Dissertations / Theses on the topic 'Intrinsic optical signal imaging'
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Berwick, Jason. "Investigation of the V-signal oscillation using intrinsic optical imaging and imaging spectroscopy and its relevance to cortical metabolism." Thesis, University of Sheffield, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312793.
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Harel, Noam. "Functional organization of auditory cortex revealed by optical imaging of intrinsic signals." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0025/NQ49983.pdf.
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Labron, Mark William. "Imaging the effects of acute osmotic stress on the rat neocortical slice using intrinsic optical signals and calcein fluorescence." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp01/MQ36047.pdf.
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Xu, Wei. "Analog Signal Processing for Optical Coherence Imaging Systems." Diss., The University of Arizona, 2006. http://hdl.handle.net/10150/195225.
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Optical coherence tomography (OCT) and optical coherence microscopy (OCM) are non-invasive optical coherence imaging techniques, which enable micron-scale resolution, depth resolved imaging capability. Both OCT and OCM are based on Michelson interferometer theory. They are widely used in ophthalmology, gastroenterology and dermatology, because of their high resolution, safety and low cost. OCT creates cross sectional images whereas OCM obtains en face images. In this dissertation, the design and development of three increasingly complicated analog signal processing (ASP) solutions for optical coherence imaging are presented.The first ASP solution was implemented for a time domain OCT system with a Rapid Scanning Optical Delay line (RSOD)-based optical signal modulation and logarithmic amplifier (Log amp) based demodulation. This OCT system can acquire up to 1600 A-scans per second. The measured dynamic range is 106dB at 200A-scan per second. This OCT signal processing electronics includes an off-the-shelf filter box with a Log amp circuit implemented on a PCB board.The second ASP solution was developed for an OCM system with synchronized modulation and demodulation and compensation for interferometer phase drift. This OCM acquired micron-scale resolution, high dynamic range images at acquisition speeds up to 45,000 pixels/second. This OCM ASP solution is fully custom designed on a perforated circuit board.The third ASP solution was implemented on a single 2.2 mm x 2.2 mm complementary metal oxide semiconductor (CMOS) chip. This design is expandable to a multiple channel OCT system. A single on-chip CMOS photodetector and ASP channel was used for coherent demodulation in a time domain OCT system. Cross-sectional images were acquired with a dynamic range of 76dB (limited by photodetector responsivity). When incorporated with a bump-bonded InGaAs photodiode with higher responsivity, the expected dynamic range is close to 100dB.
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Raguet, Hugo. "A Signal Processing Approach to Voltage-Sensitive Dye Optical Imaging." Thesis, Paris 9, 2014. http://www.theses.fr/2014PA090031/document.
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L’imagerie optique par colorant potentiométrique est une méthode d’enregistrement de l’activité corticale prometteuse, mais dont le potentiel réel est limité par la présence d’artefacts et d’interférences dans les acquisitions. À partir de modèles existant dans la littérature, nous proposons un modèle génératif du signal basé sur un mélange additif de composantes, chacune contrainte dans une union d’espaces linéaires déterminés par son origine biophysique. Motivés par le problème de séparation de composantes qui en découle, qui est un problème inverse linéaire sous-déterminé, nous développons : (1) des régularisations convexes structurées spatialement, favorisant en particulier des solutions parcimonieuses ; (2) un nouvel algorithme proximal de premier ordre pour minimiser efficacement la fonctionnelle qui en résulte ; (3) des méthodes statistiques de sélection de paramètre basées sur l’estimateur non biaisé du risque de Stein. Nous étudions ces outils dans un cadre général, et discutons leur utilité pour de nombreux domaines des mathématiques appliqués, en particulier pour les problèmes inverses ou de régression en grande dimension. Nous développons par la suite un logiciel de séparation de composantes en présence de bruit, dans un environnement intégré adapté à l’imagerie optique par colorant potentiométrique. Finalement, nous évaluons ce logiciel sur différentes données, synthétiques et réelles, montrant des résultats encourageants quant à la possibilité d’observer des dynamiques corticales complexesVoltage-sensitive dye optical imaging is a promising recording modality for the cortical activity, but its practical potential is limited by many artefacts and interferences in the acquisitions. Inspired by existing models in the literature, we propose a generative model of the signal, based on an additive mixtures of components, each one being constrained within an union of linear spaces, determined by its biophysical origin. Motivated by the resulting component separation problem, which is an underdetermined linear inverse problem, we develop: (1) convex, spatially structured regularizations, enforcing in particular sparsity on the solutions; (2) a new rst-order proximal algorithm for minimizing e›ciently the resulting functional; (3) statistical methods for automatic parameters selection, based on Stein’s unbiased risk estimate.We study thosemethods in a general framework, and discuss their potential applications in variouselds of applied mathematics, in particular for large scale inverse problems or regressions. We develop subsequently a soŸware for noisy component separation, in an integrated environment adapted to voltage-sensitive dye optical imaging. Finally, we evaluate this soŸware on dišerent data set, including synthetic and real data, showing encouraging perspectives for the observation of complex cortical dynamics
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R, S. Umesh. "Algorithms for processing polarization-rich optical imaging data." Thesis, Indian Institute of Science, 2004. http://hdl.handle.net/2005/96.
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This work mainly focuses on signal processing issues related to continuous-wave, polarization-based direct imaging schemes. Here, we present a mathematical framework to analyze the performance of the Polarization Difference Imaging (PDI) and Polarization Modulation Imaging (PMI). We have considered three visualization parameters, namely, the polarization intensity (PI), Degree of Linear Polarization (DOLP) and polarization orientation (PO) for comparing these schemes. The first two parameters appear frequently in literature, possibly under different names. The last parameter, polarization orientation, has been introduced and elaborated in this thesis. We have also proposed some extensions/alternatives for the existing imaging and processing schemes and analyzed their advantages.
Theoretically and through Monte-Carlo simulations, we have studied the performance of these schemes under white and coloured noise conditions, concluding that, in general, the PMI gives better estimates of all the parameters. Experimental results corroborate our theoretical arguments. PMI is shown to give asymptotically efficient estimates of these parameters, whereas PDI is shown to give biased estimates of the first two and is also shown to be incapable of estimating PO. Moreover, it is shown that PDI is a particular case of PMI. The property of PDI, that it can yield estimates at lower variances has been recognized as its major strength. We have also shown that the three visualization parameters can be fused to form a colour image, giving a holistic view of the scene. We report the advantages of analyzing chunks of data and bootstrapped data under various circumstances.
Experiments were conducted to image objects through calibrated scattering media and natural media like mist, with successful results. Scattering media prepared with polystyrene microspheres of diameters 2.97m, 0.06m and 0.13m dispersed in water were used in our experiments. An intensified charge coupled device (CCD) camera was used to capture the images. Results showed that imaging could be performed beyond optical thickness of 40, for particles with 0.13m diameter. For larger particles, the depth to which we could image was much lesser. An experiment using an incoherent source yielded better results than with coherent sources, which we attribute to the speckle noise induced by coherent sources. We have suggested a harmonic based imaging scheme, which can perhaps be used when we have a mixture of scattering particles. We have also briefly touched upon the possible post processing that can be performed on the obtained results, and as an example, shown segmentation based on a PO imaging result.
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Brookshire, Charles Thomas. "Illumination Recovery For Optical Microscopy." University of Dayton / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=dayton1588936914060945.
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Koh, P. H. "Methodology of optical topography measurements for functional brain imaging and the development and implementation of functional optical signal analysis software." Thesis, University College London (University of London), 2007. http://discovery.ucl.ac.uk/1444898/.
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Near-infrared spectroscopy (N1RS) has been used extensively in recent years as a non invasive tool for investigating cerebral hemodynamics and oxygenation. The technique exploits the different optical absorption of oxy-haemoglobin and deoxy-haemoglobin in the near infrared region to measure changes in their concentrations in tissue. By making multiple NIRS measurement simultaneously, optical topography (OT) provides spatial maps of the changes in haemoglobin concentration levels from specific regions of the cerebral cortex. The thesis describes several key developments in optical topography studies of functional brain activation. These include the development of a novel data analysis software to process the experimental data and a new statistical methodology for examining the spatial and temporal variance of OT data. The experimental work involved the design of a cognitive task to measure the haemodynamic response using a 24-channeI Hitachi ETG-100 OT system. Following a series of pilot studies, a study on twins with opposite handedness was conducted to study the functional changes in the parietal region of the brain. Changes in systemic variables were also investigated. A dynamic phantom with optical properties similar to those of biological tissues was developed with the use of liquid crystals to simulate spatially varying changes in haemodynamics. A new software tool was developed to provide a flexible processing approach with real time analysis of the optical signals and advanced statistical analysis. Unlike conventional statistical measures which compare a pre-defined activation and task periods, the thesis describes the incorporation of a Statistical Parametric Mapping toolbox which enables statistical inference about the spatially-resolved topographic data to be made. The use of the general linear model computes the temporal correlations between the defined model and optical signals but also corrects for the spatial correlations between neighbouring measurement points. The issues related to collecting functional activation data using optical topography are fully discussed with a view that the work presented in this thesis will extend the applicability of this technology.
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Balu, Ramani. "Intrinsic and Synaptic Properties of Olfactory Bulb Neurons and Their Relation to Olfactory Sensory Processing." Case Western Reserve University School of Graduate Studies / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=case1173540900.
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Martin, Phillip A., and Phillip A. Martin. "Investigation of the Feasibility of an Optical Imaging System for the Application of In Vivo Flow Cytometry." Thesis, The University of Arizona, 2016. http://hdl.handle.net/10150/621197.
