1. Articles from bioRxiv.org

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    1. Differentiation of semi-transparent tissue phantom inclusions using optical coherence tomography towards label-free neurography and lymphography

      Differentiation of semi-transparent tissue phantom inclusions using optical coherence tomography towards label-free neurography and lymphography

      Significance: Lymphatic and peripheral nervous system imaging is of prime importance for monitoring various important pathologic processes including cancer development, metastasis, and response to therapy. Aim: Optical coherence tomography (OCT) is a promising approach for this imaging task but is challenged by the near-transparent nature of these structures. Our aim is to detect and differentiate semi-transparent materials using OCT texture analysis, towards label-free neurography and lymphography. Approach: We have recently demonstrated a novel OCT texture analysis-based approach that used speckle statistics to image lymphatics and nerves in-vivo that does not rely on negative contrast. However, these two near-transparent structures could ...

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    2. Multiple forward scattering reduces the measured scattering coefficient of whole blood in visible-light optical coherence tomography

      Multiple forward scattering reduces the measured scattering coefficient of whole blood in visible-light optical coherence tomography

      Preview PDF Abstract Optical properties of blood encode oxygen-dependent information. Noninvasive optical detection of these properties is increasingly desirable to extract biomarkers for tissue health. Recently, visible-light optical coherence tomography (vis-OCT) demonstrated retinal oxygen saturation (sO2) measurements using the depth-resolved spectrum of blood. Such measurements rely on differences between the absorption and scattering coefficients of oxygenated and deoxygenated blood.

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    3. Using the Dynamic Forward Scattering Signal for Optical Coherence Tomography based Blood Flow Quantification

      Using the Dynamic Forward Scattering Signal for Optical Coherence Tomography based Blood Flow Quantification

      To our knowledge, all existing optical coherence tomography approaches for quantifying blood flow, whether Doppler-based or decorrelation-based, analyze the light that is back-scattered by moving red blood cells (RBCs). This work investigates the potential advantages of basing these measurements of the light that is forward-scattered by RBCs, i.e., by looking at the signals back-scattered from below the vessel. We show experimentally that this results in a flowmetry measure that is insensitive to vessel orientation for vessels that are approximately orthogonal to the imaging beam. We further provide proof-of-principle demonstrations that DFS can be used to measure flow in human ...

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    4. Longitudinal Morphological and Functional Characterization of Human Heart Organoids Using Optical Coherence Tomography

      Longitudinal Morphological and Functional Characterization of Human Heart Organoids Using Optical Coherence Tomography

      Organoids play an increasingly important role as in vitro models for studying organ development, disease mechanisms, and drug discovery. Organoids are self-organizing, organ-like three-dimensional (3D) cell cultures developing organ-specific cell types and functions. Recently, three groups independently developed self-assembling human heart organoids (hHOs) from human pluripotent stem cells (hPSCs). In this study, we utilized a customized spectral-domain optical coherence tomography (SD-OCT) system to characterize the growth of hHOs. Development of chamber structures and beating patterns of the hHOs were observed via OCT and calcium imaging. We demonstrated the capability of OCT to produce 3D images in a fast, label-free, and ...

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    5. Interferometric imaging of thermal expansion for temperature control in retinal laser therapy

      Interferometric imaging of thermal expansion for temperature control in retinal laser therapy

      Precise control of the temperature rise is a prerequisite for proper photothermal therapy. In retinal laser therapy, the heat deposition is primarily governed by the melanin concentration, which can significantly vary across the retina and from patient to patient. In this work, we present a method for determining the optical and thermal properties of layered materials, directly applicable to the retina, using low-energy laser heating and phase-resolved optical coherence tomography (pOCT). The method is demonstrated on a polymer-based tissue phantom heated with a laser pulse focused onto an absorbing layer buried below the phantom's surface. Using a line-scan spectral-domain ...

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    6. Capillary stall quantification from optical coherence tomography angiogram maximum intensity projections

      Capillary stall quantification from optical coherence tomography angiogram maximum intensity projections

      Optical coherence tomography (OCT) is applicable to the study of cerebral microvasculature in vivo. Optimised acquisition schemes enable the generation of three-dimensional OCT angiograms, i.e., volumetric images of red blood cell flux in capillary networks, currently at a repetition rate of up to 1/10 seconds. This makes testable a new class of hypotheses that strive to bridge the gap between microscopic phenomena occurring at the spatial scale of neurons, and less invasive but crude techniques to measure macroscopic blood flow dynamics. Here we present a method for quantifying the occurrence of transient capillary stalls in OCT angiograms, i ...

