3,107 results match your criteria Biomed Opt Express[Journal]


Automated detection of shadow artifacts in optical coherence tomography angiography.

Biomed Opt Express 2019 Mar 28;10(3):1514-1531. Epub 2019 Feb 28.

Casey Eye Institute, Oregon Health & Science University, Portland, OR, 97239, USA.

Frequently, when imaging retinal vasculature with optical coherence tomography angiography (OCTA) in diseased eyes, there are unavoidable obstacles to the propagation of light such as vitreous floaters or the pupil boundary. These obstacles can block the optical coherence tomography (OCT) beam and impede the visualization of the underlying retinal microcirculation. Detecting these shadow artifacts is especially important in the quantification of metrics that assess retinal disease progression because they might masquerade as regional perfusion loss. Read More

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https://www.osapublishing.org/abstract.cfm?URI=boe-10-3-1514
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http://dx.doi.org/10.1364/BOE.10.001514DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420267PMC
March 2019
2 Reads

Analysis of spatial resolution in phase-sensitive compression optical coherence elastography.

Biomed Opt Express 2019 Mar 28;10(3):1496-1513. Epub 2019 Feb 28.

BRITElab, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia and Centre for Medical Research, The University of Western Australia, Crawley, Western Australia, 6009, Australia.

Optical coherence elastography (OCE) is emerging as a method to image the mechanical properties of tissue on the microscale. However, the spatial resolution, a main advantage of OCE, has not been investigated and is not trivial to evaluate. To address this, we present a framework to analyze resolution in phase-sensitive compression OCE that incorporates the three main determinants of resolution: mechanical deformation of the sample, detection of this deformation using optical coherence tomography (OCT), and signal processing to estimate local axial strain. Read More

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http://dx.doi.org/10.1364/BOE.10.001496DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420276PMC

Dynamic optical coherence tomography imaging of the lacrimal passage with an extrinsic contrast agent.

Biomed Opt Express 2019 Mar 28;10(3):1482-1495. Epub 2019 Feb 28.

Systems Engineering Inc., 2-19-24 Honkomagome, Bunkyo-ku, Tokyo 113-0021, Japan.

Recently, trans-conjunctiva optical coherence tomography (OCT) imaging of the lacrimal passage was demonstrated using a turbid commercial eye drop as an extrinsic contrast agent. However, static OCT images are not sufficient to unambiguously delineate the lumen boundary to render 3D lumen images of the lacrimal passage by segmentation. The turbid eye drop is expected to include small particles that flow and undergo Brownian motion and can be used as an extrinsic contrast agent for dynamic OCT. Read More

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http://dx.doi.org/10.1364/BOE.10.001482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420300PMC

Single etalon design for two-stage cross-axis VIPA spectroscopy.

Biomed Opt Express 2019 Mar 28;10(3):1475-1481. Epub 2019 Feb 28.

Fischell Department of Bioengineering, University of Maryland, 8278 Paint Branch Drive, College Park, MD 20742, USA.

Two-stage cross axis VIPA spectrometers have been widely used in Brillouin microscopy since they provide single shot spectral measurements at high throughput and extinction. However, this spectrometer configuration presents challenges such as size, cost and alignment difficulties between the two cascaded etalons. Here, we present a cross-axis VIPA spectrometer that implements a single etalon, using a light recirculation architecture to achieve the multistage configuration. Read More

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http://dx.doi.org/10.1364/BOE.10.001475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420281PMC

Brillouin-Raman mapping of natural fibers with spectral moment analysis.

Biomed Opt Express 2019 Mar 28;10(3):1469-1474. Epub 2019 Feb 28.

School of Physics and Astronomy, University of Exeter, Stocker Road, EX4 4QL Exeter, United Kingdom.

Brillouin spectroscopy has emerged as a novel analytical tool for biophotonic research and applications. It operates on a microscopic scale and in the GHz spectral range, providing a new spatial and frequency window for the analysis of the materials elasticity. Here we investigate spectral moments calculation as a means of analysing Brillouin and Raman spectra, providing rapid access to peak intensity and frequency shift, with robust application to fast scanning measurements. Read More

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http://dx.doi.org/10.1364/BOE.10.001469DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420284PMC

Computational simulations of the penetration of 0.30 THz radiation into the human ear.

Biomed Opt Express 2019 Mar 28;10(3):1462-1468. Epub 2019 Feb 28.

Swinburne University of Technology Melbourne, Australia.

There is an increasing interest in industrial and security applications and the establishment of wireless communication operating at frequencies of up to 0.30 THz. Soft tissue has a high coefficient of absorption at 0. Read More

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http://dx.doi.org/10.1364/BOE.10.001462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420278PMC

Bleaching effects and fluorescence lifetime imaging ophthalmoscopy.

Biomed Opt Express 2019 Mar 28;10(3):1446-1461. Epub 2019 Feb 28.

Institute of Biomedical Engineering and Informatics, Technische Universität Ilmenau, POB 100565, 98694 Ilmenau, Germany.

