1
|
Seesan T, Mukherjee P, Abd El-Sadek I, Lim Y, Zhu L, Makita S, Yasuno Y. Optical-coherence-tomography-based deep-learning scatterer-density estimator using physically accurate noise model. BIOMEDICAL OPTICS EXPRESS 2024; 15:2832-2848. [PMID: 38855681 PMCID: PMC11161371 DOI: 10.1364/boe.519743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 06/11/2024]
Abstract
We demonstrate a deep-learning-based scatterer density estimator (SDE) that processes local speckle patterns of optical coherence tomography (OCT) images and estimates the scatterer density behind each speckle pattern. The SDE is trained using large quantities of numerically simulated OCT images and their associated scatterer densities. The numerical simulation uses a noise model that incorporates the spatial properties of three types of noise, i.e., shot noise, relative-intensity noise, and non-optical noise. The SDE's performance was evaluated numerically and experimentally using two types of scattering phantom and in vitro tumor spheroids. The results confirmed that the SDE estimates scatterer densities accurately. The estimation accuracy improved significantly when compared with our previous deep-learning-based SDE, which was trained using numerical speckle patterns generated from a noise model that did not account for the spatial properties of noise.
Collapse
Affiliation(s)
- Thitiya Seesan
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Pradipta Mukherjee
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Ibrahim Abd El-Sadek
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
- Department of Physics, Faculty of Science, Damietta University, New Damietta City 34517, Damietta, Egypt
| | - Yiheng Lim
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Lida Zhu
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Shuichi Makita
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Yoshiaki Yasuno
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| |
Collapse
|
2
|
Kübler J, Zoutenbier VS, Buist G, Fischer J, Amelink A, de Boer JF. Confocal corrected attenuation coefficient imaging in phantoms and in vivo using chromatic focal shift calibration. BIOMEDICAL OPTICS EXPRESS 2023; 14:5282-5297. [PMID: 37854560 PMCID: PMC10581799 DOI: 10.1364/boe.498459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/25/2023] [Accepted: 09/07/2023] [Indexed: 10/20/2023]
Abstract
Optical coherence tomography (OCT) is conventionally used for structural imaging of tissue. Calibrating the intensity values of OCT images can give information on the tissue's inherent optical properties, such as the attenuation coefficient, which can provide an additional parameter to quantify possible pathological changes. To obtain calibrated intensity values, the focus position and Rayleigh length of the incident beam need to be known. We explore the feasibility of extracting the focus position from an OCT scan acquired with a single focus setting using the chromatic aberration of the system. The chromatic focal shift of an OCT system is exploited to achieve different focus positions for sub-spectrum reconstructed OCT images. The ratios of these images are used to estimate the focus position. Reconstruction of a high-resolution B-scan from coherent addition of sub-spectrum confocal function corrected B-scans and subsequent high-resolution OCT attenuation coefficient imaging is demonstrated. Furthermore, we introduce a method to experimentally determine the chromatic focal shifts of an OCT system in phantoms and an in vivo human retina. These shifts are compared to the theoretically expected shifts calculated with ray tracing.
Collapse
Affiliation(s)
- Johannes Kübler
- LaserLaB, Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, The Netherlands
- Heidelberg Engineering GmbH, Heidelberg, Germany
| | - Vincent S. Zoutenbier
- LaserLaB, Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, The Netherlands
- Department of Optics, Netherlands Organization for Applied Scientific Research, TNO, Delft, The Netherlands
| | - Gijs Buist
- LaserLaB, Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, The Netherlands
- Department of Optics, Netherlands Organization for Applied Scientific Research, TNO, Delft, The Netherlands
| | - Jörg Fischer
- Heidelberg Engineering GmbH, Heidelberg, Germany
| | - Arjen Amelink
- LaserLaB, Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, The Netherlands
- Department of Optics, Netherlands Organization for Applied Scientific Research, TNO, Delft, The Netherlands
| | - Johannes F. de Boer
- LaserLaB, Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, The Netherlands
- Department of Ophthalmology, Amsterdam UMC, Amsterdam, The Netherlands
| |
Collapse
|
3
|
Rosenfeld PJ, Cheng Y, Shen M, Gregori G, Wang RK. Unleashing the power of optical attenuation coefficients to facilitate segmentation strategies in OCT imaging of age-related macular degeneration: perspective. BIOMEDICAL OPTICS EXPRESS 2023; 14:4947-4963. [PMID: 37791280 PMCID: PMC10545179 DOI: 10.1364/boe.496080] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/22/2023] [Accepted: 07/27/2023] [Indexed: 10/05/2023]
Abstract
The use of optical attenuation coefficients (OAC) in optical coherence tomography (OCT) imaging of the retina has improved the segmentation of anatomic layers compared with traditional intensity-based algorithms. Optical attenuation correction has improved our ability to measure the choroidal thickness and choroidal vascularity index using dense volume scans. Algorithms that combine conventional intensity-based segmentation with depth-resolved OAC OCT imaging have been used to detect elevations of the retinal pigment epithelium (RPE) due to drusen and basal laminar deposits, the location of hyperpigmentation within the retina and along the RPE, the identification of macular atrophy, the thickness of the outer retinal (photoreceptor) layer, and the presence of calcified drusen. OAC OCT algorithms can identify the risk-factors that predict disease progression in age-related macular degeneration.