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    7. Quantification of volumetric morphometry and optical property in the cortex of human cerebellum at micrometer resolution

      Quantification of volumetric morphometry and optical property in the cortex of human cerebellum at micrometer resolution

      The surface of the human cerebellar cortex is much more tightly folded than the cerebral cortex. Volumetric analysis of cerebellar morphometry in magnetic resonance imaging studies suffers from insufficient resolution, and therefore has had limited impact on disease assessment. Automatic serial polarization-sensitive optical coherence tomography (as-PSOCT) is an emerging technique that offers the advantages of microscopic resolution and volumetric reconstruction of large-scale samples. In this study, we reconstructed multiple cubic centimeters of ex vivo human cerebellum tissue using as-PSOCT. The morphometric and optical properties of the cerebellar cortex across five subjects were quantified. While the molecular and granular layers exhibited ...

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    8. Deep-learning based retinal fluid segmentation in optical coherence tomography images using a cascade of ENets

      Deep-learning based retinal fluid segmentation in optical coherence tomography images using a cascade of ENets

      Optical coherence tomography (OCT) is a non-invasive, painless and reproducible examination which allows ophthalmologists to visualize retinal layers. This imaging modality is useful to detect diseases such as diabetic macular edema (DME) or age related macular degeneration (AMD), which are associated with fluid accumulations. In this paper, a cascade of deep convolutional neural networks is proposed using ENets for the segmentation of fluid accumulations in OCT B-Scans. After denoising the B-Scans, a first ENet extracts the region of interest (ROI) between the inner limiting membrane (ILM) and the Bruch's membrane (BM), whereas the second ENet segments the fluid in ...

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    9. Refractive-index matching enhanced polarization-sensitive optical coherence tomography quantification in human brain tissue

      Refractive-index matching enhanced polarization-sensitive optical coherence tomography quantification in human brain tissue

      The importance of polarization-sensitive optical coherence tomography (PS-OCT) has been increasingly recognized in human brain imaging. Despite the recent progress of PS-OCT in revealing white matter architecture and orientation, quantification of fine-scale fiber tracts in the human brain cortex has been a challenging problem, due to a low birefringence in the gray matter. In this study, we investigated the effect of refractive index matching by 2,2'-thiodiethanol (TDE) immersion on the improvement of PS-OCT measurements in ex vivo human brain tissue. We obtain the cortical fiber orientation maps in the gray matter, which reveals the radial fibers in the ...

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    10. A high-accuracy and high-efficiency digital volume correlation method to characterize in-vivo optic nerve head biomechanics from optical coherence tomography

      A high-accuracy and high-efficiency digital volume correlation method to characterize in-vivo optic nerve head biomechanics from optical coherence tomography

      In-vivo optic nerve head (ONH) biomechanics characterization is emerging as a promising way to study eye physiology and pathology. We propose a high-accuracy and high-efficiency digital volume correlation (DVC) method for the purpose of characterizing the in-vivo ONH deformation from volumes acquired by optical coherence tomography (OCT). Using a combination of synthetic tests and analysis of OCTs from monkey ONHs subjected to acute and chronically elevated intraocular pressure, we demonstrate that our proposed methodology overcomes several challenges for conventional DVC methods. First, it accounts for large ONH rigid body motion in the OCT volumes which could otherwise lead to analysis ...

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    11. In Situ Volumetric Imaging and Analysis of FRESH 3D Bioprinted Constructs Using Optical Coherence Tomography

      In Situ Volumetric Imaging and Analysis of FRESH 3D Bioprinted Constructs Using Optical Coherence Tomography

      As 3D bioprinting has grown as a fabrication technology, so too has the need for improved analytical methods to characterize these engineered constructs. This is especially challenging for soft tissues composed of hydrogels and cells as these materials readily deform, posing a barrier when trying to assess print fidelity and other properties non-destructively. Indeed, given the importance of structure-function relationships in most tissue types, establishing that the 3D architecture of the bioprinted construct matches its intended anatomic design is critical. Here we report development of a multimaterial bioprinting platform with integrated optical coherence tomography (OCT) for in situ volumetric imaging ...

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    12. Balanced-detection visible-light optical coherence tomography

      Balanced-detection visible-light optical coherence tomography

      Increases in speed and sensitivity enabled rapid clinical adoption of optical coherence tomography (OCT) in ophthalmology. Recently visible-light OCT (vis-OCT) achieved ultrahigh axial resolution, improved tissue contrast, and new functional imaging capabilities, demonstrating the potential to improve clincal care further. However, limited speed and sensitivity caused by the high relative intensity noise (RIN) in supercontinuum lasers impeded the clinical adoption of vis-OCT. To overcome these limitations, we developed balanced-detection vis-OCT (BD-vis-OCT), which uses two calibrated spectrometers to cancel noises common to sample and reference arms, including RIN. We analyzed the RIN to achieve a robust pixel-to-pixel calibration between the two ...