This study investigates the influence of photopigment bleaching on autofluorescence lifetimes in the fundus in 21 young healthy volunteers. Three measurements of 30° retinal fields in two spectral channels (SSC: 498-560 nm, LSC: 560-720 nm) were obtained for each volunteer using fluorescence lifetime imaging ophthalmoscopy (FLIO). After dark-adaptation by wearing a custom-made lightproof mask for 30 minutes, the first FLIO-measurement was recorded (dark-adapted state). Read More

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http://dx.doi.org/10.1364/BOE.10.001446DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420301PMC

High-resolution endomicroscopy with a spectrally encoded miniature objective.

Biomed Opt Express 2019 Mar 25;10(3):1432-1445. Epub 2019 Feb 25.

Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX 77005, USA.

Fiber bundle endomicroscopy techniques have been used for numerous minimally invasive imaging applications. However, these techniques may provide limited spatial sampling due to the limited number of imaging cores inside the fiber bundle. Here, we present a custom-fabricated miniature objective that can be coupled to a fiber bundle and can overcome the fiber bundle's sampling threshold by utilizing the spectral encoding concept. Read More

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http://dx.doi.org/10.1364/BOE.10.001432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420270PMC
March 2019
1 Read

Imaging mechanical properties of sub-micron ECM in live zebrafish using Brillouin microscopy.

Biomed Opt Express 2019 Mar 25;10(3):1420-1431. Epub 2019 Feb 25.

Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

In this work, we quantify the mechanical properties of the extra-cellular matrix (ECM) in live zebrafish using Brillouin microscopy. Optimization of the imaging conditions and parameters, combined with careful spectral analysis, allows us to resolve the thin ECM and distinguish its Brillouin frequency shift, a proxy for mechanical properties, from the surrounding tissue. High-resolution mechanical mapping further enables the direct measurement of the thickness of the ECM label-free and . Read More

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http://dx.doi.org/10.1364/BOE.10.001420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420298PMC

Cylindrical illumination with angular coupling for whole-prostate photoacoustic tomography.

Biomed Opt Express 2019 Mar 22;10(3):1405-1419. Epub 2019 Feb 22.

Department of Electrical and Computer Engineering, Boston University, 8 St. Mary's Street, Boston, MA 02215, USA.

Current diagnosis of prostate cancer relies on histological analysis of tissue samples acquired by biopsy, which could benefit from real-time identification of suspicious lesions. Photoacoustic tomography has the potential to provide real-time targets for prostate biopsy guidance with chemical selectivity, but light delivered from the rectal cavity has been unable to penetrate to the anterior prostate. To overcome this barrier, a urethral device with cylindrical illumination is developed for whole-prostate imaging, and its performance as a function of angular light coupling is evaluated with a prostate-mimicking phantom. Read More

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http://dx.doi.org/10.1364/BOE.10.001405DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420282PMC
March 2019
1 Read

Development of multi-directional functional near-infrared spectroscopy system for human neuroimaging studies.

Biomed Opt Express 2019 Mar 22;10(3):1393-1404. Epub 2019 Feb 22.

ATR Neural Information Analysis Laboratories, Kyoto 619-0288, Japan.

Multi-directional measurement using multi-directional light sources and multi-directional photodetectors drastically increases the amount of observation data without increasing the number of optical probes. In this study, we developed a novel multi-directional functional near-infrared spectroscopy (fNIRS) system for human neuroimaging studies. We tested our system by measuring the cortical hemodynamic changes of a single subject during a motor task and compared them with the same subject's functional magnetic resonance imaging (fMRI) data. Read More

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http://dx.doi.org/10.1364/BOE.10.001393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420293PMC
March 2019
1 Read

Power spectrum of spontaneous cerebral homodynamic oscillation shows a distinct pattern in autism spectrum disorder.

Biomed Opt Express 2019 Mar 22;10(3):1383-1392. Epub 2019 Feb 22.

Guangdong Provincial Key Laboratory of Optical Information Materials and Technology, National Center for International Research on Green Optoelectronics, MOE International Laboratory for Optical Information Technologies, South China Academy of Advanced Optoelectronics, South China Normal University, Guangzhou 510006, China.

Spontaneous hemodynamic fluctuations recorded by functional near-infrared spectroscopy (fNIRS) from bilateral temporal lobes were analyzed on 25 children with autism spectrum disorder (ASD) and 22 typically developing (TD) children. By frequency domain analysis, a new characteristic was uncovered that the power spectrum of low frequency cerebral hemodynamic oscillation showed a distinct pattern in ASD. More specifically, at the frequency of 0. Read More

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http://dx.doi.org/10.1364/BOE.10.001383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420268PMC
March 2019
1 Read
3.648 Impact Factor

Computationally effective 2D and 3D fast phase unwrapping algorithms and their applications to Doppler optical coherence tomography.

Biomed Opt Express 2019 Mar 21;10(3):1365-1382. Epub 2019 Feb 21.

Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland.