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This thesis investigates the feasibility of employing an optical imaging system for the application of in vivo flow cytometry for detecting rare circulating tumor cells (CTCs) in vasculature. This investigation presented used three optical imaging configurations: a Nikon Eclipse E600 fluorescence microscope with a PIXIS 2048B CCD camera; a Nikon Eclipse E600 fluorescence microscope with a ThorLabs DCC 3240N CMOS camera; and a custom built confocal microendoscope with a ThorLabs DCC 3240N CMOS camera. These systems were employed to gain insight as to what signal to noise ratios and sensitivities are required to sufficiently detect fluorescently labeled cancer cells. This work presents general concepts of fluorescence and confocal microscopy, the experimental setups employed, and experimental measurements and results obtained. The experimental measurements involved the following: the simulation of flow cytometry by imaging green fluorescent microspheres, with a fluorescence excitation range of 505-515 nm and a diameter of 15µm, in a square crit tube moving on a translational stage, and imaging a selection of cells that included MCF10A breast cells (non-cancerous), OVCAR3 ovarian cancer cells, and patient derived xenogram (PDX) breast cancer cells, which express folate-receptor proteins on their surface. We fluorescently labeled these cells with the introduction of a new folate-receptor targeted fluorescent contrast agent OTL38, made by On Target Laboratories. The results established that we were able to image and detect fluorescence microspheres with a minimum signal to noise ratio (SNR) of 2.3 using the ThorLabs DCC 3240N camera on the Nikon Fluorescence microscope. We were able to image and detect the cells used on all three system configurations. Analyzing the different cell uptake efficacies of the contrast agent OTL38, we established that the SNR levels were variable when imaging PDX breast cancer cells. We propose future work to investigate possible effects on the variability of SNR results, as well as, and future steps in designing a real-time optical fluorescence imaging system for in vivo flow cytometry.
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Wang, Zhipeng. "A framework for the Analysis and Evaluation of Optical Imaging Systems with Arbitrary Response Functions." Diss., The University of Arizona, 2008. http://hdl.handle.net/10150/195108.
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The scientific applications and engineering aspects of multispectral and hyperspectral imaging systems have been studied extensively. The traditional geometric spectral imaging system model is specifically developed aiming at spectral sensors with spectrally non-overlapping bands. Spectral imaging systems with overlapping bands also exist. For example, the quantum-dot infrared photodetectors (QDIPs) for midwave- and longwave-infrared (IR) imaging systems exhibit highly overlapping spectral responses tunable through the bias voltages applied. This makes it possible to build spectrally tunable imaging system in IR range based on single QDIP. Furthermore, the QDIP based system can be operated as being adaptive to scenes. Other optical imaging systems like the human eye and some polarimetric sensing systems also have overlapping bands. To analyze such sensors, a functional analysis-based framework is provided in this dissertation. The framework starts from the mathematical description of the interaction between sensor and the radiation from scene reaching it. A geometric model of the spectral imaging process is provided based on the framework. The spectral response functions and the scene spectra are considered as vectors inside an 1-dimensional spectral space. The spectral imaging process is abstracted to represent a projection of scene spectrum onto sensor. The projected spectrum, which is the least-square error reconstruction of the scene vectors, contains the useful information for image processing. Spectral sensors with arbitrary spectral response functions are can be analyzed with this model. The framework leads directly to an image pre-processing algorithm to remove the data correlation between bands. Further discussion shows that this model can also serve the purpose of sensor evaluation, and thus facilitates comparison between different sensors. The spectral shapes and the Signal-to-Noise Ratios (SNR) of different bands are seen to influence the sensor's imaging ability in different manners, which are discussed in detail. With the newly defined SNR in spectral space, we can quantitatively characterize the photodetector noise of a spectral sensor with overlapping bands. The idea of adaptive imaging with QDIP based sensor is proposed and illustrated.
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Langer, Dominik, 't Hoff Marcel van, Andreas J. Keller, Chetan Nagaraja, Oliver A. Pfaeffli, Maurice Goeldi, Hansjoerg Kasper, and Fritjof Helmchen. "HelioScan : A software framework for controlling in vivo microscopy setups with high hardware flexibility, functional diversity and extendibility." Uppsala universitet, Genetisk utvecklingsbiologi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-201813.
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Intravital microscopy such as in vivo imaging of brain dynamics is often performed with custom-built microscope setups controlled by custom-written software to meet specific requirements. Continuous technological advancement in the field has created a need for new control software that is flexible enough to support the biological researcher with innovative imaging techniques and provide the developer with a solid platform for quickly and easily implementing new extensions. Here, we introduce HelioScan, a software package written in LabVIEW, as a platform serving this dual role. HelioScan is designed as a collection of components that can be flexibly assembled into microscope control software tailored to the particular hardware and functionality requirements. Moreover, HelioScan provides a software framework, within which new functionality can be implemented in a quick and structured manner. A specific HelioScan application assembles at run-time from individual software components, based on user-definable configuration files. Due to its component-based architecture, HelioScan can exploit synergies of multiple developers working in parallel on different components in a community effort. We exemplify the capabilities and versatility of HelioScan by demonstrating several in vivo brain imaging modes, including camera-based intrinsic optical signal imaging for functional mapping of cortical areas, standard two-photon laser-scanning microscopy using galvanometric mirrors, and high-speed in vivo two-photon calcium imaging using either acousto-optic deflectors or a resonant scanner. We recommend HelioScan as a convenient software framework for the in vivo imaging community.Paid Open Access
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Adya, Vandana. "Detection of Signal Parameters and Backscattering Polarimetric Imaging Signatures using Molecular Optical Contrast Agents and Preclinical Liquid Phantoms." University of Akron / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=akron1225204620.
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Khan, Sajjad. "Liquid Crystal Optics for Communications, Signal Processing and 3-D Microscopic Imaging." Doctoral diss., University of Central Florida, 2005. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/3389.
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This dissertation proposes, studies and experimentally demonstrates novel liquid crystal (LC) optics to solve challenging problems in RF and photonic signal processing, freespace and fiber optic communications and microscopic imaging. These include free-space optical scanners for military and optical wireless applications, variable fiber-optic attenuators for optical communications, photonic control techniques for phased array antennas and radar, and 3-D microscopic imaging. At the heart of the applications demonstrated in this thesis are LC devices that are non-pixelated and can be controlled either electrically or optically. Instead of the typical pixel-by-pixel control as is custom in LC devices, the phase profile across the aperture of these novel LC devices is varied through the use of high impedance layers. Due to the presence of the high impedance layer, there forms a voltage gradient across the aperture of such a device which results in a phase gradient across the LC layer which in turn is accumulated by the optical beam traversing through this LC device. The geometry of the electrical contacts that are used to apply the external voltage will define the nature of the phase gradient present across the optical beam. In order to steer a laser beam in one angular dimension, straight line electrical contacts are used to form a one dimensional phase gradient while an annular electrical contact results in a circularly symmetric phase profile across the optical beam making it suitable for focusing the optical beam. The geometry of the electrical contacts alone is not sufficient to form the linear and the quadratic phase profiles that are required to either deflect or focus an optical beam. Clever use of the phase response of a typical nematic liquid crystal (NLC) is made such that the linear response region is used for the angular beam deflection while the high voltage quadratic response region is used for focusing the beam. Employing an NLC deflector, a device that uses the linear angular deflection, laser beam steering is demonstrated in two orthogonal dimensions whereas an NLC lens is used to address the third dimension to complete a three dimensional (3-D) scanner. Such an NLC deflector was then used in a variable optical attenuator (VOA), whereby a laser beam coupled between two identical single mode fibers (SMF) was mis-aligned away from the output fiber causing the intensity of the output coupled light to decrease as a function of the angular deflection. Since the angular deflection is electrically controlled, hence the VOA operation is fairly simple and repeatable. An extension of this VOA for wavelength tunable operation is also shown in this dissertation. A LC spatial light modulator (SLM) that uses a photo-sensitive high impedance electrode whose impedance can be varied by controlling the light intensity incident on it, is used in a control system for a phased array antenna. Phase is controlled on the Write side of the SLM by controlling the intensity of the Write laser beam which then is accessed by the Read beam from the opposite side of this reflective SLM. Thus the phase of the Read beam is varied by controlling the intensity of the Write beam. A variable fiber-optic delay line is demonstrated in the thesis which uses wavelength sensitive and wavelength insensitive optics to get both analog as well as digital delays. It uses a chirped fiber Bragg grating (FBG), and a 1xN optical switch to achieve multiple time delays. The switch can be implemented using the 3-D optical scanner mentioned earlier. A technique is presented for ultra-low loss laser communication that uses a combination of strong and weak thin lens optics. As opposed to conventional laser communication systems, the Gaussian laser beam is prevented from diverging at the receiving station by using a weak thin lens that places the transmitted beam waist mid-way between a symmetrical transmitter-receiver link design thus saving prime optical power. LC device technology forms an excellent basis to realize such a large aperture weak lens. Using a 1-D array of LC deflectors, a broadband optical add-drop filter (OADF) is proposed for dense wavelength division multiplexing (DWDM) applications. By binary control of the drive signal to the individual LC deflectors in the array, any optical channel can be selectively dropped and added. For demonstration purposes, microelectromechanical systems (MEMS) digital micromirrors have been used to implement the OADF. Several key systems issues such as insertion loss, polarization dependent loss, wavelength resolution and response time are analyzed in detail for comparison with the LC deflector approach. A no-moving-parts axial scanning confocal microscope (ASCM) system is designed and demonstrated using a combination of a large diameter LC lens and a classical microscope objective lens. By electrically controlling the 5 mm diameter LC lens, the 633 nm wavelength focal spot is moved continuously over a 48 [micro]m range with measured 3-dB axial resolution of 3.1 [micro]m using a 0.65 numerical aperture (NA) micro-objective lens. The ASCM is successfully used to image an Indium Phosphide twin square optical waveguide sample with a 10.2 [micro]m waveguide pitch and 2.3 [micro]m height and width. Using fine analog electrical control of the LC lens, a super-fine sub-wavelength axial resolution of 270 nm is demonstrated. The proposed ASCM can be useful in various precision three dimensional imaging and profiling applications.Ph.D.
Optics and Photonics
Optics
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Morel, Sophie. "Imagerie grand champ en anatomopathologie." Thesis, Université Grenoble Alpes (ComUE), 2016. http://www.theses.fr/2016GREAY075/document.
