1. Articles from bioRxiv.org

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    1. 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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    2. 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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    3. 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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    4. 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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    5. 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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    6. 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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    7. 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
    8. 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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    9. 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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    10. 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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    11. 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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    12. 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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    13. 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
    14. 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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    15. 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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    16. Long-term in vivo Monitoring of Gliotic Sheathing of Ultrathin Entropic Coated Brain Microprobes with Fiber-based Optical Coherence Tomography

      Long-term in vivo Monitoring of Gliotic Sheathing of Ultrathin Entropic Coated Brain Microprobes with Fiber-based Optical Coherence Tomography

      Microfabricated neuroprosthetic devices have made possible important observations on neuron activity; however, long-term high-fidelity recording performance of these devices has yet to be realized. Tissue-device interactions appear to be a primary source of lost recording performance. The current state of the art for visualizing the tissue response surrounding brain implants in animals is Immunohistochemistry + Confocal Microscopy, which is mainly performed after sacrificing the animal. Monitoring the tissue response as it develops could reveal important features of the response which may inform improvements in electrode design. Optical Coherence Tomography (OCT), an imaging technique commonly used in ophthalmology, has already been adapted ...

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    17. The influence of insulin therapy on measurements of optical coherence tomography parameters in diabetic patients without retinopathy

      The influence of insulin therapy on measurements of optical coherence tomography parameters in diabetic patients without retinopathy

      Purpose To determine whether there was a change in the fundus of the eye in diabetic patients without retinopathy after insulin therapy. Methods The diabetic patients without retinopathy were included in this study. A swept-source optical coherence tomography/angiography (SS-OCT/A) was used to obtain the measurements of macular retinal nerve fibre layer (mRNFL) thickness, ganglion cell-inner plexiform layer (GC-IPL) thickness, retinal thickness (RT), macular choroidal thickness (MCT), peripapillary retinal nerve fibre layer (pRNFL) thickness, peripapillary choroidal thickness (PCT), and perfused vascular density (PVD). Univariable and multivariable regression analyses were performed to explore the influence of insulin use on measurements ...

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    18. Accuracy of a deep convolutional neural network in the detection of myopic macular diseases using swept-source optical coherence tomography

      Accuracy of a deep convolutional neural network in the detection of myopic macular diseases using swept-source optical coherence tomography

      This study examined and compared outcomes of deep learning (DL) in identifying swept-source optical coherence tomography (OCT) images without myopic macular lesions [i.e., no high myopia (nHM) vs. high myopia (HM)], and OCT images with myopic macular lesions [e.g., myopic choroidal neovascularization (mCNV) and retinoschisis (RS)]. A total of 796 SS-OCT images were included in the study as follows and analyzed by k-fold cross-validation (k = 5) using DL's renowned model, Visual Geometry Group-16: nHM, 107 images; HM, 456 images; mCNV, 122 images; and RS, 111 images (n = 796). The binary classification of OCT images with or without ...

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    19. A Spectral De-mixing Model for Triplex In Vivo Imaging of Optical Coherence Tomography Contrast Agents

      A Spectral De-mixing Model for Triplex In Vivo Imaging of Optical Coherence Tomography Contrast Agents

      The ability to detect multiple contrast agents simultaneously would greatly enhance Optical Coherence Tomography (OCT) images, providing nuanced biological context to physiological structures. However, previous OCT contrast agent work has been limited to scenarios where only a single contrast agent could be robustly detected within each voxel. We present a novel spectroscopic technique for de-mixing the spectral signal from multiple OCT contrast agents within a single voxel. We validate our technique in vitro and also demonstrate in vivo imaging of three spectrally distinct gold nanobipyramids, trafficking within the lymphatic system of a live mouse. This approach opens the door to ...

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    20. Gold Nanobipyramids as Second Near Infrared Optical Coherence Tomography Contrast Agents for Multiplexed In Vivo Lymphangiography

      Gold Nanobipyramids as Second Near Infrared Optical Coherence Tomography Contrast Agents for Multiplexed In Vivo Lymphangiography

      Developing contrast-enhanced optical coherence tomography (OCT) techniques is important for specific imaging of tissue lesions, molecular imaging, cell-tracking, and highly sensitive microangiography and lymphangiography. Multiplexed OCT imaging in the second near infrared (NIR-II) window is highly desirable since it allows simultaneous imaging and tracking of multiple biological events in high resolution with deeper tissue penetration in vivo. Here we demonstrate that gold nanobipyramids can function as OCT multiplexing contrast agents, allowing the visualization of two separate lymphatic flows occurring simultaneously from different drainage basins into the same lymph node in a live mouse. Contrast-enhanced multiplexed lymphangiography of a melanoma tumor ...

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    21. Exploring the association of collaterals and vessel density using optical coherence tomography angiography in retinal vein occlusions

      Exploring the association of collaterals and vessel density using optical coherence tomography angiography in retinal vein occlusions

      Purpose: Using optical coherence tomography angiography (OCTA) to characterize the types of collaterals in eyes with retinal vein occlusion (RVO) and further investigate their correlations with vessel densities of the superficial (SCP) and the deep capillary plexus (DCP). Methods: This cross-sectional study included 25 eyes of 23 patients with RVO. 3 x 3 mm2 OCTA macular scans were used to quantify the parafoveal vessel density (VD) of the SCP and DCP, and to classify the collaterals into one of four types (true superficial, true deep, superficial diving, and foveal collateral). Poisson regression model was used to identify significant associations between ...

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    22. Micro-indentation and optical coherence tomography for the mechanical characterization of embryos: Experimental setup and measurements on fixed chicken embryos.

      Micro-indentation and optical coherence tomography for the mechanical characterization of embryos: Experimental setup and measurements on fixed chicken embryos.

      The investigation of the mechanical properties of embryos is expected to provide valuable information on the phenomenology of morphogenesis. It is thus believed that, by mapping the viscoelastic features of an embryo at different stages of growth, it may be possible to shed light on the role of mechanics in embryonic development. To contribute to this field, we present a new instrument that can determine spatiotemporal distributions of mechanical properties of embryos over a wide area and with unprecedented accuracy. The method relies on combining ferrule-top micro-indentation, which provides local measurements of viscoelasticity, with Optical Coherence Tomography, which can reveal ...

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    23. Micro-indentation and optical coherence tomography for the mechanical characterization of embryos

      Micro-indentation and optical coherence tomography for the mechanical characterization of embryos

      The investigation of the mechanical properties of embryos is expected to provide valuable information on the phenomenology of morphogenesis. It is thus believed that, by mapping the viscoelastic features of an embryo at different stages of growth, it may be possible to shed light on the role of mechanics in embryonic development. To contribute to this field, we present a new instrument that can determine spatiotemporal distributions of mechanical properties of embryos over a wide area and with unprecedented accuracy. The method relies on combining ferrule-top micro-indentation, which provides local measurements of viscoelasticity, with Optical Coherence Tomography, which can reveal ...

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    1-24 of 31 1 2 »
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