We propose a simplification for a robust and easy to implement fast phase unwrapping (FPU) algorithm that is used to solve the phase wrapping problem encountered in various fields of optical imaging and metrology. We show that the number of necessary computations using the algorithm can be reduced compared to its original version. FPU can be easily extended from two to three spatial dimensions. Read More

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http://dx.doi.org/10.1364/BOE.10.001365DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420292PMC
March 2019
1 Read

Optical fiber technology enables smart needles for epidurals: an swine study.

Biomed Opt Express 2019 Mar 21;10(3):1351-1364. Epub 2019 Feb 21.

Optoelectronics Group, Engineering Department, University of Sannio, Benevento I-82100, Italy.

Nowadays, epidural space identification is made by using subjective and manual techniques characterized by failure rates up to 7%. In this work, we propose a fiber optic sensor technology based needle guidance system, that is directly inspired by the most common technique currently used for epidurals; through real-time strain measurements, the fiber Bragg grating integrated inside the needle lumen is able to effectively perceive the typical force drop occurring when the needle enters the epidural space. An swine study demonstrates the validity of our approach, paving the way for the development of lab-in-a-needle systems. Read More

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http://dx.doi.org/10.1364/BOE.10.001351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420287PMC
March 2019
1 Read

Digital staining through the application of deep neural networks to multi-modal multi-photon microscopy.

Biomed Opt Express 2019 Mar 19;10(3):1339-1350. Epub 2019 Feb 19.

Optics Laboratory, School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland.

Deep neural networks have been used to map multi-modal, multi-photon microscopy measurements of a label-free tissue sample to its corresponding histologically stained brightfield microscope colour image. It is shown that the extra structural and functional contrasts provided by using two source modes, namely two-photon excitation microscopy and fluorescence lifetime imaging, result in a more faithful reconstruction of the target haematoxylin and eosin stained mode. This modal mapping procedure can aid histopathologists, since it provides access to unobserved imaging modalities, and translates the high-dimensional numerical data generated by multi-modal, multi-photon microscopy into traditionally accepted visual forms. Read More

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http://dx.doi.org/10.1364/BOE.10.001339DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420275PMC

Image analysis applied to Brillouin images of tissue-mimicking collagen gelatins.

Biomed Opt Express 2019 Mar 19;10(3):1329-1338. Epub 2019 Feb 19.

School of Physics and Astronomy, University of Exeter, Stocker Road, EX4 4QL Exeter, UK.

Brillouin spectroscopy is an emerging analytical tool in biomedical and biophysical sciences. It probes viscoelasticity through the propagation of thermally induced acoustic waves at gigahertz frequencies. Brillouin light scattering (BLS) measurements have traditionally been performed using multipass Fabry-Pérot interferometers, which have high contrast and resolution, however, as they are scanning spectrometers they often require long acquisition times in poorly scattering media. Read More

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http://dx.doi.org/10.1364/BOE.10.001329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420274PMC

Automated segmentation of dermal fillers in OCT images of mice using convolutional neural networks.

Biomed Opt Express 2019 Mar 19;10(3):1315-1328. Epub 2019 Feb 19.

Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria.

We present a system for automatic determination of the intradermal volume of hydrogels based on optical coherence tomography (OCT) and deep learning. Volumetric image data was acquired using a custom-built OCT prototype that employs an akinetic swept laser at ~1310 nm with a bandwidth of 87 nm, providing an axial resolution of ~6.5 μm in tissue. Read More

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http://dx.doi.org/10.1364/BOE.10.001315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420291PMC
March 2019
2 Reads

Precision analysis and optimization in phase decorrelation OCT velocimetry.

Biomed Opt Express 2019 Mar 19;10(3):1297-1314. Epub 2019 Feb 19.

LaserLaB, Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.

Quantitative flow velocimetry in Optical Coherence Tomography is used to determine both the axial and lateral flow component at the level of individual voxels. The lateral flow is determined by analyzing the statistical properties of reflected electro-magnetic fields for repeated measurements at (nearly) the same location. The precision or statistical fluctuation of the quantitative velocity estimation depends on the number of repeated measurements and the method to determine quantitative flow velocity. Read More

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http://dx.doi.org/10.1364/BOE.10.001297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420279PMC

Multi-fiber distributed thermal profiling of minimally invasive thermal ablation with scattering-level multiplexing in MgO-doped fibers.

Biomed Opt Express 2019 Mar 19;10(3):1282-1296. Epub 2019 Feb 19.

Nazarbayev University, Department of Electrical and Computer Engineering, 010000 Astana, Kazakhstan.

We propose a setup for multiplexed distributed optical fiber sensors capable of resolving temperature distribution in thermo-therapies, with a spatial resolution of 2.5 mm over multiple fibers interrogated simultaneously. The setup is based on optical backscatter reflectometry (OBR) applied to optical fibers having backscattered power significantly larger than standard fibers (36. Read More

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http://dx.doi.org/10.1364/BOE.10.001282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420269PMC

Video-rate quantitative phase analysis by a DIC microscope using a polarization camera.