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L’objectif de cette thèse a été de développer une méthode simple et rapide (35 minutes) d'imagerie afin d’enregistrer des images grand champ (jusqu’à 2,5 cm x 2,5 cm) et multi-échelles (µm-cm) de lames de tissus colorés et non colorés en anatomopathologie.La solution proposée est basée sur l’imagerie sans lentille. C’est une méthode simple, bas coût, qui permet d’enregistrer des images grand champ (10-30 mm²) d’objets épars, comme des virus, des bactéries ou des cellules. Dans ces travaux, nous montrons qu’il est possible d'obtenir en imagerie sans lentille des images d'objets denses tels que des lames de tissus colorés ou non marqués. Pour ce faire, l’échantillon est illuminé sous différentes longueurs d’onde, et un nouvel algorithme de reconstruction holographique multi-longueurs d’onde permet de reconstruire le module et la phase d’objets denses. Chaque image est reconstruite en 1,1 seconde couvrant un champ de 10 mm². Une image totale de la lame de tissu, couvrant un champ de 6,25 cm², est obtenue en 35 minutes en scannant l’échantillon au-dessus du capteur. Les images reconstruites sont multi-échelles, permettant à l’utilisateur d’observer en une seule fois la structure générale du tissu, et de zoomer jusqu’à la cellule individuelle (3-4 µm). La méthode a été testée sur différents échantillons anatomopathologiques colorés et non colorés. Au-delà des lames de tissus, l’imagerie sans lentille multi-longueurs d’onde montre des résultats encourageants pour le diagnostic de la méningite, le suivi au cours du temps d’une population bactérienne pour l’identification et la réalisation d’antibiogrammes, et le suivi au cours du temps de cultures cellulairesThis PhD project aims to develop a simple, fast (35 minutes), wide-field (up to 2.5 cm x 2.5 cm) multiscale (µm-cm) imaging method for stained and unstained tissue slides for digital pathology application. We present a solution based on lensfree imaging. It is a simple, low-cost technique that enables wide field imaging (10-30 mm²) of sparse objects, like viruses, bacteria or cells. In this project, we adapted lensfree imaging for dense objects observation, like stained or unstained tissue slides. The sample is illuminated under multiple illumination wavelengths, and a new multiwavelength holographic reconstruction algorithm was developed in order to reconstruct the modulus and phase of dense objects. Each image covers 10 mm² field of view, and is reconstructed in 1.1 second. An image of the whole tissue slide covers 6.25 cm². It is recorded in 35 minutes by scanning the sample over the sensor. The reconstructed images are multiscale, allowing the user to observe the overall tissue structure and to zoom down to the single cell level (3-4 µm). The method was tested on various stained and unstained pathology samples. Besides tissue slides, multiwavelength lensfree imaging shows encouraging results for meningitis diagnosis, bacteria population monitoring for identification and antibiotic susceptibility testing, and cell culture monitoring
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Akin, Ryan E. "Minimally invasive assessment of lymphatic pumping pressure using near infrared imaging." Thesis, Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/47536.
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Although the major functions of the lymphatic system are fairly well defined, its vasculature has yet to be well characterized in comparison to its blood vasculature counterpart. Recent advances in optical imaging techniques have allowed for more detailed and quantitative evaluations of lymph flow dynamics and mechanism. A rat tail is often used for investigations of lymph flow because of the simple geometry, superficial nature, and disease progression models of its collecting lymphatic vessels. In this study, a pressure cuff system was fabricated and coupled with an existing functional near infrared (NIR) imaging system to measure the overall pumping pressure of the lymphatic vessels of a rat tail. In addition to adapting the system for use on rodents, previous systems used for measuring lymphatic pumping pressure in humans were improved upon in several ways. The system defined here utilizes closed-loop feedback control of pressure application at smaller, more precise intervals. Using this device, a significant difference in lymphatic vessel pumping pressure was detected between a control case and a treatment case in which a vasoactive substance with a nitric oxide donor (GTNO ointment) was applied to the tail. Although it is known that nitric oxide plays a crucial physiologic role in propagation of flow through lymphatic vessels, this study has quantified its significant pharmacological reduction of pumping pressure for the first time.
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Qureshi, Muhammad Shakeel. "Integrated front-end analog circuits for mems sensors in ultrasound imaging and optical grating based microphone." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/29613.
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Thesis (Ph.D)--Electrical and Computer Engineering, Georgia Institute of Technology, 2009.Committee Chair: Hasler, Paul; Committee Co-Chair: Degertekin, Levent; Committee Member: Anderson, David; Committee Member: Ayazi, Farrokh; Committee Member: Brand, Oliver; Committee Member: Hesketh, Peter. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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Zenteno, Omar. "Markerless tracking of a fiber-optical probe by endoscopic vision : Towards multispectral enhanced biopsy." Thesis, Orléans, 2020. https://theses.univ-orleans.fr/public/2020ORLE3181_va.pdf.
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Un prototype d’endoscope augmenté d’une sonde multispectrale a été développé au moyen d’un fibroscope inséré dans le canal opérateur d’un système endoscopique commercial et connecté à une caméra multispectrale snapshot (41 bandes dans la gamme de 470 à 975 nm). La sonde multispectrale fonctionne comme une biopsie optique localisée pour une exploration médicale complémentaire avec un champ de vision beaucoup plus petit que l’endoscope. Cette thèse aborde le problème d’un recalage in vivo des images bimodales (RGB endoscope/MS fibroscope) afin de fournir au chirurgien une localisation précise de la biopsie dans l’image endoscopique pendant l’examen. Ce recalage est critique car l’absence de texture dans la paroi gastrique fait que les méthodes classiques exploitant une mise en correspondance des contenus des images échouent le plus souvent. De plus, par mesure d’asepsie, la sonde doit être retirée et nettoyée entre chaque patient. C’est pourquoi nous abordons le problème de recalage comme une estimation de pose relative entre deux caméras hétérogènes et non rigidement liées(endoscope et fibroscope). Les deux caméras peuvent être calibrées séparément à l’aide d’un motif en damier de sorte que leur pose relative instantanée puisse être estimée en suivant la caméra mobile (fibroscope). Pour ce faire, on profite de la présence du fibroscope dans les images endoscopiques et de sa géométrie. Ainsi, la pose du fibroscope est estimée en minimisant l’erreur de re-projection d’un cylindre virtuel en utilisant une pose estimée en quatre étapes : (i) la segmentation du fibroscope est réalisée à l’aide de modèles CNN formés sur nos séquences endoscopiques ; (ii) un axe de cylindre 3D est initialisé en utilisant la segmentation initiale et les coordonnées de Plücker ; (iii) l’estimation de la pose est optimisée en maximisant l’indice de similarité de Jaccard entre une segmentation automatique du fibroscope dans l’image et la projection du cylindre virtuel dans le cadre de référence endoscopique ; (iv) nous utilisons la pose des deux caméras pour estimer la transformation par homographie directe entre les points projetés virtuellement, ce qui permet d’obtenir un suivi sans marque. Cette approche a été validée en utilisant une simulation réaliste des mouvements du fibroscope à l’intérieur du canal opérateur (c’est-à-dire l’insertion et le béquillage) et les séquences in vivo acquises avec le prototype multimodal dans un centre médical. L’estimation en temps réel de la position relative entre les deux caméras permet au chirurgien de visualiser la zone ciblée par le fibroscope sur la paroi gastrique au cours de l’examen et de superposer les deux modalités d’images en donnant accès aux données spectrales pour la biopsie optique. Dans un processus hors ligne, il est également possible pour le suivi des patients de localiser les biopsies sur une carte panoramique construite par des techniques de mosaïquage d’images à partir de la vidéo endoscopique acquise lors de l’examen. D’une manière générale, la méthode proposée pour localiser la biopsie optique peut être étendue à n’importe quel type d’imagerie, en particulier pour une sonde sans marqueur et des images peu texturéesThis work addresses the problem of bi-modal registration to provide the surgeon with an accurate optical biopsy location in endoscopic frames during image guided examination. A multispectral-augmented endoscopic prototype was developed based on a commercial endoscopic system: A fiberscope is inserted into the operating channel and connected to a snapshot multispectral camera (41 bands in the range of 470 to 975 nm), working as a localized optical biopsy for a complementary medical exploration with a much smaller field of view. The registration between modalities is challenging due to the lack of texture in gastric wall which causes direct image-content registration methods to fail. Therefore, we approach the registration problem as a relative pose estimation between two non-homogeneous cameras (endoscope and fiberscope) not rigidly linked. Both cameras can be separately calibrated using a chessboard pattern so their instantaneous relative pose can be estimated by tracking the moving camera (fiberscope). To do this, we take advantage of the fiberscope presence in the endoscopic images and its geometry. Therefore, the pose of the fiberscope is estimated by minimizing the re-projection error of a virtual cylinder using a predicted pose in four steps: (i) the segmentation of the fiberscope is achieved through CNNs models trained on our endoscopic sequences;(ii) a 3D cylinder axis is initialized using the initial segmentation and Plücker’s coordinates;(iii) the pose estimate is optimized by maximizing Jaccard’s similarity index between an automatic segmentation of the fiberscope in the image and the virtual cylinder projection in the endoscopic reference frame; (iv) we use the pose of both cameras to estimate the transformation through direct homography between virtually projected points achieving a markerless tracking. This approach was validated using a virtual framework to realistically simulate the movements of the fiberscope inside the operating channel (i.e, insertion and precession) and in-vivo sequences acquired with our multimodal prototype in a medical center. The final registered images offer the surgeon real time visualization of the area targeted by the fiberscopeat the gastric wall and its corresponding spectral data. In an off-line process, it is also possible to locate the hyperspectral biopsy on a panoramic map constructed by image mosaicing techniques from the endoscopic video acquired during examination. In a general way, the proposed method for locating optical biopsy can be extended to any type of imaging, specially in the presence of poorly textured images or when markerless probe tracking is necessary, and could be valuable for patient monitoring
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Elsner, Mark Michael. "Analyse epileptischer Aktivität anhand intrinsischer optischer Signale und elektrophysiologischer Methoden in vitro nach Status epilepticus in vivo." Doctoral thesis, Humboldt-Universität zu Berlin, Medizinische Fakultät - Universitätsklinikum Charité, 2004. http://dx.doi.org/10.18452/15146.