Collapse
Affiliation(s)
- Philip J. Rosenfeld
- Department of Ophthalmology, Bascom Palmer
Eye Institute, University of Miami Miller School of
Medicine, Miami, Florida, USA
| | - Yuxuan Cheng
- Department of Bioengineering,
University of Washington, Seattle,
Washington, USA
| | - Mengxi Shen
- Department of Ophthalmology, Bascom Palmer
Eye Institute, University of Miami Miller School of
Medicine, Miami, Florida, USA
| | - Giovanni Gregori
- Department of Ophthalmology, Bascom Palmer
Eye Institute, University of Miami Miller School of
Medicine, Miami, Florida, USA
| | - Ruikang K. Wang
- Department of Bioengineering,
University of Washington, Seattle,
Washington, USA
- Department of Ophthalmology,
University of Washington, Seattle,
Washington, USA
| |
Collapse
|
4
|
Glandorf L, Marchand PJ, Lasser T, Razansky D. Digital aberration correction enhances field of view in visible-light optical coherence microscopy. OPTICS LETTERS 2022; 47:5088-5091. [PMID: 36181193 DOI: 10.1364/ol.464405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
In optical coherence microscopy, optical aberrations commonly result in astigmatism-dominated wavefront errors in the peripheral regions of the optical objective, primarily elongating the microscope's point-spread function along the radial direction in the vicinity of the focal plane. We report on enhanced-field-of-view optical coherence microscopy through computational aberration correction in the visible-light range. An isotropic spatial resolution of 2.5 µm was achieved over an enhanced lateral field of view spanning 1.3 mm × 1.6 mm, as experimentally verified in a micro-bead phantom and further demonstrated in ex vivo tissue samples. The extended field of view achieved by the digital aberration correction facilitates the use of low-cost systems by averting the need for high-quality objectives.
Collapse
|
5
|
Kübler J, Zoutenbier VS, Amelink A, Fischer J, de Boer JF. Investigation of methods to extract confocal function parameters for the depth resolved determination of attenuation coefficients using OCT in intralipid samples, titanium oxide phantoms, and in vivo human retinas. BIOMEDICAL OPTICS EXPRESS 2021; 12:6814-6830. [PMID: 34858682 PMCID: PMC8606142 DOI: 10.1364/boe.440574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/21/2021] [Accepted: 09/29/2021] [Indexed: 05/18/2023]
Abstract
The attenuation coefficient provides a quantitative parameter for tissue characterization and can be calculated from optical coherence tomography (OCT) data, but accurate determination requires compensation for the confocal function. We present extensive measurement series for extraction of the focal plane and the apparent Rayleigh length from the ratios of OCT images acquired with different focus depths and compare these results with two alternative approaches. By acquiring OCT images for a range of different focus depths the optimal focus plane difference is determined for intralipid and titanium oxide (TiO2) phantoms with different scatterer concentrations, which allows for calculation of the attenuation coefficient corrected for the confocal function. The attenuation coefficient is determined for homogeneous intralipid and TiO2 samples over a wide range of concentrations. We further demonstrate very good reproducibility of the determined attenuation coefficient of layers with identical scatter concentrations in a multi-layered phantom. Finally, this method is applied to in vivo retinal data.