Biomed Opt Express 2019 Mar 19;10(3):1273-1281. Epub 2019 Feb 19.

Department of Optical Engineering, Utsunomiya University, 7-1-2 Yoto, Utsunomiya, Tochigi, Japan.

This paper describes how to take advantage of the replacement of an intensity camera with a polarization camera in a standard differential interference contrast (DIC) microscope. Using a polarization camera enables snapshot quantitative phase analysis so that real-time imaging of living transparent tissues become possible. Using our method, we quantify the phase measurement accuracy using a phantom consisting of glass beads embedded in lacquer. Read More

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http://dx.doi.org/10.1364/BOE.10.001273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420286PMC
March 2019
3.648 Impact Factor

Rapid pathology of lumpectomy margins with open-top light-sheet (OTLS) microscopy.

Biomed Opt Express 2019 Mar 19;10(3):1257-1272. Epub 2019 Feb 19.

Department of Mechanical Engineering, University of Washington, Seattle, WA 98195, USA.

Open-top light-sheet microscopy is a technique that can potentially enable rapid inspection of large tissue surfaces and volumes. Here, we have optimized an open-top light-sheet (OTLS) microscope and image-processing workflow for the comprehensive examination of surgical margin surfaces, and have also developed a novel fluorescent analog of H&E staining that is robust for staining fresh unfixed tissues. Our tissue-staining method can be achieved within 2. Read More

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http://dx.doi.org/10.1364/BOE.10.001257DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420271PMC

Jaundice Eye Color Index (JECI): quantifying the yellowness of the sclera in jaundiced neonates with digital photography.

Biomed Opt Express 2019 Mar 14;10(3):1250-1256. Epub 2019 Feb 14.

The Neonatal Care Unit, Elizabeth Garrett Anderson Wing, University College London Hospitals Trust, UK.

The sclera is arguably a better site than the skin to measure jaundice-especially in dark-skinned patients-since it is free of skin pigment (melanin), a major confounding factor. This work aims to show how the yellowness of the sclera can be quantified by digital photography in color spaces including the native RGB and CIE XYZ. We also introduce a new color metric we call "Jaundice Eye Color Index" (JECI) which allows the yellowness of jaundiced sclerae to be predicted for a specific total serum bilirubin level in the neonatal population. Read More

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http://dx.doi.org/10.1364/BOE.10.001250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420273PMC
March 2019
6 Reads

Contrast improvement in indocyanine green fluorescence sensing in thick tissue using a time-gating method.

Authors:
Goro Nishimura

Biomed Opt Express 2019 Mar 12;10(3):1234-1249. Epub 2019 Feb 12.

Research Institute for Electronic Science, Hokkaido University, N20W10, Sapporo 001-0020, Japan.

Indocyanine green-based fluorescence imaging techniques are very powerful in clinical applications, but the imaging is restricted to the signal from the near-surface region of tissue. Here, we focus on the method to discriminate the fluorescence signal from the background using a time-domain gating technique. The contrast of the fluorescence image from a fluorescence object at more than 1 cm depth in a meat phantom could be enhanced about 4-5 times relative to the continuous wave method if the time-gate range was properly selected. Read More

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http://dx.doi.org/10.1364/BOE.10.001234DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420283PMC

Fluorescence lifetime detection with particle counting devices.

Biomed Opt Express 2019 Mar 12;10(3):1223-1233. Epub 2019 Feb 12.

Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA.

Fluorescence-based single particle counting devices have become very powerful tools for human health-related applications such as the detection of blood-borne pathogens. Instead of passing the sample fluid through a thin tube or microfluidic chip, as it is commonly practiced in flow cytometers and sorter devices, single particle counters scan the fluid volume by rotation and translation of the sample container. Hence, single particle counters are not limited by the fluid flow friction and can scan a large volume in a short timeframe while maintaining high sensitivity. Read More

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http://dx.doi.org/10.1364/BOE.10.001223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420272PMC

Optical coherence tomography-guided laser marking with tethered capsule endomicroscopy in unsedated patients.

Biomed Opt Express 2019 Mar 12;10(3):1207-1222. Epub 2019 Feb 12.

Wellman Center for Photomedicine, Harvard Medical School and Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA.

Tethered capsule endomicroscopy (TCE) is an emerging screening technology that comprehensively obtains microstructural OCT images of the gastrointestinal (GI) tract in unsedated patients. To advance clinical adoption of this imaging technique, it will be important to validate TCE images with co-localized histology, the current diagnostic gold standard. One method for co-localizing OCT images with histology is image-targeted laser marking, which has previously been implemented using a driveshaft-based, balloon OCT catheter, deployed during endoscopy. Read More

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http://dx.doi.org/10.1364/BOE.10.001207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420285PMC
March 2019
1 Read

Label-free self-referenced sensing of living cells by terahertz metamaterial-based reflection spectroscopy.

Biomed Opt Express 2019 Mar 11;10(3):1196-1206. Epub 2019 Feb 11.

Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.