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Eine wichtige Folge des Status epilepticus ist die Entwicklung einer chronischen Epilepsie. Die genauen Mechanismen und die Kinetik der Epileptogenese sind weitestgehend unklar. Ziel der vorliegenden Arbeit war ein besseres Verständnis des Prozesses durch die In-vitro-Analyse von Lokalisation und Kinetik funktioneller Folgen des Status epilepticus in vivo. In kombinierten Hippokampus-entorhinaler Kortex Hirnschnittpräparaten von Wistar-Ratten nach elektrisch induziertem selbsterhaltendem Status epilepticus (self-sustaining status epilepticus, SSSE) wurden im Niedrig-Magnesium-Modell anfallsartige Ereignisse (AE) ausgelöst und untersucht. Die In-vitro-Analyse der AE wurde eine, vier und acht Wochen nach SSSE durchgeführt. Um das räumliche Verhalten der epileptischen Aktivität beurteilen zu können, wurde die Messung des extrazellulären Feldpotenzials mit der Analyse intrinsischer optischer Signale kombiniert. Im Verlauf nach SSSE kam es zu einer Latenzverkürzung bis zum Auftreten epileptischer Aktivität und zu einer Zunahme der AE-Frequenz. Vier und acht Wochen nach SSSE stieg der Anteil der AE mit großflächigem Ursprung signifikant an. Im Verlauf nach SSSE wurden außerdem zunehmend diskontinuierliche Ausbreitungsmuster der Anfallsaktivität beobachtet. Acht Wochen nach SSSE zeigten 50% der Präparate zudem eine zeitlich und räumlich von den AE unabhängige, hochfrequente Aktivität im Gyrus dentatus. Zusammenfassend wurden eine Latenzverkürzung und eine Zunahme der AE-Frequenz als Hinweise für eine gesteigerte Exzitabilität des Hirngewebes nach SSSE gesehen. Neben dem großflächigen Ursprung deutet auch die Zunahme diskontinuierlicher Ausbreitungsmuster auf eine gesteigerte Synchronizität des neuronalen Netzwerkes nach SSSE hin. Die autonome Aktivität im Gyrus dentatus spricht dafür, dass die in vorangegangenen Studien beschriebenen strukturellen Änderungen in dieser Region mit einer veränderten Funktionalität einhergehen.The development of chronic epilepsy is a serious consequence of Status epilepticus. Little is known about the mechanisms and kinetic of the epileptogenic process. The aim of this md-thesis was the analysis of localisation and kinetic of functional deficits in vitro after Status epilepticus in vivo. Using the Low-Magnesium-Model, seizure-like events (SLE) were induced in combined hippocampal-entorhinal cortex slices of wistar rats after electrically induced self-sustaining Status epilepticus (SSSE). One, four and eight weeks after SSSE the in-vitro-analysis of SLE was performed. In order to determine onset and spread-pattern of epileptic activity, the measurement of the extracellular field-potential was combined with the imaging of intrinsic optical signals (IOS). In the time course after SSSE there was a reduction of the latency to onset of seizure activity and an increase of the SLE-frequency. Four and eight weeks after SSSE a significant increase of SLE with regional onset was found. In Addition, there was an increase of non-contiguous propagation of seizure activity. Eight weeks after SSSE 50% of the brain-slices showed autonomous high-frequent activity in the dentate gyrus. In conclusion a reduction of the latency to onset of seizure activity and an increase of the SLE-frequency were found. These changes are indicators of increased excitability after SSSE. Other than the regional onset, the non-contiguous spread-pattern also indicates increased synchronicity of the neuronal network after SSSE. The autonomous activity in the dentate Gyrus shows, that the previously described structural changes in this region lead to functional deficits.
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Hallum, Luke Edward Graduate School of Biomedical Engineering Faculty of Engineering UNSW. "Prosthetic vision : Visual modelling, information theory and neural correlates." Publisher:University of New South Wales. Graduate School of Biomedical Engineering, 2008. http://handle.unsw.edu.au/1959.4/41450.
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Electrical stimulation of the retina affected by photoreceptor loss (e.g., cases of retinitis pigmentosa) elicits the perception of luminous spots (so-called phosphenes) in the visual field. This phenomenon, attributed to the relatively high survival rates of neurons comprising the retina's inner layer, serves as the cornerstone of efforts to provide a microelectronic retinal prosthesis -- a device analogous to the cochlear implant. This thesis concerns phosphenes -- their elicitation and modulation, and, in turn, image analysis for use in a prosthesis. This thesis begins with a comparative review of visual modelling of electrical epiretinal stimulation and analogous acoustic modelling of electrical cochlear stimulation. The latter models involve coloured noise played to normal listeners so as to investigate speech processing and electrode design for use in cochlear implants. Subsequently, four experiments (three psychophysical and one numerical), and two statistical analyses, are presented. Intrinsic signal optical imaging in cerebral cortex is canvassed appendically. The first experiment describes a visual tracking task administered to 20 normal observers afforded simulated prosthetic vision. Fixation, saccade, and smooth pursuit, and the effect of practice, were assessed. Further, an image analysis scheme is demonstrated that, compared to existing approaches, assisted fixation and pursuit (but not saccade) accuracy (35.8% and 6.8%, respectively), and required less phosphene array scanning. Subsequently, (numerical) information-theoretic reasoning is provided for the scheme's superiority. This reasoning was then employed to further optimise the scheme (resulting in a filter comprising overlapping Gaussian kernels), and may be readily extended to arbitrary arrangements of many phosphenes. A face recognition study, wherein stimuli comprised either size- or intensity-modulated phosphenes, is then presented. The study involved unpracticed observers (n=85), and showed no 'size' --versus--'intensity' effect. Overall, a 400-phosphene (100-phosphene) image afforded subjects 89.0% (64.0%) correct recognition (two-interval forced-choice paradigm) when five seconds' scanning was allowed. Performance fell (64.5%) when the 400-phosphene image was stabilised on the retina and presented briefly. Scanning was similar in 400- and 100-phosphene tasks. The final chapter presents the statistical effects of sampling and rendering jitter on the phosphene image. These results may generalise to low-resolution imaging systems involving loosely packed pixels.
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Lindberg, Arvid. "Development of rigid polarimetric endoscope for early detection of cancer in vivo." Thesis, Institut polytechnique de Paris, 2020. http://www.theses.fr/2020IPPAX010.
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Le diagnostic précoce d’une lésion cancéreuse et l’ablation chirurgicale complète des zones malades restent les deux points cruciaux pour améliorer considérablement les chances de guérison d’un patient. Cependant la détection d’un cancer dans la phase initiale de son développement reste une tache très difficile à accomplir car liée à une prise aléatoire de biopsies alors que les parties pathologiques, à ce stade de la maladie, demeurent difficilement identifiables aux techniques d’imagerie classiques (imagerie visible, ultrasons, résonance magnétique, scanner rayon X, tomographie par émission de positrons). En plus l’évaluation des marges d’exérèse chirurgicale reste une tache encore très difficiles à accomplir, voire impossibles, dans certains cas.L’imagerie polarimétrique est une technique très prometteuse pour la détection précoce des lésions cancéreuses sur la surface des organes et pour une meilleure définition des limites de résection pendant la chirurgie. Les activités de recherche biomédicale développées à l’intérieur de l’équipe « Optique Appliquée et Polarimétrie » du LPICM sont centrées sur le développement d’imageurs polarimétriques de Mueller pour l’amélioration de la prise en charge des cancers épithéliaux, également appelés carcinomes, qui représentent le 80 – 90% de tous les cancers. A ce sujet le LPICM est porteur d’un projet financé par l’Institut National du Cancer (INCa) sur l’utilisation de l’imagerie polarimétrique pour l’amélioration de la prise en charge du cancer du col utérin à différents stades de son évolution. Actuellement une campagne extensive de mesures sur les lésions précancéreuses présentes au niveau du col utérin est en cours dans trois hôpitaux parisiens (Institut Gustave Roussy, Kremlin Bicêtre, Institut Mutualiste Montsouris). Cette étude ex vivo qui utilise un polarimètre de type Mueller grand champ en réflexion, va conduire à établir la performance du diagnostic de l’imagerie polarimétrique de Mueller, en termes de sensibilité et spécificité, comparée à celle fournie par les pathologistes et considérée comme le « gold standard » pour le diagnostic du cancer. Cette phase représente un point de départ pour l’utilisation in vivo de cette technique, car elle va apporter une connaissance précise des effets systématiques pouvant dégrader ses performances. A l’intérieur du projet INCa l’extension de la mesure du col utérin in vivo est prévue, utilisant un colposcope classique modifié pour obtenir les images polarimétriques de Mueller.L’endoscope est un autre instrument utilisé aussi pour diagnostiquer des lésions cancéreuses ou précancéreuses dans les muqueuses internes (œsophage, colon, rectum…). Le sujet de thèse proposé consiste à développer un endoscope polarimétrique de Mueller rigide et à établir ses performances. Le travail du doctorant comportera une partie d’instrumentation en optique, d’acquisition de données, de traitement de signal et d’évaluation de la performance statistique de la méthode. Le sujet de cette thèse se situe donc à l’interface entre la physique et le diagnostic médical et montre un fort potentiel de développement industriel avec un impact social significatifEarly diagnosis of a cancerous lesion and complete surgical resection of the diseased areas are both crucial points in order to greatly improve the chances for recovery of a patient. However, early detection of cancer is a very difficult task. It relies on random biopsies of suspicious areas which are not easy to identify at this stage of the disease using conventional imaging techniques (visible imaging, ultrasound, magnetic resonance, X-ray scanner, positron emission tomography). In addition, the correct evaluation of surgical resection margins remains often very difficult or even impossible in some cases.Polarimetric imaging is a promising technique for the early detection of cancerous lesions on the surface of the organs and for a better definition of the resection limits during surgery. Biomedical research activity, conducted within the 'Applied Optics and Polarimetry' team of the LPICM, focuses on the development of Mueller polarimetric imaging systems for improving the management of epithelial cancers, also known as carcinomas, which represent 80-90% of all cancers. In this regard the LPICM leads a project funded by the “Institut National du Cancer (INCa)”, on the use of Mueller polarimetric imaging for improving the management of cervical cancer at different stages of its evolution. At present an extensive series of ex vivo measurements is in progress in three different hospitals of Paris (Institut Gustave Roussy, Kremlin Bicêtre and Institut Mutualiste Montsouris). The final goal of this study is to evaluate the performance of Mueller polarimetric imaging technique in terms of sensitivity and specificity, while using an interpretation of corresponding histology slides by pathologists as a “golden standard” of cancer diagnostics. Ex vivo measurements provide a precise knowledge of the systematic effects which can negatively affect image quality. Hence, the results of this study represent a good starting point for in vivo applications of polarimetric imaging technique. Within the frame of INCa project the analysis of uterine cervix in vivo is planned, using a classical colposcope modified to obtain polarimetric Mueller images.The endoscope is another medical instrument used also to detect cancerous or precancerous lesions in the internal cavities of human body (esophagus, colon, rectum, etc.). The proposed thesis subject consists in developing a Mueller polarimetric rigid endoscope and evaluating its performance in terms of sensitivity and specificity. The work of PhD student will be concerned with instrumentation in optics, acquisition of data, signal processing and statistical evaluation of the performance of technique. Thus, the subject of this thesis is on the interface between physics and medical diagnostics and it shows a strong potential for industrial development with a significant societal impact
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Yoo, Thomas. "Application of a Multimodal Polarimetric Imager to Study the Polarimetric Response of Scattering Media and Microstructures." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLX106/document.