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    13. Adaptive spectroscopic visible-light optical coherence tomography for human retinal oximetry

      Adaptive spectroscopic visible-light optical coherence tomography for human retinal oximetry

      Alterations in the retinal oxygen saturation (sO2) and oxygen consumption are associated with nearly all blinding diseases. A technology that can accurately measure retinal sO2 has the potential to improve ophthalmology care significantly. Recently, visible-light optical coherence tomography (vis-OCT) showed great promise for noninvasive, depth-resolved measurement of retinal sO2 as well as ultra-high resolution anatomical imaging. We discovered that spectral contaminants (SC), if not correctly removed, could lead to incorrect vis-OCT sO2 measurements. There are two main types of SCs associated with vis-OCT systems and eye conditions, respectively. Their negative influence on sO2 accuracy is amplified in human eyes due ...

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    14. Scalable mapping of myelin and neuron density in the human brain with micrometer resolution

      Scalable mapping of myelin and neuron density in the human brain with micrometer resolution

      Optical Coherence Tomography (OCT) is an emerging 3D imaging technique that allows quantification of intrinsic optical properties such as scattering coefficient and back-scattering coefficient, and has proved useful in distinguishing delicate microstructures in the human brain. The origins of scattering in brain tissues are contributed by the myelin content, neuron size and density primarily; however, no quantitative relationships between them have been reported, which hampers the use of OCT in fundamental studies of architectonic areas in the human brain and the pathological evaluations of diseases. To date, histology remains the golden standard, which is prone to errors and can only ...

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    15. Watching Death in the Gerbil Cochlea Using Optical Coherence Tomography (OCT)

      Watching Death in the Gerbil Cochlea Using Optical Coherence Tomography (OCT)

      Because it is difficult to directly observe the morphology of the living cochlea, our ability to infer the mechanical functioning of the living ear has been limited. Nearly all of our knowledge about cochlear morphology comes from postmortem tissue that was fixed and processed using procedures that possibly distort the structures and fluid spaces of the organ of Corti. In this study, optical coherence tomography was employed to obtain in vivo and postmortem micron-scale volumetric images of the high-frequency hook region of the gerbil cochlea through the round-window membrane. The anatomical structures and fluid spaces of the organ of Corti ...

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    16. Segmentation of the Urothelium in Optical Coherence Tomography Images with Dynamic Contrast

      Segmentation of the Urothelium in Optical Coherence Tomography Images with Dynamic Contrast

      Significance: Speckle variations induced by intracellular motion (IM) in the urothelium was observed in optical coherence tomography (OCT) images. It is feasible to use the IM as a dynamic contrast to segment the urothelium with only two sequential OCT images. This new method opens the possibility of tracking the distribution of the urothelial cells to identify the microinvasion of bladder tumors. Approach: With fresh porcine bladder tissue, IM was analyzed by tracking speckle variations using autocorrelation function, then quantified with CONTINE algorism to identify the decorrelation time (DT) of the speckle variations. Variance analysis is conducted to show IM amplitude ...

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      Mentions: Cleveland Clinic
    17. In Vivo Sublayer Analysis Of Human Retinal Inner Plexiform Layer Obtained By Visible-Light Optical Coherence Tomography

      In Vivo Sublayer Analysis Of Human Retinal Inner Plexiform Layer Obtained By Visible-Light Optical Coherence Tomography

      Purpose: Growing evidence suggests, in glaucoma, the dendritic degeneration of subpopulation of the retinal ganglion cells (RGCs) may precede RGCs soma death. Since different RGCs synapse in different IPL sublayers, visualization of the lamellar structure of the IPL could enable both clinical and fundamental advances in glaucoma understanding and management. In this pilot study, we investigated whether visible-light optical coherence tomography (vis-OCT) could detect the difference in the inner plexiform layer (IPL) sublayers thicknesses between small cohorts of healthy and glaucomatous subjects. Method: We investigated vis-OCT retinal images from nine healthy and five glaucomatous subjects. Four of the healthy subjects ...

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    18. Automated Deep Learning-based Multi-class Fluid Segmentation in Swept-Source Optical Coherence Tomography Images

      Automated Deep Learning-based Multi-class Fluid Segmentation in Swept-Source Optical Coherence Tomography Images

      Purpose: To evaluate the performance of a deep learning-based, fully automated, multi-class, macular fluid segmentation algorithm relative to expert annotations in a heterogeneous population of confirmed wet age-related macular degeneration (wAMD) subjects. Methods: Twenty-two swept-source optical coherence tomography (SS-OCT) volumes of the macula from 22 from different individuals with wAMD were manually annotated by two expert graders. These results were compared using cross-validation (CV) to automated segmentations using a deep learning-based algorithm encoding spatial information about retinal tissue as an additional input to the network. The algorithm detects and delineates fluid regions in the OCT data, differentiating between intra- and ...