Terahertz (THz) metamaterial-based reflection spectroscopy is proposed for label-free sensing of living cells by a self-referenced method. When sensing the living Madin-Darby canine kidney cell monolayer and phosphate buffered saline solution, self-referenced signals showed significant differences in peak intensity because of inherent discrepancy in the imaginary part of their complex refractive indices, as confirmed by 3D-FDTD simulations. The resonance peak intensity was unaffected by cell monolayer thickness variation, demonstrating feasibility for sensing various cells. Read More

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http://dx.doi.org/10.1364/BOE.10.001196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420280PMC

monitoring and high-resolution characterizing of the prednisolone-induced osteoporotic process on adult zebrafish by optical coherence tomography.

Biomed Opt Express 2019 Mar 11;10(3):1184-1195. Epub 2019 Feb 11.

School of Basic Medical Science, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 511436, China.

Because of its similar genetic makeup with humans, zebrafish are an available and well-established osteoporosis model for anti-osteoporosis drug development as well as the drug safety-evaluation process. However, few optical imaging methods could effectively visualize the bone of adult zebrafish due to their limited penetration depth. In this paper, high-resolution and long-term characterization of a prednisolone-induced osteoporotic zebrafish model was achieved with spectral-domain optical coherence tomography (SD-OCT). Read More

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https://www.osapublishing.org/abstract.cfm?URI=boe-10-3-1184
Publisher Site
http://dx.doi.org/10.1364/BOE.10.001184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420289PMC
March 2019
4 Reads
3.648 Impact Factor

Integrated multi-channel optical system for bacteria characterization and its potential use for monitoring of environmental bacteria.

Biomed Opt Express 2019 Mar 11;10(3):1165-1183. Epub 2019 Feb 11.

Bio-Optics Group, Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeże S. Wyspiańskiego Street, Wroclaw, Poland.

The potential use of a novel multichannel optical system towards fast and non-destructive bacteria identification and its application for environmental bacteria characterisation on the strain level is presented. It is the first attempt to use the proposed optical method to study various bacteria species (Gram-negative, Gram-positive) commonly present in the environment. The novel configuration of the optical system enables multichannel examination of bacterial colonies and provides additional functionality such as registration of two-dimensional (2D) distribution of monochromatic transmission coefficient of examined colonies, what can be used as a novel optical signature for bacteria characterization. Read More

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http://dx.doi.org/10.1364/BOE.10.001165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420290PMC

Multimodal virtual histology of rabbit vocal folds by nonlinear microscopy and nano computed tomography.

Biomed Opt Express 2019 Mar 11;10(3):1151-1164. Epub 2019 Feb 11.

Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada.

Human vocal folds (VFs) possess a unique anatomical structure and mechanical properties for human communication. However, VFs are prone to scarring as a consequence of overuse, injury, disease or surgery. Accumulation of scar tissue on VFs inhibits proper phonation and leads to partial or complete loss of voice, with significant consequences for the patient's quality of life. Read More

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http://dx.doi.org/10.1364/BOE.10.001151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420294PMC
March 2019
1 Read

3,3'-thiodipropanol as a versatile refractive index-matching mounting medium for fluorescence microscopy.

Biomed Opt Express 2019 Mar 11;10(3):1136-1150. Epub 2019 Feb 11.

Centro de Investigaciones en Óptica, Loma Del Bosque 115, León C.P. 37150, Mexico.

High resolution fluorescence microscopy requires optimization of the protocols for biological sample preparation. The optical and chemical characteristics of mounting media are among the things that could be modified to achieve optimal image formation. In our search for chemical substances that could perform as mounting media, 3,3'-thiodipropanol (TDP) emerged as a sulfide with potentially interesting characteristics. Read More

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http://dx.doi.org/10.1364/BOE.10.001136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420295PMC

Parallel deep neural networks for endoscopic OCT image segmentation.

Biomed Opt Express 2019 Mar 7;10(3):1126-1135. Epub 2019 Feb 7.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.

We report parallel-trained deep neural networks for automated endoscopic OCT image segmentation feasible even with a limited training data set. These U-Net-based deep neural networks were trained using a modified dice loss function and manual segmentations of ultrahigh-resolution cross-sectional images collected by an 800 nm OCT endoscopic system. The method was tested on guinea pig esophagus images. Read More

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http://dx.doi.org/10.1364/BOE.10.001126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420296PMC
March 2019
2 Reads

Micromachined phase-shifted array-type Mirau interferometer for swept-source OCT imaging: design, microfabrication and experimental validation.

Biomed Opt Express 2019 Mar 7;10(3):1111-1125. Epub 2019 Feb 7.

Fraunhofer Institute for Electronic Nanosystems, Technologie Campus 3, 09126 Chemnitz, Germany.

OCT instruments permit fast and non-invasive 3D optical biopsies of biological tissues. However, they are bulky and expensive, making them only affordable at the hospital and thus, not sufficiently used as an early diagnostic tool. Significant reduction of system cost and size is achieved by implementation of MOEMS technologies. Read More

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http://dx.doi.org/10.1364/BOE.10.001111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420266PMC

One-step deconvolution for multi-angle TIRF microscopy with enhanced resolution.