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Les travaux réalisés au cours cette thèse ont eu comme objectif l’étude de l’interaction de la lumière polarisée avec des milieux et des particules diffusants. Ces travaux s’inscrivent dans un contexte collaboratif fort entre le LPICM et différents laboratoires privés et publics. Des aspects très variées ont été traités en profondeur dont le développement instrumental, la simulation numérique avancée et la création de protocoles de mesure pour l’interprétation de donnés à caractère complexe.La partie instrumentale de la thèse a été consacrée au développement d’un instrument novateur, adapté à la prise d’images polarimétriques à différents échelles (du millimètre au micron) pouvant être rapidement reconfigurable pour offrir différents modes d’imagerie du même échantillon. Les deux aspects principaux qui caractérisent l’instrument sont i) la possibilité d’obtenir des images polarimétriques réelles de l’échantillon et des images de la distribution angulaire de lumière diffusé par une zone sur l’échantillon dont sa taille et position peuvent être sélectionnée par l’utilisateur à volonté, ii) le contrôle total de l’état de polarisation, de la taille et de la divergence des faisceaux utilisés pour l’éclairage de l’échantillon et pour la réalisation des images de celui-ci. Ces deux aspects ne se trouvent réunis sur aucun autre appareil commercial ou expérimental actuel.Le premier objet d’étude en utilisant le polarimètre imageur multimodal a été l’étude de l’effet de l’épaisseur d’un milieu diffusant sur sa réponse optique. En imagerie médicale il existe un large consensus sur les avantages de l’utilisation de différentes propriétés polarimétriques pour améliorer l’efficacité de techniques optiques de dépistage de différentes maladies. En dépit de ces avantages, l’interprétation des observables polarimétriques en termes de propriétés physiologiques des tissus se trouve souvent obscurcie par l’influence de l’épaisseur, souvent inconnue, de l’échantillon étudié.L’objectif des travaux a été donc, de mieux comprendre la dépendance des propriétés polarimétriques de différents matériaux diffusants avec l’épaisseur de ceux-ci. En conclusion, il a été possible de montrer que, de manière assez universelle, les propriétés polarimétriques des milieux diffusants varient proportionnellement au chemin optique que la lumière a parcouru à l’intérieur du milieu, tandis que le dégrée de polarisation dépend quadratiquement de ce chemin. Cette découverte a pu être ensuite utilisée pour élaborer une méthode d’analyse de données qui permet de s’affranchir de l’effet des variations d’épaisseur des tissus, rendant ainsi les mesures très robustes et liées uniquement aux propriétés intrinsèques des échantillons étudiés.Un deuxième objet d’étude a été la réponse polarimétrique de particules de taille micrométrique. La sélection des particules étudiées par analogie à la taille des cellules qui forment les tissus biologiques et qui sont responsables de la dispersion de la lumière. Grâce à des mesures polarimétriques, il a été découvert que lorsque les microparticules sont éclairées avec une incidence oblique par rapport à l’axe optique du microscope, celles-ci semblent se comporter comme si elles étaient optiquement actives. D’ailleurs, il a été trouvé que la valeur de cette activité optique apparente dépend de la forme des particules étudiées. L’explication de ce phénomène est basée sur l’apparition d’une phase topologique dans le faisceau de lumière. Cette phase topologique dépend du parcours de la lumière diffusée à l’intérieur du microscope. L’observation inédite de cette phase topologique a été possible grâce au fait que l’imageur polarimétrique multimodale permet un éclairage des échantillons à l’incidence oblique. Cette découverte peut améliorer significativement l’efficacité de méthodes optiques pour la détermination de la forme de micro-objetsThe work carried out during this thesis was aimed to study the interaction of polarized light from the scattering media and particles. This work is part of a strong collaborative context between the LPICM and various private and public laboratories. A wide variety of aspects have been treated deeply, including instrumental development, advanced numerical simulation and the creation of measurement protocols for the interpretation of complex data.The instrumental part of the thesis was devoted to the development of an innovative instrument, suitable for taking polarimetric images at different scales (from millimeters to microns) that can be quickly reconfigured to offer different imaging modes of the same sample. The two main aspects that characterize the instrument are i) the possibility of obtaining real polarimetric images of the sample and the angular distribution of light scattered by an illuminated zone whose size and position can be controlled, ii) the total control of the polarization state, size and divergence of the beams. These two aspects are not united on any other commercial or experimental apparatus today.The first object of the study using the multimodal imaging polarimeter was to study the effect of the thickness from a scattering medium on its optical response. In medical imaging, there is a broad consensus on the benefits of using different polarimetric properties to improve the effectiveness of optical screening techniques for different diseases. Despite these advantages, the interpretation of the polarimetric responses in terms of the physiological properties of tissues has been obscured by the influence of the unknown thickness of the sample.The objective of the work was, therefore, to better understand the dependence of the polarimetric properties of different scattering materials with the known thickness. In conclusion, it is possible to show that the polarimetric properties of the scattering media vary proportionally with the optical path that the light has traveled inside the medium, whereas the degree of polarization depends quadratically on the optical path. This discovery could be used to develop a method of data analysis that overcomes the effect of thickness variations, thus making the measurements very robust and related only to the intrinsic properties of the samples studied.The second object of study was to study the polarimetric responses from particles of micrometric size. The selection of the particles studied by analogy to the size of the cells that form the biological tissues, and which are responsible for the dispersion of light. By means of the polarimetric measurements, it has been discovered that when the microparticles are illuminated with an oblique incidence with respect to the optical axis of the microscope, they appear to behave as if they were optically active. Moreover, it has been found that the value of this apparent optical activity depends on the shape of the particles. The explanation of this phenomenon is based on the appearance of a topological phase of the beam. This topological phase depends on the path of the light scattered inside the microscope. The unprecedented observation of this topological phase has been done by the fact that the multimodal polarimetric imager allows illumination of the samples at the oblique incidence. This discovery can significantly improve the efficiency of optical methods for determining the shape of micro-objects
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Witomski, Arnaud. "Imagerie laser à synthèse d'ouverture par réinjection optique." Phd thesis, Grenoble 1, 2007. http://tel.archives-ouvertes.fr/tel-00144904.
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Nous présentons dans ce mémoire une technique d'imagerie laser à synthèse d'ouverture par réinjection optique. L'imageur de base, appelé Laser Optical Feedback Imaging (LOFI), détecte la faible quantité de lumière rétrodiffusée par la cible à analyser, qui est décalée en fréquence et réinjectée dans la source laser pour être amplifiée par la dynamique du laser. Le grand avantage de cette technique est qu'elle est auto-alignée, c'est à dire que le laser est à la fois la source et le détecteur. La résolution spatiale des images LOFI est limitée par la diffraction : nous proposons d'adapter la technique de synthèse d'ouverture, bien connue dans le domaine radar, pour nous affranchir de ce problème. En mettant à profit le balayage du laser sur la cible pour faire l'acquisition de l'image pixel par pixel, nous montrons qu'il est possible d'augmenter synthétiquement l'ouverture de collection du système et donc la résolution de l'image. Nous présentons le traitement du signal adapté à la reconstruction de l'image super-résolue à partir des données acquises pour les différentes positions successives du laser. Nous montrons qu'on peut étendre cette technique utilisée en balayage linéaire à un balayage angulaire et que nous pouvons obtenir une résolution, non seulement meilleure que la limite de diffraction, mais également meilleure que celle obtenue avec un balayage linéaire. Nous validons cette technique expérimentalement en comparant des images LOFI obtenues avec et sans synthèse d'ouverture.Nous présentons ensuite dans ce mémoire le dispositif LOFI en régime paramétrique soumis à une modulation de pompage. Nous présentons l'analyse d'un laser soumis de manière synchronisée à une réinjection optique décalée en fréquence et une modulation de pompage et nous montrons qu'il est possible d'amplifier paramétriquement le signal rétrodiffusé par la cible. Nous validons cette analyse par des résultats numériques et expérimentaux et nous démontrons qu'il est possible de déterminer la quantité de lumière réinjectée dans le laser.
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Fredenberg, Erik. "Spectral Mammography with X-Ray Optics and a Photon-Counting Detector." Doctoral thesis, KTH, Medicinsk avbildning, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-11641.
