927 research outputs found

    PhyCV: The First Physics-inspired Computer Vision Library

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    PhyCV is the first computer vision library which utilizes algorithms directly derived from the equations of physics governing physical phenomena. The algorithms appearing in the current release emulate, in a metaphoric sense, the propagation of light through a physical medium with natural and engineered diffractive properties followed by coherent detection. Unlike traditional algorithms that are a sequence of hand-crafted empirical rules or deep learning algorithms that are usually data-driven and computationally heavy, physics-inspired algorithms leverage physical laws of nature as blueprints for inventing algorithms. PhyCV features low-dimensionality and high- efficiency, making it ideal for edge computing applications. We demonstrate real-time video processing on NVIDIA Jetson Nano using PhyCV. In addition, these algorithms have the potential to be implemented in real physical devices for fast and efficient computation in the form of analog computing. The open-sourced code is available at https://github.com/JalaliLabUCLA/phyc

    Generalizable automated pixel-level structural segmentation of medical and biological data

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    Over the years, the rapid expansion in imaging techniques and equipments has driven the demand for more automation in handling large medical and biological data sets. A wealth of approaches have been suggested as optimal solutions for their respective imaging types. These solutions span various image resolutions, modalities and contrast (staining) mechanisms. Few approaches generalise well across multiple image types, contrasts or resolution. This thesis proposes an automated pixel-level framework that addresses 2D, 2D+t and 3D structural segmentation in a more generalizable manner, yet has enough adaptability to address a number of specific image modalities, spanning retinal funduscopy, sequential fluorescein angiography and two-photon microscopy. The pixel-level segmentation scheme involves: i ) constructing a phase-invariant orientation field of the local spatial neighbourhood; ii ) combining local feature maps with intensity-based measures in a structural patch context; iii ) using a complex supervised learning process to interpret the combination of all the elements in the patch in order to reach a classification decision. This has the advantage of transferability from retinal blood vessels in 2D to neural structures in 3D. To process the temporal components in non-standard 2D+t retinal angiography sequences, we first introduce a co-registration procedure: at the pairwise level, we combine projective RANSAC with a quadratic homography transformation to map the coordinate systems between any two frames. At the joint level, we construct a hierarchical approach in order for each individual frame to be registered to the global reference intra- and inter- sequence(s). We then take a non-training approach that searches in both the spatial neighbourhood of each pixel and the filter output across varying scales to locate and link microvascular centrelines to (sub-) pixel accuracy. In essence, this \link while extract" piece-wise segmentation approach combines the local phase-invariant orientation field information with additional local phase estimates to obtain a soft classification of the centreline (sub-) pixel locations. Unlike retinal segmentation problems where vasculature is the main focus, 3D neural segmentation requires additional exibility, allowing a variety of structures of anatomical importance yet with different geometric properties to be differentiated both from the background and against other structures. Notably, cellular structures, such as Purkinje cells, neural dendrites and interneurons, all display certain elongation along their medial axes, yet each class has a characteristic shape captured by an orientation field that distinguishes it from other structures. To take this into consideration, we introduce a 5D orientation mapping to capture these orientation properties. This mapping is incorporated into the local feature map description prior to a learning machine. Extensive performance evaluations and validation of each of the techniques presented in this thesis is carried out. For retinal fundus images, we compute Receiver Operating Characteristic (ROC) curves on existing public databases (DRIVE & STARE) to assess and compare our algorithms with other benchmark methods. For 2D+t retinal angiography sequences, we compute the error metrics ("Centreline Error") of our scheme with other benchmark methods. For microscopic cortical data stacks, we present segmentation results on both surrogate data with known ground-truth and experimental rat cerebellar cortex two-photon microscopic tissue stacks.Open Acces

    Biomedical Applications of Mid-Infrared Spectroscopic Imaging and Multivariate Data Analysis: Contribution to the Understanding of Diabetes Pathogenesis