Biomed Opt Express 2019 Mar 5;10(3):1097-1110. Epub 2019 Feb 5.

Key Laboratory of Image Processing and Intelligent Control of Ministry of Education of China, School of Automation, Huazhong University of Science and Technology, Wuhan 430074, China.

Total internal reflection fluorescence microscopy (TIRF microscopy) uses a rapid decay of evanescent waves to excite fluorophores within several hundred nanometers () beneath the plasma membrane, which can effectively suppress excitation of fluorescence signals in the deep layers. From image stacks obtained with a plurality of different incident angles, a three-dimensional spatial structure of the observed sample can be reconstructed by a Multi-Angle-TIRF (MA-TIRF) algorithm that provides an axial resolution of ~50 . Taking into account the point spread function (PSF) of the TIRF microscopes, we further increase its lateral resolution by introducing a fast deconvolution algorithm into the reconstruction of MA-TIRF data (DMA-TIRF), which is approached in just one step of minimizing the reconstruction function. Read More

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http://dx.doi.org/10.1364/BOE.10.001097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420288PMC

Active photonic sensing for super-resolved reading performance in simulated prosthetic vision.

Biomed Opt Express 2019 Mar 4;10(3):1081-1096. Epub 2019 Feb 4.

Faculty of Life Sciences, School of Optometry and Vision Science, Bar Ilan University, Ramat Gan, Israel.

In this work, we study the enhancement of simulated prosthetic reading performance through "active photonic sensing" in normally sighted subjects. Three sensing paradigms were implemented: active sensing, in which the subject actively scanned the presented words using the computer mouse, with an option to control text size; passive scanning produced by software-initiated horizontal movements of words; and no scanning. Our findings reveal a 30% increase in word recognition rate with active scanning as compared to no or passive scanning and up to 14-fold increase with zooming. Read More

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http://dx.doi.org/10.1364/BOE.10.001081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420299PMC

Layer boundary evolution method for macular OCT layer segmentation.

Biomed Opt Express 2019 Mar 4;10(3):1064-1080. Epub 2019 Feb 4.

Dept. of Electrical and Computer Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA.

Optical coherence tomography (OCT) is used to produce high resolution depth images of the retina and is now the standard of care for in-vivo ophthalmological assessment. It is also increasingly being used for evaluation of neurological disorders such as multiple sclerosis (MS). Automatic segmentation methods identify the retinal layers of the macular cube providing consistent results without intra- and inter-rater variation and is faster than manual segmentation. Read More

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http://dx.doi.org/10.1364/BOE.10.001064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420297PMC
March 2019
2 Reads

High-throughput, high-resolution deep learning microscopy based on registration-free generative adversarial network.

Biomed Opt Express 2019 Mar 4;10(3):1044-1063. Epub 2019 Feb 4.

School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, 430074, China.

We combine a generative adversarial network (GAN) with light microscopy to achieve deep learning super-resolution under a large field of view (FOV). By appropriately adopting prior microscopy data in an adversarial training, the neural network can recover a high-resolution, accurate image of new specimen from its single low-resolution measurement. Its capacity has been broadly demonstrated via imaging various types of samples, such as USAF resolution target, human pathological slides, fluorescence-labelled fibroblast cells, and deep tissues in transgenic mouse brain, by both wide-field and light-sheet microscopes. Read More

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http://dx.doi.org/10.1364/BOE.10.001044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420277PMC
March 2019
3.648 Impact Factor

Scanning optical coherence tomography probe for in vivo imaging and displacement measurements in the cochlea.

Biomed Opt Express 2019 Feb 1;10(2):1032-1043. Epub 2019 Feb 1.

Department of Biomedical Engineering, Columbia University, 1210 Amsterdam Ave, New York, NY 10027, USA.

We developed a spectral domain optical coherence tomography (SDOCT) fiber optic probe for imaging and sub-nanometer displacement measurements inside the mammalian cochlea. The probe, 140 μm in diameter, can scan laterally up to 400 μm by means of a piezoelectric bender. Two different sampling rates are used, 10 kHz for high-resolution B-scan imaging, and 100 kHz for displacement measurements in order to span the auditory frequency range of gerbil (~50 kHz). Read More

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http://dx.doi.org/10.1364/BOE.10.001032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377895PMC
February 2019
2 Reads

Quality improvement of OCT angiograms with elliptical directional filtering.

Biomed Opt Express 2019 Feb 1;10(2):1013-1031. Epub 2019 Feb 1.

Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland.

We present a method of OCT angiography (OCTA) data filtering for noise suppression and improved visualization of the retinal vascular networks in projection images. In our approach, we use a set of filters applied in three orthogonal axes in the three-dimensional (3-D) data sets. Minimization of artifacts generated in B-scan-wise data processing is accomplished by filtering the cross-sections along the slow scanning axis. Read More

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http://dx.doi.org/10.1364/BOE.10.001013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377873PMC
February 2019
1 Read

Choroidal vasculature imaging with laser Doppler holography.