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Early detection is vital to successfully treating breast cancer, and mammography screening is the most efficient and wide-spread method to reach this goal. Imaging low-contrast targets, while minimizing the radiation exposure to a large population is, however, a major challenge. Optimizing the image quality per unit radiation dose is therefore essential. In this thesis, two optimization schemes with respect to x-ray photon energy have been investigated: filtering the incident spectrum with refractive x-ray optics (spectral shaping), and utilizing the transmitted spectrum with energy-resolved photon-counting detectors (spectral imaging). Two types of x-ray lenses were experimentally characterized, and modeled using ray tracing, field propagation, and geometrical optics. Spectral shaping reduced dose approximately 20% compared to an absorption-filtered reference system with the same signal-to-noise ratio, scan time, and spatial resolution. In addition, a focusing pre-object collimator based on the same type of optics reduced divergence of the radiation and improved photon economy by about 50%. A photon-counting silicon detector was investigated in terms of energy resolution and its feasibility for spectral imaging. Contrast-enhanced tumor imaging with a system based on the detector was characterized and optimized with a model that took anatomical noise into account. Improvement in an ideal-observer detectability index by a factor of 2 to 8 over that obtained by conventional absorption imaging was found for different levels of anatomical noise and breast density. Increased conspicuity was confirmed by experiment. Further, the model was extended to include imaging of unenhanced lesions. Detectability of microcalcifications increased no more than a few percent, whereas the ability to detect large tumors might improve on the order of 50% despite the low attenuation difference between glandular and cancerous tissue. It is clear that inclusion of anatomical noise and imaging task in spectral optimization may yield completely different results than an analysis based solely on quantum noise.QC 20100714
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Turley, Jordan Alexander. "An analysis of signal processing techniques for intrinsic optical signal brain imaging." Thesis, 2018. http://hdl.handle.net/1959.13/1383963.
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Masters Research - Master of Philosophy (MPhil)Intrinsic Optical Signal (IOS) imaging uses light in the visible spectrum to visualise activity related changes within the cerebral cortex. A limiting issue with IOS is the presence of large disturbance components. Appropriate signal processing is therefore important in obtaining quality IOS imaging results. Our aim was to simplify the choice of post processing techniques, by comparing a variety of those previously performed. To reach our goal, we have designed and constructed our own IOS imaging system, including hardware and software. We carried out preliminary tests on real mice to improve our understanding of the IOS imaging modality and the signal components involved. We then created a mathematical model of the mouse brains' IOS response and analysed the performance of a variety of signal processing techniques, including those typically applied to IOS imaging. Next, we compared these techniques on real imaging data. These include: averaging over trials, spatial Gaussian filtering, temporal low pass filtering, temporal band pass filtering, global signal regression, principal component analysis, truncated differences. We were particularly focused on comparing the effectiveness of each technique’s ability to remove noise and extract the IOS signal for both spatial and temporal responses, both quantitatively and qualitatively. We performed careful analysis of the techniques and the advantages and disadvantages are presented such that the best choice can be made for a given IOS imaging setup. Our results concluded that Gaussian filtering is the most effective choice for improving the spatial IOS response with minimal complexity. For temporal data, low pass filtering and band pass filtering provided a significant improvement over averaging with reasonable complexity, however if periodic stimuli is not possible, GSR or truncated difference should be considered as these techniques also significantly improve the signal and do not require a periodic stimuli. Other PCA variations can be considered but require careful consideration of the component selection technique to be used and are highly dependent on the quality of the raw data.
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Naderian, Azadeh. "Retinal optical imaging of intrinsic signals." Thèse, 2017. http://hdl.handle.net/1866/20273.
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Akhlagh, Moayed Alireza. "In vivo Imaging of Light Induced Intrinsic Optical Signals in the Chicken Retina with a Combined Ultra-High Resolution Optical Coherence Tomography and Electroretinography System." Thesis, 2012. http://hdl.handle.net/10012/7208.
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The main objective of this thesis is to investigate the intrinsic optical signals (IOSs) with an ultra-high resolution optical coherence tomography system (UHROCT). In order to study the retinal IOSs evoked by visible light, an UHROCT and an Electroretinogram (ERG) system was combined. An animal model (chicken retina) based on its retinal avascularity and cone dominance, was selected. Imaging the chicken retina with OCT resulted in high contrast, high resolution (~3μm axial and ~5 μm lateral resolution) 2D and 3D volumetric tomograms, in which all retina layers were clearly distinguishable. Using the combined UHROCT and ERG system to image IOSs from the chicken retina exposed to visible light (7ms green flash) resulted in highly reproducible IOS recordings from all retinal layers for the first time. All inner retinal layers showed an initial increase and subsequently a decrease in the intensity of the backreflected imaging light within the first 100 ms after the onset of the stimulus. Outer segments of the photoreceptors also showed a decrease in the backreflected imaging light within 100 ms after the onset of the flash. All retinal layers showed a strong decrease in the backreflected light within 150 to 175 ms after the onset of the flash. Imaging the pupil dynamics of the chicken with a modified combined UHROCT and ERG system showed that part of the strong negative IOSs observed in all retinal layers resulted from the vignetting of the imaging beam due to the light induced pupil constriction. Thorough analysis of the pupil dynamics acquired with UHROCT showed a time dependent effect of the anesthesia agent on pupil constriction. Further experiments to investigate an anesthesia effects on retinal function showed significant changes in ERG components. Statistical analysis showed that Isoflurane anesthesia severely affects the inner retinal response.
In conclusion, it was hypothesized that the fast IOSs within ~50-100 ms after the onset of the visual stimulus originated from the neuronal tissue in the retina and are related to tissue optical property changes as a result of the electrical signal propagation in the light activated retina. Longer term decreases in backreflected light are likely due to pupil changes.
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Ringuette, Dene. "Application of Vertical-cavity Surface-emitting Lasers for Simultaneous Laser Speckle Contrast and Intrinsic Optical Signal Imaging: Toward Chronic Portable Cortical Hemodynamic Imaging." Thesis, 2012. http://hdl.handle.net/1807/32620.
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We demonstrated simultaneous intrinsic optical signal imaging (IOSI) and laser speckle contrast imaging (LSCI) using coherence modulation of vertical-cavity surface-emitting laser (VCSEL) diodes. The unique properties of VCSELs were exploited to deliver rapidly switched coherent and non-coherent illumination suitable for high resolution LSCI and IOSI, respectively. Utilizing three near-infrared VCSELs we were able to map changes in cortical blood oxygenation and flow during ischemia. Additionally, the subtle reflectance changes associated with cortical spreading depression were imaged using non-coherent VCSEL illumination. We are currently using two-photon laser-scanning microscopy to quantify the accuracy of LSCI and IOSI implementations.
The small size and efficiency of VCSELs and modern photo diodes, makes the development of implantable dual-mode imaging devices feasible. Devices capable of chronic imaging of cortical hemodynamics could significantly enhance the range of studies available to neuroscientists and significantly aid clinicians postoperatively. The research presented in this thesis significantly furthers this objective.
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Guy, Julien. "Order under the guise of chaos: functional neuroanatomy of the somatosensory "barrel" cortex of the reeler mutant mouse." Doctoral thesis, 2015. http://hdl.handle.net/11858/00-1735-0000-0028-8752-9.
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Ranjbar-Salmloo, Yadollah. "Sensory coding in supragranular cells of the vibrissal cortex in anesthetized and awake mice." Phd thesis, 2017. http://hdl.handle.net/1885/147598.
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Sensory perception entails reliable representation of the
external stimuli as impulse activity of individual neurons (i.e.
spikes) and neuronal populations in the sensory area. An ongoing
challenge in neuroscience is to identify and characterize the
features of the stimuli which are relevant to a specific sensory
modality and neuronal strategies to effectively and efficiently
encode those features. It is widely hypothesized that the
neuronal populations employ “sparse coding” strategies to
optimize the stimulus representations with a low energetic cost
(i.e. low impulse activity). In the past two decades, a wealth of
experimental evidence has supported this hypothesis by showing
spatiotemporally sparse activity in sensory area. Despite
numerous studies, the extent of sparse coding and its underlying
mechanisms are not fully understood, especially in primary
vibrissal somatosensory cortex (vS1), which is a key model system
in sensory neuroscience. Importantly, it is not clear yet whether
sparse activation of supragranular vS1 is due to insufficient
synaptic input to the majority of the cells or the absence of
effective stimulus features.
In this thesis, first we asked how the choice of stimulus could
affect the degree of sparseness and/or the overall fraction of
the responsive vS1 neurons. We presented whisker deflections
spanning a broad range of intensities, including “standard
stimuli” and a high-velocity, “sharp” stimulus, which
simulated the fast slip events that occur during whisker mediated
object palpation. We used whole-cell and cell-attached recording
and calcium imaging to characterize the neuronal responses to
these stimuli. Consistent with previous literature, whole-cell
recording revealed a sparse response to the standard range of
velocities: although all recorded cells showed tuning to velocity
in their postsynaptic potentials, only a small fraction produced
stimulus-evoked spikes. In contrast, the sharp stimulus evoked
reliable spiking in a large fraction of regular spiking neurons
in the supragranular vS1. Spiking responses to the sharp stimulus
were binary and precisely timed, with minimum trial-to-trial
variability. Interestingly, we also observed that the sharp
stimulus produced a consistent and significant reduction in
action potential threshold.
In the second step we asked whether the stimulus dependent sparse
and dense activations we found in anesthetized condition would
generalize to the awake condition. We employed cell-attached
recordings in head-fixed awake mice to explore the degree of
sparseness in awake cortex. Although, stimuli delivered by a
piezo-electric actuator evoked significant response in a small
fraction of regular spiking supragranular neurons (16%-29%), we
observed that a majority of neurons (84%) were driven by manual
probing of whiskers. Our results demonstrate that despite sparse
activity, the majority of neurons in the superficial layers of
vS1 contribute to coding by representing a specific feature of
the tactile stimulus.
Thesis outline: Chapter 1 provides a review of the current
knowledge on sparse coding and an overview of the whisker-sensory
pathway. Chapter 2 represents our published results regarding
sparse and dense coding in vS1 of anesthetized mice
(Ranjbar-Slamloo and Arabzadeh 2017). Chapter 3 represents our
pending manuscript with results obtained with piezo and manual
stimulation in awake mice. Finally, in Chapter 4 we discuss and
conclude our findings in the context of the literature. The
appendix provides unpublished results related to Chapter 2. This
section is referenced in the final chapter for further
discussion.
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Stodieck, Sophia Katharina. "The role of postsynaptic density (PSD) proteins PSD-95 and PSD-93 for mouse visual cortical plasticity and vision." Doctoral thesis, 2016. http://hdl.handle.net/11858/00-1735-0000-0023-3F15-A.
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Shankar, Mohan. "Sampling and Signal Estimation in Computational Optical Sensors." Diss., 2007. http://hdl.handle.net/10161/445.
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Aksoylar, Aydan. "Modeling and model-aware signal processing methods for enhancement of optical systems." Thesis, 2016. https://hdl.handle.net/2144/19504.