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    Diabetic retinopathy (DR) is a microvascular complication of diabetes and a leading cause of adult vision loss. Although a great deal of progress has been made in ophthalmological examinations and clinical approaches to detect the signs of retinopathy in patients with diabetes, there still remain outstanding questions regarding the molecular and biochemical changes involved. To discover the biochemical mechanisms underlying the development and progression of changes in the retina as a result of diabetes, a more comprehensive understanding of the bio-molecular processes, in individual retinal cells subjected to hyperglycemia, is required. Animal models provide a suitable resource for temporal detection of the underlying pathophysiological and biochemical changes associated with DR, which is not fully attainable in human studies. In the present study, I aimed to determine the nature of diabetes-induced, highly localized biochemical changes in the retinal tissue from Ins2Akita/+ (Akita/+; a model of Type I diabetes) male mice with different duration of diabetes. Employing label-free, spatially resolved Fourier transform infrared (FT-IR) imaging engaged with chemometric tools enabled me to identify temporal-dependent reproducible biomarkers of the diabetic retinal tissue from mice with 6 or 12 weeks, and 6 or 10 months of diabetes. I report, for the first time, the origin of molecular changes in the biochemistry of individual retinal layers with different duration of diabetes. A robust classification between distinctive retinal layers - namely photoreceptor layer (PRL), outer plexiform layer (OPL), inner nuclear layer (INL), and inner plexiform layer (IPL) - and associated temporal-dependent spectral biomarkers, were delineated. Spatially-resolved super resolution chemical images revealed oxidative stress-induced structural and morphological alterations within the nucleus of the photoreceptors. Comparison among the PRL, OPL, INL, and IPL suggested that the photoreceptor layer is the most susceptible layer to the oxidative stress with short-duration of diabetes. Moreover, for the first time, we present the temporal-dependent molecular alterations for the PRL, OPL, INL, and IPL from Akita/+ mice, with progression of diabetes. These findings are potentially important and may be of particular benefit in understanding the molecular and biological activity of retinal cells during oxidative stress in diabetes. Our integrating paradigm provides a new conceptual framework and a significant rationale for a better understanding of the molecular and cellular mechanisms underlying the development and progression of DR. This approach may yield alternative and potentially complimentary methods for the assessment of diabetes changes. It is expected that the conclusions drawn from this work will bridge the gap in our knowledge regarding the biochemical mechanisms of the DR and address some critical needs in the biomedical community

    FY10 Engineering Innovations, Research and Technology Report

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    Development of Molecular Contrast-enhanced Imaging for Optical Coherence Tomography