Biomed Opt Express 2019 Feb 31;10(2):995-1012. Epub 2019 Jan 31.

Institut Langevin, Centre National de la Recherche Scientifique (CNRS), Paris Sciences & Lettres (PSL University), École Supérieure de Physique et de Chimie Industrielles (ESPCI Paris), 1 rue Jussieu, 75005 Paris, France.

The choroid is a highly vascularized tissue supplying the retinal pigment epithelium and photoreceptors. Its implication in retinal diseases is gaining increasing interest. However, investigating the anatomy and flow of the choroid remains challenging. Read More

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http://dx.doi.org/10.1364/BOE.10.000995DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377881PMC
February 2019
5 Reads

Fast esophageal layer segmentation in OCT images of guinea pigs based on sparse Bayesian classification and graph search.

Biomed Opt Express 2019 Feb 30;10(2):978-994. Epub 2019 Jan 30.

School of Electronic and Information Engineering, Soochow University, Suzhou 215006, China.

Endoscopic optical coherence tomography (OCT) devices are capable of generating high-resolution images of esophageal structures at high speed. To make the obtained data easy to interpret and reveal the clinical significance, an automatic segmentation algorithm is needed. This work proposes a fast algorithm combining sparse Bayesian learning and graph search (termed as SBGS) to automatically identify six layer boundaries on esophageal OCT images. Read More

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http://dx.doi.org/10.1364/BOE.10.000978DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377884PMC
February 2019
5 Reads
3.648 Impact Factor

Diffuse reflectance spectroscopy-enhanced drill for bone boundary detection.

Biomed Opt Express 2019 Feb 30;10(2):961-977. Epub 2019 Jan 30.

Tyndall National Institute, Lee Maltings Complex, Dyke parade, Cork, Ireland, T12R5CP.

Intramedullary nailing is a routine orthopedic procedure used for treating fractures of femoral or tibial shafts. A critical part of this procedure involves the drilling of pilot holes in both ends of the bone for the placement of the screws that will secure the IM rod to sections of the fractured bone. This step introduces a risk of soft tissue damage because the drill bit, if not stopped in time, can transverse the bone-tissue boundary into the overlying muscle, causing unnecessary injury and prolonging healing time due to periosteum damage. Read More

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http://dx.doi.org/10.1364/BOE.10.000961DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377869PMC
February 2019
2 Reads

Physiological and structural characterization of human skin in vivo using combined photothermal radiometry and diffuse reflectance spectroscopy.

Biomed Opt Express 2019 Feb 29;10(2):944-960. Epub 2019 Jan 29.

Jožef Stefan Institute, Department of Complex Matter, Jamova 39, Ljubljana, 1000, Slovenia.

In this proof-of-concept study we combine two optical techniques to enable assessment of structure and composition of human skin in vivo: Pulsed photothermal radiometry (PPTR), which involves measurements of transient dynamics in mid-infrared emission from sample surface after exposure to a light pulse, and diffuse reflectance spectroscopy (DRS) in visible part of the spectrum. The analysis involves simultaneous fitting of measured PPTR signals and DRS with corresponding predictions of a Monte Carlo model of light-tissue interaction. By using a four-layer optical model of skin we obtain a good match between the experimental and model data when scattering properties of the epidermis and dermis are also optimized on an individual basis. Read More

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http://dx.doi.org/10.1364/BOE.10.000944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377901PMC
February 2019
2 Reads

Multi-wavelength photo-acoustic microscopy in the frequency domain for simultaneous excitation and detection of dyes.

Biomed Opt Express 2019 Feb 29;10(2):932-943. Epub 2019 Jan 29.

Univ. Grenoble Alpes, CNRS, LiPhy, F-38000 Grenoble, France.

An optical-resolution photoacoustic microscope with modulated CW laser diodes allowing multi-channel imaging is presented that can be used for both imaging biological tissues and for targeted photo-dynamic therapy (PDT) varying the optical power and exposure time. The effects of this therapy are immediately monitored in order to optimize the time of irradiation. After the description of the experimental setup, and applications are presented on a synthetic sample and on the mouse ear using hemoglobin as endogenous and methylene blue as exogenous dye for imaging and PDT, respectively. Read More

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http://dx.doi.org/10.1364/BOE.10.000932DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377889PMC
February 2019
1 Read

Drusen diagnosis comparison between hyper-spectral and color retinal images.

Biomed Opt Express 2019 Feb 28;10(2):914-931. Epub 2019 Jan 28.

Department of Ophthalmology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.

Age-related macular degeneration (AMD) is a degenerative aging disorder, which can lead to irreversible vision loss in older individuals. The emergence of clinical applications of retinal hyper-spectral imaging provides a unique opportunity to capture important spectral signatures, with the potential to enhance the molecular diagnosis of retinal diseases. In this study, we use a machine learning classification approach to explore whether hyper-spectral images offer an improved outcome compared to standard RGB images. Read More

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http://dx.doi.org/10.1364/BOE.10.000914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377880PMC
February 2019
1 Read

Automatic glaucoma classification using color fundus images based on convolutional neural networks and transfer learning.