Collapse
Affiliation(s)
- Johannes Kübler
- LaserLaB, Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, The Netherlands
- Heidelberg Engineering GmbH, Heidelberg, Germany
| | - Vincent S. Zoutenbier
- LaserLaB, Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, The Netherlands
| | - Arjen Amelink
- LaserLaB, Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, The Netherlands
- Department of Optics, Netherlands Organization for Applied Scientific Research, TNO, Delft, The Netherlands
| | - Jörg Fischer
- Heidelberg Engineering GmbH, Heidelberg, Germany
| | - Johannes F. de Boer
- LaserLaB, Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, The Netherlands
- Department of Ophthalmology, Amsterdam UMC, Amsterdam, The Netherlands
| |
Collapse
|
6
|
Ghafaryasl B, Vermeer KA, Kalkman J, Callewaert T, de Boer JF, van Vliet LJ. Attenuation coefficient estimation in Fourier-domain OCT of multi-layered phantoms. BIOMEDICAL OPTICS EXPRESS 2021; 12:2744-2758. [PMID: 34123501 PMCID: PMC8176795 DOI: 10.1364/boe.415079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 05/11/2023]
Abstract
Optical properties, such as the attenuation coefficients of multi-layer tissue samples, could be used as a biomarker for diagnosis and disease progression in clinical practice. In this paper, we present a method to estimate the attenuation coefficients in a multi-layer sample by fitting a single scattering model for the OCT signal to the recorded OCT signal. In addition, we employ numerical simulations to obtain the theoretically achievable precision and accuracy of the estimated parameters under various experimental conditions. Finally, the method is applied to two sets of measurements obtained from a multi-layer phantom by two experimental OCT systems: one with a large and one with a small Rayleigh length. Numerical and experimental results show an accurate estimation of the attenuation coefficients when using multiple B-scans.
Collapse
Affiliation(s)
- Babak Ghafaryasl
- Rotterdam Ophthalmic Institute, Rotterdam Eye Hospital, 3011 BH, Rotterdam, The Netherlands
- Department of Imaging Physics, Delft University of Technology, 2628 CJ, Delft, The Netherlands
| | - Koenraad A. Vermeer
- Rotterdam Ophthalmic Institute, Rotterdam Eye Hospital, 3011 BH, Rotterdam, The Netherlands
| | - Jeroen Kalkman
- Department of Imaging Physics, Delft University of Technology, 2628 CJ, Delft, The Netherlands
| | - Tom Callewaert
- Department of Imaging Physics, Delft University of Technology, 2628 CJ, Delft, The Netherlands
| | - Johannes F. de Boer
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Lucas J. van Vliet
- Department of Imaging Physics, Delft University of Technology, 2628 CJ, Delft, The Netherlands
| |
Collapse
|
7
|
Ghafaryasl B, Vermeer KA, Kalkman J, Callewaert T, de Boer JF, Van Vliet LJ. Analysis of attenuation coefficient estimation in Fourier-domain OCT of semi-infinite media. BIOMEDICAL OPTICS EXPRESS 2020; 11:6093-6107. [PMID: 33282477 PMCID: PMC7687928 DOI: 10.1364/boe.403283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 05/05/2023]
Abstract
The attenuation coefficient (AC) is an optical property of tissue that can be estimated from optical coherence tomography (OCT) data. In this paper, we aim to estimate the AC accurately by compensating for the shape of the focused beam. For this, we propose a method to estimate the axial PSF model parameters and AC by fitting a model for an OCT signal in a homogenous sample to the recorded OCT signal. In addition, we employ numerical analysis to obtain the theoretical optimal precision of the estimated parameters for different experimental setups. Finally, the method is applied to OCT B-scans obtained from homogeneous samples. The numerical and experimental results show accurate estimations of the AC and the focus location when the focus is located inside the sample.