Full textAbstract:
Theoretical and numerical modeling of optical systems are increasingly being utilized in a wide range of areas in physics and engineering for characterizing and improving existing systems or developing new methods. This dissertation focuses on determining and improving the performance of imaging and non-imaging optical systems through modeling and developing model-aware enhancement methods. We evaluate the performance, demonstrate enhancements in terms of resolution and light collection efficiency, and improve the capabilities of the systems through changes to the system design and through post-processing techniques. We consider application areas in integrated circuit (IC) imaging for fault analysis and malicious circuitry detection, and free-form lens design for creating prescribed illumination patterns.
The first part of this dissertation focuses on sub-surface imaging of ICs for fault analysis using a solid immersion lens (SIL) microscope. We first derive the Green's function of the microscope and use it to determine its resolution limits for bulk silicon and silicon-on-insulator (SOI) chips. We then propose an optimization framework for designing super-resolving apodization masks that utilizes the developed model and demonstrate the trade-offs in designing such masks. Finally, we derive the full electromagnetic model of the SIL microscope that models the image of an arbitrary sub-surface structure.
With the rapidly shrinking dimensions of ICs, we are increasingly limited in resolving the features and identifying potential modifications despite the resolution improvements provided by the state-of-the-art microscopy techniques and enhancement methods described here. In the second part of this dissertation, we shift our focus away from improving the resolution and consider an optical framework that does not require high resolution imaging for detecting malicious circuitry. We develop a classification-based high-throughput gate identification method that utilizes the physical model of the optical system. We then propose a lower-throughput system to increase the detection accuracy, based on higher resolution imaging to supplement the former method.
Finally, we consider the problem of free-form lens design for forming prescribed illumination patterns as a non-imaging application. Common methods that design free-form lenses for forming patterns consider the input light source to be a point source, however using extended light sources with such lenses lead to significant blurring in the resulting pattern. We propose a deconvolution-based framework that utilizes the lens geometry to model the blurring effects and eliminates this degradation, resulting in sharper patterns.
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Mathevula, Langutani Eulenda. "Optical and magnetic properties of rare earth Doped α-Fe2O3 for future bio-imaging applications." Thesis, 2018. http://hdl.handle.net/10500/26881.
Full textAbstract:
Imaging techniques have been developed for decades for the detection of biomolecules in
biomedicine cells, in vitro or in living cells and organisms. The application however, often
constrained by the available probes, whose optical properties may limit the imaging possibilities.
It is very essential to improve the sensitivity of these devices by enhancing efficiency to detection.
Recently, Fe3O4 has been used primarily in cancer theranostic application such as magnetic
resonance imaging (MRI). However, its toxicity towards normal cells has been pointed out by
scientific communities, when they are involved in in vitro (helics) cancer treatment. In this work,
we have chosen to use α-Fe2O3, because it has proven to be less toxic than Fe3O4. Hematite is
antiferromagnetic (AFM) at room temperature with a small canted moment lying within the crystal
symmetry plane. At low temperature, hematite undergoes a magnetic phase transition from weak
ferromagnetic (WFM) to a pure antiferromagnetic configuration (AF), which is known as the
Morin transition. This magnetic property makes it possible for hematite to be applied in imaging
technique. To enhance the optical properties, the α-Fe2O3 is doped with lanthanide ions due to their
unique optical properties. Incorporation of these rare earth ions, enable the α-Fe2O3 to have
enhance luminescence properties.
Imaging techniques have been developed for decades for the detection of biomolecules in
biomedicine cells, in vitro or in living cells and organisms. The application however, often
constrained by the available probes, whose optical properties may limit the imaging possibilities.
It is very essential to improve the sensitivity of these devices by enhancing efficiency to detection.
Recently, Fe3O4 has been used primarily in cancer theranostic application such as magnetic
resonance imaging (MRI). However, its toxicity towards normal cells has been pointed out by
scientific communities, when they are involved in in vitro (helics) cancer treatment. In this work,
we have chosen to use α-Fe2O3, because it has proven to be less toxic than Fe3O4. Hematite is
antiferromagnetic (AFM) at room temperature with a small canted moment lying within the crystal
symmetry plane. At low temperature, hematite undergoes a magnetic phase transition from weak
ferromagnetic (WFM) to a pure antiferromagnetic configuration (AF), which is known as the
Morin transition. This magnetic property makes it possible for hematite to be applied in imaging
technique. To enhance the optical properties, the α-Fe2O3 is doped with lanthanide ions due to their
unique optical properties. Incorporation of these rare earth ions, enable the α-Fe2O3 to have
enhance luminescence properties.
These lanthanide-doped nanoparticles (UCNPs) undergoes up-conversion process which have
remarkable ability to combine two or more low energy photons to generate a singly high energy
photon by an anti-stokes process and hold great promise for bio-imaging. These nanoparticles
exhibit excellent photostability, continuous emission capability and sharp multi-peak line
emission. With near infrared excitation, light scattering by biological tissues is substantially
reduced. α-Fe2O3 have been singly and co-doped with Holmium, Thulium, and Ytterbium by both
sol-gel and microwave methods. The doping of these lanthanides have shown improved
luminescent properties of α-Fe2O3. The up-conversion has been observed from co-doping Thulium
and Ytterbium. This work is a proof of concept to show the up-conversion in α-Fe2O3. However,
the up-conversion intensity is low about 200000 CPS maximum observed, this could be due to the
nature of the host structure quenching the luminescence. There is rather, a need to increase the
intensity for the maximum application to be achieved.Physics
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Nattar, Ranganath Gayathri. "Signal propagation in recurrent networks of mouse barrel cortex." Thesis, 2011. http://hdl.handle.net/2152/ETD-UT-2011-12-4577.
Full textAbstract:
Sensory signals are represented and propagated as spiking activity in multiple neuronal populations to lead to cognitive or motor behavior in organisms. Neural processing underlying sensory-motor behavior is understood by uncovering the governing computational principles and the biophysical mechanisms that implement the principles. While these mechanisms have been studied extensively at the single-neuron and system levels, activity within neuronal networks significantly impact neural processing. For example, there are spatiotemporal interactions (neural correlations) between responses of neurons within populations that could potentially impact signal representation and propagation. Furthermore, the effects of associative plasticity are also expected to alter network activity and its propagation. The effects of plasticity on network activity cannot be predicted from individual neuronal responses due to the complex, non-linear interactions within neuronal networks. Thus examining neural correlations in network activity and the propagation of network activity, requires recording spiking activity from large, heterogeneous, populations of spatially distributed neurons simultaneously. Studies addressing the propagation of network activity have been limited to theoretical approaches. Empirical studies have been limited by the technical difficulties in recording from a large number of neurons simultaneously. To overcome this challenge we developed a novel technique, dithered random-access functional calcium imaging. This imaging technique records and extracts suprathreshold activity from a large number of neurons. This technique also has a high spike detection efficiency and millisecond temporal precision. We applied this technique to measure the propagation of activity and neural correlations in activity evoked by afferent, thalamocortical inputs in the recurrent cortical networks of the mouse barrel cortex. We found that the cortical activity evoked by novel (naïve), thalamocortical inputs showed limited propagation of activity and decrease in propagation of neural correlations (measured from neuronal pairs within each population) from L4 to L2/3 network of the responding column. However, associative cortical plasticity was induced from pairing thalamocortical inputs with intracortical inputs. This pairing resulted in increased propagation of activity. The pairing also modified the propagation of neural correlations. Our results suggest that synaptic plasticity in intracortical circuits contributes to the modified propagation of activity and neural correlations. The modified propagation of neural correlations could in turn contribute to behavioral performance in vivo following perceptual learning.text
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Truong, Van Tri. "Optical imaging and two-photon microscopy study of hemodynamic changes contralateral to ictal focus during epileptiform discharges." Thèse, 2015. http://hdl.handle.net/1866/12441.
Full textAbstract:
Il est relativement bien établi que les crises focales entraînent une augmentation régionale du flot sanguin dans le but de soutenir la demande énergétique en hémoglobine oxygénée des neurones épileptiques. Des changements hémodynamiques précoces ont également été rapportés dans la région homologue controlatérale, bien que ceci ait été moins bien caractérisé. Dans cette étude, notre objectif est de mieux caractériser, lors de crises focales, la nature des changements hémodynamiques précoces dans la région homologue controlatérale au foyer épileptique. L'imagerie optique intrinsèque (IOI) et la microscopie deux-photons sont utilisées pour étudier les changements hémodynamiques dans la région homologue controlatérale au site de crises focales induites par l’injection de 4-aminopyridine (4-AP) dans le cortex somatosensitif ipsilatéral de souris. Dans l'étude d'IOI, des changements de l’oxyhémoglobine (HbO), de la désoxyhémoglobine (HbR) et du débit sanguin cérébral ont été observées dans la région homologue controlatérale au site de crises focales lors de toutes les crises. Toutefois, ces changements étaient hétérogènes, sans patron cohérent et reproduisible. Nos expériences avec la microscopie deux-photons n’ont pas révélé de changements hémodynamiques significatifs dans la région homotopique controlatérale lors de trains de pointes épileptiques. Nos résultats doivent être interprétés avec prudence compte tenu de plusieurs limitations: d’une part absence de mesures électrophysiologiques dans la région d’intérêt controlatérale au foyer simultanément à l’imagerie deux-photons et à l'IOI; d’autre part, lors des expériences avec le deux-photons, incapacité à générer de longues décharges ictales mais plutôt des trains de pointes, couverture spatiale limitée de la région d’intérêt controlatérale, et faible puissance suite au décès prématuré de plusieurs souris pour diverses raisons techniques. Nous terminons en discutant de divers moyens pour améliorer les expériences futures.It has been well demonstrated that focal seizures are associated with a significant increase in regional cerebral blood flow to actively supply discharging neurons with oxygenated hemoglobin. There is also some evidence to suggest that focal seizures elicit early hemodynamic changes in the contralateral homotopic area, although this has been less well documented. In this study, we aim to better characterize the nature of early hemodynamic responses contralateral to the epileptic focus during seizures. We used intrinsic optical imaging (IOI) and two-photon laser microscopy to measure the hemodynamic changes in the homotopic contralateral area following focal seizures induced by an injection of 4-aminopyridine (4-AP) in the mouse somatosensory neocortex. In the study using IOI, oxyhemoglobin (HbO), deoxyhemoglobin (HbR) and cerebral blood flow (CBF) changes were observed in the homotopic area contralateral to the focus during all seizures. However, these changes were rather heterogenous, lacking any consistent or reproducible pattern. Our two-photon study showed no significant hemodynamic changes at the capillary level in the homotopic area contralateral to the ictal focus during epileptic spike trains. However, these findings must be interpreted cautiously in light of several limitations we encountered during the experiments. Specifically, we were unable to simultaneously record electrophysiology in the contralateral homotopic area. Furthermore, during our two-photon experiments, we failed to induce long ictal discharges (inducing only spike trains) had a limited sampling of the contralateral homotopic area and reduced power as a result of low mice survival rate. We conclude by providing alternatives to possibly improve future experiments.