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    19. Segmentation boosting with compensation methods in optical coherence tomography angiography ...

      Segmentation boosting with compensation methods in optical coherence tomography angiography ...

      Optical coherence tomography angiography is a noninvasive imaging modality to establish the diagnosis of retinal vascular diseases. However, angiography images are significantly interfered if patients jitter or blink. In this study, a novel retinal image analysis method to accurately detect blood vessels and compensate the effect of interference was proposed. We call this the patch U-Net compensation (PUC) system, which is based on the famous U-Net. Several techniques, including a better training mechanism, direction criteria, area criteria, gap criteria, and probability map criteria, have been proposed to improve its accuracy. Simulations show that the proposed PUC achieves much better performance ...

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    20. Physiological, Biochemical and Microstructural Changes in Rice (Oryza sativa L.) under Varying pH Levels

      Physiological, Biochemical and Microstructural Changes in Rice (Oryza sativa L.) under Varying pH Levels

      Soil acidification exerts detrimental effects on rice plant leading to severe reduction in its yield. In the present study, we investigated the physiological, biochemical and microstructural changes in the leaves of rice cultivars, namely, Jhilli Dhan (JD) and Gora Dhan (GD), under varying pH conditions (pH 6.5, 5.5, 4.5 and 3.5). Seedlings were grown at varying pH levels for 14 days under controlled conditions. Root and shoot growth and chlorophyll content were found to be decreased with increasing acidity, whereas electrolyte leakage was increased with increasing acidity. Overall, seedling growth was significantly reduced at pH 3 ...

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    21. Effect of chlorination and pressure flushing of drippers fed by reclaimed wastewater on biofouling

      Effect of chlorination and pressure flushing of drippers fed by reclaimed wastewater on biofouling

      Dripper clogging reduces the performance and service life of a drip irrigation system. The impact of chlorination (1.5 ppm of free chlorine during 1 h application) and pressure flushing (0.18 MPa) on the biofouling of non-pressure-compensating drippers fed by real reclaimed wastewater was studied at lab scale using Optical Coherence Tomography. The effect of these treatments on microbial composition (bacteria and eukaryotes) was also investigated by High-throughput DNA sequencing. Biofouling was mainly observed in inlet, outlet and return areas of the drippers. Chlorination limited biofilm development mainly in the mainstream of the milli-labyrinth channel. It was more efficient ...

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    22. Full-field optical coherence tomography for the diagnosis of giant cell arteritis

      Full-field optical coherence tomography for the diagnosis of giant cell arteritis

      Histopathological examination of temporal artery biopsy (TAB) remains the gold standard for the diagnosis of giant cell arteritis (GCA) but is associated with essential limitations that emphasize the need for an upgraded pathological process. This study pioneered the use of full-field optical coherence tomography (FF-OCT) for rapid and automated on-site pathological diagnosis of GCA. Sixteen TABs (12 negative and 4 positive for GCA) were selected according to major histopathological criteria of GCA following hematoxylin-eosin-saffron-staining for subsequent acquisition with FF-OCT to compare structural modifications of the artery cell wall and thickness of each tunica. Gabor filtering of FF-OCT images was then ...

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      Mentions: ESPCI ParisTech
    23. Visible light optical coherence tomography angiography (vis-OCTA)

      Visible light optical coherence tomography angiography (vis-OCTA)

      We report herein the first visible light optical coherence tomography angiography (vis-OCTA) for human retinal imaging. Compared to the existing vis-OCT systems, we devised a spectrometer with a narrower bandwidth to increase the spectral power density for OCTA imaging, while retaining the major spectral contrast in the blood. We achieved a 100 kHz A-line rate, the fastest acquisition speed reported so far for human retinal vis-OCT. We rigorously optimized the imaging protocol such that a single acquisition takes <6 seconds with a field of view (FOV) of 3x7.8 mm2. The angiography enables accurate localization of microvasculature down to the ...

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    24. In vivo characterization of chick embryo mesoderm by optical coherence tomography assisted microindentation

      In vivo characterization of chick embryo mesoderm by optical coherence tomography assisted microindentation

      Embryos are growing organisms with highly heterogeneous properties in space and time. Understanding the mechanical properties is a crucial prerequisite for the investigation of morphogenesis. During the last ten years, new techniques have been developed to evaluate the mechanical properties of biological tissues in vivo . To address this need, we employed a new instrument that, via the combination of micro-indentation with Optical Coherence Tomography (OCT), allows us to determine both, the spatial distribution of mechanical properties of chick embryos and the structural changes in real-time provided by OCT. We report here the stiffness measurements on live chicken mesoderm during somite ...

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    1-24 of 40 1 2 »
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