Biomed Opt Express 2019 Feb 25;10(2):892-913. Epub 2019 Jan 25.

Biomedical Image Technologies Laboratory (BIT), ETSI Telecomunicación, Universidad Politécnica de Madrid, 28040 Madrid, Spain.

Glaucoma detection in color fundus images is a challenging task that requires expertise and years of practice. In this study we exploited the application of different Convolutional Neural Networks (CNN) schemes to show the influence in the performance of relevant factors like the data set size, the architecture and the use of transfer learning vs newly defined architectures. We also compared the performance of the CNN based system with respect to human evaluators and explored the influence of the integration of images and data collected from the clinical history of the patients. Read More

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http://dx.doi.org/10.1364/BOE.10.000892DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377910PMC
February 2019
1 Read

Smartphone-based multispectral imaging and machine-learning based analysis for discrimination between seborrheic dermatitis and psoriasis on the scalp.

Biomed Opt Express 2019 Feb 24;10(2):879-891. Epub 2019 Jan 24.

Department of Information and Communication Engineering, Daegu Gyeongbuk Institute of Science & Technology, Daegu, 42988, South Korea.

For appropriate treatment, accurate discrimination between seborrheic dermatitis and psoriasis in a timely manner is crucial to avoid complications. However, when they occur on the scalp, differential diagnosis can be challenging using conventional dermascopes. Thus, we employed smartphone-based multispectral imaging and analysis to discriminate between them with high accuracy. Read More

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http://dx.doi.org/10.1364/BOE.10.000879DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377911PMC
February 2019
2 Reads

Monte Carlo simulation of light scattering in tissue for the design of skin-like optical devices.

Biomed Opt Express 2019 Feb 24;10(2):868-878. Epub 2019 Jan 24.

AML, Department of Engineering Mechanics, Tsinghua University, Beijing, 100084, China.

Measurement techniques based on optics, with the characteristics of noninvasive or non-destructive detection and high accuracy, offer excellent properties for application in various scenarios. Skin-like optical devices capable of deforming with human skin play major roles in future biomedical applications such as clinical diagnostics or biological healthcare. Unlike traditional rigid devices, the skin-like optical device is conformal to the skin because of the flexibility and stretchability. Read More

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http://dx.doi.org/10.1364/BOE.10.000868DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377905PMC
February 2019
3 Reads

Tissue effects of intra-tissue refractive index shaping (IRIS): insights from two-photon autofluorescence and second harmonic generation microscopy.

Biomed Opt Express 2019 Feb 24;10(2):855-867. Epub 2019 Jan 24.

The Institute of Optics, University of Rochester, Rochester, NY 14627, USA.

Intra-tissue refractive index shaping (IRIS) is a novel, non-ablative form of vision correction by which femtosecond laser pulses are tightly focused into ocular tissues to induce localized refractive index (RI) change via nonlinear absorption. Here, we examined the effects of Blue-IRIS on corneal microstructure to gain insights into underlying mechanisms. Three-layer grating patterns were inscribed with IRIS ~180 µm below the epithelial surface of rabbit globes using a 400 nm femtosecond laser. Read More

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http://dx.doi.org/10.1364/BOE.10.000855DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377903PMC
February 2019
1 Read

Chromatin laser imaging reveals abnormal nuclear changes for early cancer detection.

Biomed Opt Express 2019 Feb 24;10(2):838-854. Epub 2019 Jan 24.

Department of Biomedical Engineering, University of Michigan, 1101 Beal Ave., Ann Arbor, MI 48109, USA.

We developed and applied rapid scanning laser-emission microscopy (LEM) to detect abnormal changes in cell nuclei for early diagnosis of cancer and cancer precursors. Regulation of chromatins is essential for genetic development and normal cell functions, while abnormal nuclear changes may lead to many diseases, in particular, cancer. The capability to detect abnormal changes in "apparently normal" tissues at a stage earlier than tumor development is critical for cancer prevention. Read More

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http://dx.doi.org/10.1364/BOE.10.000838DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377874PMC
February 2019
2 Reads

Is it possible to measure hemodynamic changes in the prefrontal cortex through the frontal sinus using continuous wave DOT systems?

Biomed Opt Express 2019 Feb 24;10(2):817-837. Epub 2019 Jan 24.

Department of Basic Medical Science (Physiology), Faculty of Health Sciences, Medicine Section, Universidad de La Laguna 38071, Spain.

The present work shows the capability of near infrared (NIR) light to reach the cerebral cortex through the frontal sinus using continuous-wave techniques (CW-DOT) in a dual study. On the one hand, changes in time during the tracking of a blood dye in the prefrontal cortex were monitored. On the other hand, hemodynamic changes induced by low frequency of transcranial magnetic stimulation applied on the prefrontal cortex were recorded. Read More

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http://dx.doi.org/10.1364/BOE.10.000817DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377888PMC
February 2019