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Castonguay, Alexandre. "Modulation de l'activité de structures cérébrales sous-corticales par optogénétique." Thèse, 2013. http://hdl.handle.net/1866/10247.
Full textAbstract:
L’optogénétique est une technique prometteuse pour la modulation de l’activité neuronale. Par l’insertion d’une opsine microbienne dans la membrane plasmique de neurones et par son activation photonique, il devient possible de réguler l’activité neuronale avec une grande résolution temporelle et spatiale. Beaucoup de travaux ont été faits pour caractériser et synthétiser de nouvelles opsines. Ainsi, plusieurs variétés d’opsines sont désormais disponibles, chacune présentant des cinétiques et sensibilités à des longueurs d’onde différentes. En effet, il existe des constructions optogénétiques permettant de moduler à la hausse ou à la baisse l’activité neuronale, telles la channelrhodopsine-2 (ChR2) ou la halorhodopsine (NpHR), respectivement. Les promesses de cette technologie incluent le potentiel de stimuler une région restreinte du cerveau, et ce, de façon réversible. Toutefois, peu d’applications en ce sens ont été réalisées, cette technique étant limitée par l’absorption et la diffusion de la lumière dans les tissus.
Ce mémoire présente la conception d’une fibre optique illuminant à un angle de 90° à sa sortie, capable de guider la lumière à des structures bien précises dans le système nerveux central. Nous avons conduit des tests in vivo dans le système visuel de souris transgéniques exprimant la ChR2 dans l’ensemble du système nerveux central. Dans le système visuel, les signaux rétiniens sont conduits au corps genouillé latéral (CGL) avant d’être relayés au cortex visuel primaire (V1). Pour valider la capacité de mon montage optogénétique à stimuler spécifiquement une sous-population de neurones, nous avons tiré profit de l’organisation rétinotopique existant dans le système visuel. En stimulant optogénétiquement le CGL et en tournant la fibre optique sur elle-même à l’aide d’un moteur, il devient possible de stimuler séquentiellement différentes portions de cette structure thalamique et conséquemment, différentes représentations du champ visuel. L’activation des projections thalamiques sera enregistrée au niveau de l’aire V1 à l’aide de l’imagerie optique intrinsèque, une technique qui permet d’imager les variations de la concentration d’oxygène et du volume sanguin dans le tissu neuronal, sur une grande surface corticale. Comme l’organisation rétinotopique est maintenue au niveau de l’aire V1, l’espace activé au niveau du cortex révèlera l’étendue spatiale de notre stimulation optogénétique du CGL. Les expériences in vivo démontrèrent qu’en déplaçant la fibre optique dans le CGL, il nous était possible de stimuler différents sous- ensembles de neurones dans cette structure thalamique. En conclusion, cette étude montre notre capacité à développer un système à base de fibre optique capable de stimuler optogénétiquement une population de neurone avec une grande précision spatiale.Optogentics is a promising technic for neuronal activity modulation. By inserting a microbial opsin in the plasma membrane and by its photonic activation, it is possible to regulate neuronal activity with high temporal and spatial resolution. A lot of work has been done to characterize and synthetize new opsins. Thus, a wide variety of opsins are now available, presenting different kinetics and sensibility to specific wavelengths. Indeed, different opsins can either increase or decrease neuronal activity such as channelrhodopsin-2 (ChR2) or halorhodopsin (NpHR), respectively. This technology has the potential to stimulate a specific region within the brain in a highly reversible manner. However, little work was accomplished in this way, because to limitations due to absorption and scattering of light in biological tissue. This master’s thesis presents the conception of a side-firing optical fiber, capable of guiding light to specific structures within the brain. We conducted in vivo experiments in the visual system of transgenic mice expressing ChR2 in the entire central nervous system. In the visual system, retinal inputs are relayed to the lateral geniculate nucleus (LGN) before reaching the primary visual cortex (V1). To validate the capacity of the designed optogenetic assembly to stimulate specific sub-populations of neurons, we took advantage of the retinotopic organization existing in the visual system. By optogenetically stimulating the LGN and rotating the optical fiber around its axis with a motor, it is possible to sequentially stimulate different portions of this thalamic structure and consequently, different portions of the visual field. Activation of thalamic projections will be recorded in area V1 using intrinsic optical imaging, a technic allowing to image variations of blood oxygenation and blood volume in neuronal tissue over large cortical areas. Activation at the level of the cortex will reveal the spatial extent of the optogenetic stimulation in the LGN as retinotopic organization is maintained in V1 cortical area. In vivo experiments showed that displacing the optical fiber in the LGN allowed stimulation of different neuronal populations within this thalamic structure. In conclusion, this study demonstrates our capacity to develop a fiber-based system capable of optogenetically stimulating neuronal tissue with high spatial precision.
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Mané, Maria. "Spektrale Eigenschaften des intrinsischen optischen Signals während hypoxieinduzierter Spreading Depression im Hippokampus der Ratte." Doctoral thesis, 2011. http://hdl.handle.net/11858/00-1735-0000-0006-B204-0.
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Vanni, Matthieu P. "Les cartes fonctionnelles dans le cortex visuel du chat : nouvelles stratégies d’évaluation en imagerie optique et mise en évidence de l’organisation anatomo-fonctionnelle." Thèse, 2010. http://hdl.handle.net/1866/4105.
Full textAbstract:
Le regroupement des neurones de propriétés similaires est à l’origine de modules permettant d’optimiser l’analyse de l’information. La conséquence est la présence de cartes fonctionnelles dans le cortex visuel primaire de certains mammifères pour de nombreux paramètres tels que l’orientation, la direction du mouvement ou la position des stimuli (visuotopie).
Le premier volet de cette thèse est consacré à caractériser l’organisation modulaire dans le cortex visuel primaire pour un paramètre fondamental, la suppression centre / pourtour et au delà du cortex visuel primaire (dans l’aire 21a), pour l’orientation et la direction. Toutes les études ont été effectuées à l’aide de l’imagerie optique des signaux intrinsèques sur le cortex visuel du chat anesthésié.
La quantification de la modulation par la taille des stimuli à permis de révéler la présence de modules de forte et de faible suppression par le pourtour dans le cortex visuel primaire (aires 17 et 18). Ce type d’organisation n’avait été observé jusqu’ici que dans une aire de plus haut niveau hiérarchique chez le primate. Une organisation modulaire pour l’orientation, similaire à celle observée dans le cortex visuel primaire a été révélée dans l’aire 21a. Par contre, contrairement à l’aire 18, l’aire 21a ne semblait pas être organisée en domaine de direction. L’ensemble de ces résultats pourront permettre d’alimenter les connaissances sur l’organisation anatomo-fonctionnelle du cortex visuel du chat mais également de mieux comprendre les facteurs qui déterminent la présence d’une organisation modulaire.
Le deuxième volet abordé dans cette thèse s’est intéressé à l’amélioration de l’aspect quantitatif apporté par l’analyse temporelle en imagerie optique des signaux intrinsèques. Cette nouvelle approche, basée sur l’analyse de Fourier a permis d’augmenter considérablement le rapport signal / bruit des enregistrements. Toutefois, cette analyse ne s’est basée jusqu’ici que sur la quantification d’une seule harmonique ce qui a limité son emploi à la cartographie de l’orientation et de rétinotopie uniquement. En exploitant les plus hautes harmoniques, un modèle a été proposé afin d’estimer la taille des champs récepteurs et la sélectivité à la direction. Ce modèle a par la suite été validé par des approches conventionnelles dans le cortex visuel primaire.The clustering of neurons of similar properties is at the basis of the brain modular architecture and is considered as a strategy to optimized processing. One consequence of this clustering is the presence of functional maps in the primary visual cortex of several mammals based on features such as orientation, direction of motion and stimulus position (retinotopy). The first section of this thesis was aimed at characterizing the modular organization of functions in primary and higher-order areas. First, we investigated the possibility that a fundamental cell property, the receptive field center / surround suppression, could be orderly represented in the primary visual cortex. Second, we determined the level of modular organization in area 21a for two key properties, orientation and direction of motion. All studies were based on the optical imaging of intrinsic signals in anesthetized cats. Results indicate the presence of high and low surround suppression modules in the primary visual cortex (areas 17 and 18). To date, such organization has been discovered only in a higher-order area in primate. A modular organization for orientation, similar to the one observed in areas 17 and 18 was observed in area 21a. On the other hand, in contrast to area 18, no direction modules were discovered in area 21a. Overall, the first part of this thesis increased our knowledge about the anatomo-fonctional organization of cat visual cortex. They will also be instrumental to better understand the factors leading to the presence of a modular organization in the cortex. The second section of this thesis was directed to the development of a novel quantitative tool for the temporal analysis of optical imaging intrinsic signals. This new approach, based on Fourier decomposition, allowed to greatly increase the signal to noise ratio of the recordings. Until now, this analysis was only been based on single harmonic quantification, limiting its application for orientation and rétinotopy mapping only. A model exploiting higher harmonics was then developed to estimate additional parameters such as the receptive field size and direction selectivity. Thereafter, this model was validated with success by conventional approaches on the primary visual cortex.
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Haller, Mirjam. "Structure and function of KATP-channels in inspiratory neurons of mice." Doctoral thesis, 2000. http://hdl.handle.net/11858/00-1735-0000-0006-B5A4-C.
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