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    Biological imaging techniques that are able to detect a contrast-enhanced signal from the target molecules have been widely applied to various techniques in the imaging field. The complex biological environment provides numerous and more efficient pathways along which the chromophores (light absorber) may release its energy. This energy can provide not only morphological information, but also specific molecular information such as a biochemical map of a sample. All diseases correlate with both morphological and biochemical changes. Optical coherence tomography (OCT) system is one of the biological imaging techniques. OCT has widely been applied to many medical/clinical fields, giving benefit from a penetration depth of a few millimeters while maintaining a spatial resolution on the order of a micron. Unfortunately, OCT lacks the straightforward functional molecular imaging extensions available for other technologies, e.g. confocal fluorescence microscopy and fluorescence diffuse optical tomography. This is largely because incoherent processes such as fluorescence emission and Raman scattering are not readily detectable with low coherence interferometry that is the central technique that underlies all OCT systems. Despite a drawback of molecular imaging with OCT, it is highly desirable to measure not only morphological, but also molecular information from either endogenous or exogenous molecules. In order to overcome the limitation of molecular contrast imaging for OCT, our group has been researched the hybrid OCT imaging technique and a new exogenous contrast agent. Our contrast-enhanced imaging technique integrates OCT with a well-researched and well-established technique: two-colored pump-probe absorption spectroscopy. Our novel imaging technique is called Pump-Probe OCT (PPOCT). Based upon current successful results, molecular imaging with OCT potentially gives us the ability to identify pathologies. In order to expand the capacity of PPOCT, this dissertation focuses on development of molecular contrast-enhanced imaging for optical coherence tomography (OCT). In the first phase of the research, we developed and optimized for sensitivity a two-color ground state recovery Pump-Probe Optical Coherence Tomography (gsrPPOCT) system and signal algorithm to measure the contrast-enhanced signal of endogenous and exogenous contrast agents such as Hemoglobin (Hb) and Methylene blue (MB) from in vivo samples. Depending on the absorption peak of a target molecule, the pump light sources for PPOCT used 532nm Q-switched laser or 663nm diode laser. Based on different experimental application, Ti:sapp or SLD of 830nm center wavelength were utilized. The PPCOT system was firstly used to image Hb of in vivo vasulature in a Xenopus laevis as the endogenous contrast agent and a larval stage zebrafish using MB as the exogenous contrast agent via transient changes in light absorption. Their morphological in addition to molecular specific information from a live animal was described. The incorporation of a pump laser in an otherwise typical spectrometer based OCT system is sufficient to enable molecular imaging with PPOCT. In the second phase of this research, based on endoscopic molecular contrast-enhanced applications for OCT, we invented an ultra-wideband lensless fiber optic rotary joint based on co-aligning two optical fibers has excellent performance (~0.38 dB insertion loss). The developed rotary joint can cover a wavelength range of at least 355- 1360 nm with single mode, multimode, and double clad fibers with rotational velocities up to 8800 rpm (146 Hz). In the third phase of this research, we developed and manufactured a microencapsulated methylene blue (MB) contrast agent for PPOCT. The poly lactic coglycolic acid (PLGA) microspheres loaded with MB offer several advantages over bare MB. The microsphere encapsulation improves the PPOCT signal both by enhancing the scattering and preventing the reduction of MB to leucomethylene blue. The surface of the microsphere can readily be functionalized to enable active targeting of the contrast agent without modifying the excited state dynamics of MB that enable PPOCT imaging. Both MB and PLGA are used clinically. PLGA is FDA approved and used in drug delivery and tissue engineering applications. 2.5 µm diameter microspheres were synthesized with an inner core containing 0.01% (w/v) aqueous MB. As an initial demonstration the MB microspheres were imaged in a 100 µm diameter capillary tube submerged in a 1% intralipid emulsion. By varying the oxygen concentration both 0% and 21%, we observed he lifetime of excited triple state using time-resolved Pump-Probe spectroscopy and also the relative phase shift between the pump and probe is a reliable indicator of the oxygen concentration. Furthermore, these results are in good agreement with our theoretical predictions. This development opens up the possibility of using MB for 3-D oxygen sensing with PPOCT

    Retinal imaging tool for assessment of the parapapillary atrophy and the optic disc

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    Ophthalmic diseases such as glaucoma are associated with progressive changes in the structure of the optic disc (OD) and parapapillary atrophy (PPA). These structural changes may therefore have relevance to other systemic diseases. The size and location of OD and PPA can be used as registration landmarks for monitoring changes in features of the fundus of the eye. Retinal vessel evaluation, for example, can be used as a biomarker for the effects of multiple systemic diseases, or co-morbidities. This thesis presents the first computer-aided measuring tool that detects and quantifies the progression of PPA automatically on a 2D retinal fundus image in the presence of image noise. An automated segmentation system is described that can detect features of the optic nerve. Three novel approaches are explored that extract the PPA and OD region approximately from a 2D fundus image. The OD region is segmented using (i) a combination of active contour and morphological operations, (ii) a modified Chan-Vese algorithm and (iii) a combination of edge detection and ellipse fitting methods. The PPA region is identified from the presence of bright pixels in the temporal zone of the OD, and segmented using a sequence of techniques, including a modified Chan-Vese approach, thresholding, scanning filter and multi-seed region growing methods. The work demonstrates for the first time how the OD and PPA regions can be identified and quantified from 2D fundus images using a standard fundus camera

    Development of Molecular Contrast-enhanced Imaging for Optical Coherence Tomography

