Australia, M010, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
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23
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Hahn D, Thibault P, Bech M, Stockmar M, Schleede S, Zanette I, Rack A, Weitkamp T, Sztrókay A, Schlossbauer T, Bamberg F, Reiser M, Pfeiffer F. Numerical comparison of X-ray differential phase contrast and attenuation contrast. Biomed Opt Express 2012; 3:1141-1148. [PMID: 22741063 PMCID: PMC3370957 DOI: 10.1364/boe.3.001141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/14/2012] [Accepted: 03/14/2012] [Indexed: 06/01/2023]
Abstract
We present a numerical tool to compare directly the contrast-to-noise-ratio (CNR) of the attenuation- and differential phase-contrast signals available from grating-based X-ray imaging for single radiographs. The attenuation projection is differentiated to bring it into a modality comparable to the differential phase projection using a Gaussian derivative filter. A Relative Contrast Gain (RCG) is then defined as the ratio of the CNR of image values in a region of interest (ROI) in the differential phase projection to the CNR of image values in the same ROI in the differential attenuation projection. We apply the method on experimental data of human breast tissue acquired using a grating interferometer to compare the two contrast modes for two regions of interest differing in the type of tissue. Our results indicate that the proposed method can be used as a local estimate of the spatial distribution of the ratio δ/β, i.e., real and imaginary part of the complex refractive index, across a sample.
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Affiliation(s)
- Dieter Hahn
- Technische Universität München - 85748 Garching,
Germany
| | | | - Martin Bech
- Technische Universität München - 85748 Garching,
Germany
| | - Marco Stockmar
- Technische Universität München - 85748 Garching,
Germany
| | | | - Irene Zanette
- European Synchrotron Radiation Facility - 38043 Grenoble,
France
| | - Alexander Rack
- European Synchrotron Radiation Facility - 38043 Grenoble,
France
| | | | - Aniko Sztrókay
- Institute for Clinical Radiology, Ludwig Maximilians University - 81377 Munich,
Germany
| | - Thomas Schlossbauer
- Institute for Clinical Radiology, Ludwig Maximilians University - 81377 Munich,
Germany
| | - Fabian Bamberg
- Institute for Clinical Radiology, Ludwig Maximilians University - 81377 Munich,
Germany
| | - Maximilian Reiser
- Institute for Clinical Radiology, Ludwig Maximilians University - 81377 Munich,
Germany
| | - Franz Pfeiffer
- Technische Universität München - 85748 Garching,
Germany
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24
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Zhang K, Kang JU. Real-time intraoperative 4D full-range FD-OCT based on the dual graphics processing units architecture for microsurgery guidance. Biomed Opt Express 2011; 2:764-70. [PMID: 21483601 PMCID: PMC3072119 DOI: 10.1364/boe.2.000764] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 02/25/2011] [Accepted: 02/25/2011] [Indexed: 05/04/2023]
Abstract
Real-time 4D full-range complex-conjugate-free Fourier-domain optical coherence tomography (FD-OCT) is implemented using a dual graphics processing units (dual-GPUs) architecture. One GPU is dedicated to the FD-OCT data processing while the second one is used for the volume rendering and display. GPU accelerated non-uniform fast Fourier transform (NUFFT) is also implemented to suppress the side lobes of the point spread function to improve the image quality. Using a 128,000 A-scan/second OCT spectrometer, we obtained 5 volumes/second real-time full-range 3D OCT imaging. A complete micro-manipulation of a phantom using a microsurgical tool is monitored by multiple volume renderings of the same 3D date set with different view angles. Compared to the conventional surgical microscope, this technology would provide the surgeons a more comprehensive spatial view of the microsurgical site and could serve as an effective intraoperative guidance tool.
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