Collapse
Affiliation(s)
- Babak Ghafaryasl
- Rotterdam Ophthalmic Institute, Rotterdam Eye Hospital, Rotterdam, 3011 BH, The Netherlands
- Department of Imaging Physics, Delft University of Technology, Delft, 2628 BL, The Netherlands
| | - Koenraad A. Vermeer
- Rotterdam Ophthalmic Institute, Rotterdam Eye Hospital, Rotterdam, 3011 BH, The Netherlands
| | - Jeroen Kalkman
- Department of Imaging Physics, Delft University of Technology, Delft, 2628 BL, The Netherlands
| | - Tom Callewaert
- Department of Imaging Physics, Delft University of Technology, Delft, 2628 BL, The Netherlands
| | - Johannes F. de Boer
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV, The Netherlands
| | - Lucas J. Van Vliet
- Department of Imaging Physics, Delft University of Technology, Delft, 2628 BL, The Netherlands
| |
Collapse
|
8
|
Li K, Liang W, Yang Z, Liang Y, Wan S. Robust, accurate depth-resolved attenuation characterization in optical coherence tomography. BIOMEDICAL OPTICS EXPRESS 2020; 11:672-687. [PMID: 32206392 PMCID: PMC7041483 DOI: 10.1364/boe.382493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/21/2019] [Accepted: 12/23/2019] [Indexed: 05/06/2023]
Abstract
Depth-resolved optical attenuation coefficient is a valuable tissue parameter that complements the intensity-based structural information in optical coherent tomography (OCT) imaging. Herein we systematically analyzed the under- and over-estimation bias of existing depth-resolved methods when applied to real biological tissues, and then proposed a new algorithm that remedies these issues and accommodates general OCT data that contain incomplete decay and noise floor, thereby affording consistent estimation accuracy for practical biological samples of different scattering properties. Compared with other algorithms, our method demonstrates remarkably improved estimation accuracy and numerical robustness, as validated via numerical simulations and on experimental OCT data obtained from both silicone-TiO2 phantoms and human ventral tongue leukoplakia samples.
Collapse
Affiliation(s)
- Kaiyan Li
- School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
- Equal contribution
| | - Wenxuan Liang
- Depart of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205, USA
- Currently with the Department of Biomedical Engineering, Columbia University, New York, New York 10027, USA
- Equal contribution
| | - Zihan Yang
- Institute of Modern Optics, Nankai University, Tianjin 300350, China
| | - Yanmei Liang
- Institute of Modern Optics, Nankai University, Tianjin 300350, China
| | - Suiren Wan
- School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| |
Collapse
|
9
|
Amaral MM, Zezell DM, Monte AFG, de Cara ACB, Araújo JCR, Antunes A, Freitas AZ. General model for depth-resolved estimation of the optical attenuation coefficients in optical coherence tomography. JOURNAL OF BIOPHOTONICS 2019; 12:e201800402. [PMID: 31012263 DOI: 10.1002/jbio.201800402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 05/22/2023]
Abstract
We present the proof of concept of a general model that uses the tissue sample transmittance as input to estimate the depth-resolved attenuation coefficient of tissue samples using optical coherence tomography (OCT). This method allows us to obtain an image of tissue optical properties instead of intensity contrast, guiding diagnosis and tissues differentiation, extending its application from thick to thin samples. The performance of our method was simulated and tested with the assistance of a home built single-layered and multilayered phantoms (~100 μm each layer) with known attenuation coefficient on the range of 0.9 to 2.32 mm-1 . It is shown that the estimated depth-resolved attenuation coefficient recovers the reference values, measured by using an integrating sphere followed by the inverse adding doubling processing technique. That was corroborated for all situations when the correct transmittance value is used with an average difference of 7%. Finally, we applied the proposed method to estimate the depth-resolved attenuation coefficient for a thin biological sample, demonstrating the ability of our method on real OCT images.