    Get PDF
    Biological imaging techniques that are able to detect a contrast-enhanced signal from the target molecules have been widely applied to various techniques in the imaging field. The complex biological environment provides numerous and more efficient pathways along which the chromophores (light absorber) may release its energy. This energy can provide not only morphological information, but also specific molecular information such as a biochemical map of a sample. All diseases correlate with both morphological and biochemical changes. Optical coherence tomography (OCT) system is one of the biological imaging techniques. OCT has widely been applied to many medical/clinical fields, giving benefit from a penetration depth of a few millimeters while maintaining a spatial resolution on the order of a micron. Unfortunately, OCT lacks the straightforward functional molecular imaging extensions available for other technologies, e.g. confocal fluorescence microscopy and fluorescence diffuse optical tomography. This is largely because incoherent processes such as fluorescence emission and Raman scattering are not readily detectable with low coherence interferometry that is the central technique that underlies all OCT systems. Despite a drawback of molecular imaging with OCT, it is highly desirable to measure not only morphological, but also molecular information from either endogenous or exogenous molecules. In order to overcome the limitation of molecular contrast imaging for OCT, our group has been researched the hybrid OCT imaging technique and a new exogenous contrast agent. Our contrast-enhanced imaging technique integrates OCT with a well-researched and well-established technique: two-colored pump-probe absorption spectroscopy. Our novel imaging technique is called Pump-Probe OCT (PPOCT). Based upon current successful results, molecular imaging with OCT potentially gives us the ability to identify pathologies. In order to expand the capacity of PPOCT, this dissertation focuses on development of molecular contrast-enhanced imaging for optical coherence tomography (OCT). In the first phase of the research, we developed and optimized for sensitivity a two-color ground state recovery Pump-Probe Optical Coherence Tomography (gsrPPOCT) system and signal algorithm to measure the contrast-enhanced signal of endogenous and exogenous contrast agents such as Hemoglobin (Hb) and Methylene blue (MB) from in vivo samples. Depending on the absorption peak of a target molecule, the pump light sources for PPOCT used 532nm Q-switched laser or 663nm diode laser. Based on different experimental application, Ti:sapp or SLD of 830nm center wavelength were utilized. The PPCOT system was firstly used to image Hb of in vivo vasulature in a Xenopus laevis as the endogenous contrast agent and a larval stage zebrafish using MB as the exogenous contrast agent via transient changes in light absorption. Their morphological in addition to molecular specific information from a live animal was described. The incorporation of a pump laser in an otherwise typical spectrometer based OCT system is sufficient to enable molecular imaging with PPOCT. In the second phase of this research, based on endoscopic molecular contrast-enhanced applications for OCT, we invented an ultra-wideband lensless fiber optic rotary joint based on co-aligning two optical fibers has excellent performance (~0.38 dB insertion loss). The developed rotary joint can cover a wavelength range of at least 355- 1360 nm with single mode, multimode, and double clad fibers with rotational velocities up to 8800 rpm (146 Hz). In the third phase of this research, we developed and manufactured a microencapsulated methylene blue (MB) contrast agent for PPOCT. The poly lactic coglycolic acid (PLGA) microspheres loaded with MB offer several advantages over bare MB. The microsphere encapsulation improves the PPOCT signal both by enhancing the scattering and preventing the reduction of MB to leucomethylene blue. The surface of the microsphere can readily be functionalized to enable active targeting of the contrast agent without modifying the excited state dynamics of MB that enable PPOCT imaging. Both MB and PLGA are used clinically. PLGA is FDA approved and used in drug delivery and tissue engineering applications. 2.5 µm diameter microspheres were synthesized with an inner core containing 0.01% (w/v) aqueous MB. As an initial demonstration the MB microspheres were imaged in a 100 µm diameter capillary tube submerged in a 1% intralipid emulsion. By varying the oxygen concentration both 0% and 21%, we observed he lifetime of excited triple state using time-resolved Pump-Probe spectroscopy and also the relative phase shift between the pump and probe is a reliable indicator of the oxygen concentration. Furthermore, these results are in good agreement with our theoretical predictions. This development opens up the possibility of using MB for 3-D oxygen sensing with PPOCT
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