Collapse
Affiliation(s)
- Marcello M Amaral
- Instituto Cientifico e Tecnologico, Universidade Brasil, São Paulo, Brazil
- Universidade de Sao Paulo USP - IPEN - CNEN/SP, Instituto de Pesquisas Energeticas e Nucleares, São Paulo, Brazil
| | - Denise M Zezell
- Universidade de Sao Paulo USP - IPEN - CNEN/SP, Instituto de Pesquisas Energeticas e Nucleares, São Paulo, Brazil
| | - Adamo F G Monte
- Instituto de Fisica, Universidade Federal de Uberlandia, Uberlândia, Brazil
| | - Ana C B de Cara
- Universidade de Sao Paulo USP - IPEN - CNEN/SP, Instituto de Pesquisas Energeticas e Nucleares, São Paulo, Brazil
| | - Jeann C R Araújo
- Instituto de Fisica, Universidade Federal de Uberlandia, Uberlândia, Brazil
| | - Andrea Antunes
- Instituto de Fisica, Universidade Federal de Uberlandia, Uberlândia, Brazil
| | - Anderson Z Freitas
- Universidade de Sao Paulo USP - IPEN - CNEN/SP, Instituto de Pesquisas Energeticas e Nucleares, São Paulo, Brazil
| |
Collapse
|
10
|
Feroldi F, Willemse J, Davidoiu V, Gräfe MGO, van Iperen DJ, Goorsenberg AWM, Annema JT, Daniels JMA, Bonta PI, de Boer JF. In vivo multifunctional optical coherence tomography at the periphery of the lungs. BIOMEDICAL OPTICS EXPRESS 2019; 10:3070-3091. [PMID: 31259075 PMCID: PMC6583343 DOI: 10.1364/boe.10.003070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 05/04/2023]
Abstract
Remodeling of tissue, such as airway smooth muscle (ASM) and extracellular matrix, is considered a key feature of airways disease. No clinically accepted diagnostic method is currently available to assess airway remodeling or the effect of treatment modalities such as bronchial thermoplasty in asthma, other than invasive airway biopsies. Optical coherence tomography (OCT) generates cross-sectional, near-histological images of airway segments and enables identification and quantification of airway wall layers based on light scattering properties only. In this study, we used a custom motorized OCT probe that combines standard and polarization sensitive OCT (PS-OCT) to visualize birefringent tissue in vivo in the airway wall of a patient with severe asthma in a minimally invasive manner. We used optic axis uniformity (OAxU) to highlight the presence of uniformly arranged fiber-like tissue, helping visualizing the abundance of ASM and connective tissue structures. Attenuation coefficient images of the airways are presented for the first time, showing superior architectural contrast compared to standard OCT images. A novel segmentation algorithm was developed to detect the surface of the endoscope sheath and the surface of the tissue. PS-OCT is an innovative imaging technique that holds promise to assess airway remodeling including ASM and connective tissue in a minimally invasive, real-time manner.
Collapse
Affiliation(s)
- Fabio Feroldi
- LaserLaB Amsterdam and Department of Physics and Astronomy, VU University Amsterdam, de Boelelaan 1081, 1081HV, Amsterdam, the Netherlands
| | - Joy Willemse
- LaserLaB Amsterdam and Department of Physics and Astronomy, VU University Amsterdam, de Boelelaan 1081, 1081HV, Amsterdam, the Netherlands
- These authors contributed equally
| | - Valentina Davidoiu
- LaserLaB Amsterdam and Department of Physics and Astronomy, VU University Amsterdam, de Boelelaan 1081, 1081HV, Amsterdam, the Netherlands
- These authors contributed equally
| | - Maximilian G. O. Gräfe
- LaserLaB Amsterdam and Department of Physics and Astronomy, VU University Amsterdam, de Boelelaan 1081, 1081HV, Amsterdam, the Netherlands
| | - Dirck J. van Iperen
- LaserLaB Amsterdam and Department of Physics and Astronomy, VU University Amsterdam, de Boelelaan 1081, 1081HV, Amsterdam, the Netherlands
| | - Annika W. M. Goorsenberg
- Amsterdam University Medical Center, Department of Pulmonology, University of Amsterdam, Amsterdam, the Netherlands
| | - Jouke T. Annema
- Amsterdam University Medical Center, Department of Pulmonology, University of Amsterdam, Amsterdam, the Netherlands
| | - Johannes M. A. Daniels
- Amsterdam University Medical Center, Department of Pulmonology, VUmc Location, Amsterdam, the Netherlands
| | - Peter I. Bonta
- Amsterdam University Medical Center, Department of Pulmonology, University of Amsterdam, Amsterdam, the Netherlands
| | - Johannes F. de Boer
- LaserLaB Amsterdam and Department of Physics and Astronomy, VU University Amsterdam, de Boelelaan 1081, 1081HV, Amsterdam, the Netherlands
| |
Collapse
|