Dissertations / Theses on the topic 'Imaging systems in biology'
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1
Lux, Matthew William. "Estimation of gene network parameters from imaging cytometry data." Diss., Virginia Tech, 2013. http://hdl.handle.net/10919/23082.
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Synthetic biology endeavors to forward engineer genetic circuits with novel function. A major inspiration for the field has been the enormous success in the engineering of digital electronic circuits over the past half century. This dissertation approaches synthetic biology from the perspective of the engineering design cycle, a concept ubiquitous across many engineering disciplines. First, an analysis of the state of the engineering design cycle in synthetic biology is presented, pointing out the most limiting challenges currently facing the field. Second, a principle commonly used in electronics to weigh the tradeoffs between hardware and software implementations of a function, called co-design, is applied to synthetic biology. Designs to implement a specific logical function in three distinct domains are proposed and their pros and cons weighed. Third, automatic transitioning between an abstract design, its physical implementation, and accurate models of the corresponding system are critical for success in synthetic biology. We present a framework for accomplishing this task and demonstrate how it can be used to explore a design space. A major limitation of the aforementioned approach is that adequate parameter values for the performance of genetic components do not yet exist. Thus far, it has not been possible to uniquely attribute the function of a device to the function of the individual components in a way that enables accurate prediction of the function of new devices assembled from the same components. This lack presents a major challenge to rapid progression through the design cycle. We address this challenge by first collecting high time-resolution fluorescence trajectories of individual cells expressing a fluorescent protein, as well as snapshots of the number of corresponding mRNA molecules per cell. We then leverage the information embedded in the cell-cell variability of the population to extract parameter values for a stochastic model of gene expression more complex than typically used. Such analysis opens the door for models of genetic components that can more reliably predict the function of new combinations of these basic components.Ph. D.
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Xu, Jingjiang, and 许景江. "Development of advanced label-free optical bioimaging technologies." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/206437.
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Today label-free bioimaging has been leading to widespread and fast-growing applications, which demands for a more efficient way to keep up such momentum. To this end, the research in this thesis will study the techniques of efficiency improvement for advanced label-free bioimaging, including the time efficiency, cost efficiency and information efficiency.
Optical coherence tomography (OCT) is one of the most valuable label-free bioimaging modalities to provide noninvasive cross-sectional assessment of biological tissue. In many occasions, these applications demand for three dimensional (3D) imaging at video-rate in order to perform real-time diagnoses, which can be overcome by MHz-OCT. Here we demonstrate inertia-free all-optical ultrahigh-speed swept-source optical coherence tomography (OCT) based on amplified optical time-stretch (AOT). More importantly, the key significance of AOT-OCT is its broadband amplification stage, which greatly enhances the detection sensitivity compared with the prior attempts to employ optical time-stretch to OCT. We report an AOT-OCT system which is operated at an A-scan rate of multi-megahertz with high sensitivity (>80 dB) and perform time-stretch-based OCT of biological tissue in vivo. Moreover, using a more stable and coherent mode-locked fiber laser, we can achieve better performance without the compromise of averaging for supercontinuum-generation-based AOT-OCT system. It represents a major step forward in utilizing AOT as an alternative for achieving practical time-efficient OCT imaging at multi-MHz speed.
For the further development of this ultrahigh-speed OCT, we present a theoretical analysis of the AOT-OCT system. The spectral resolution, coherence length and sensitivity of AOT-OCT system have been discussed in detail. By theoretical model of the noise sources based on Raman amplifier, we also quantify how the input signal, amplifier gain, A-scan rate affect the sensitivity of AOT-OCT imaging. These simulation results are expected to be valuable for optimizing the design of AOT-OCT.
We also investigate in cost-effective implementation to realize efficient optical time-stretch process based on dispersive fiber. We explore and demonstrate the feasibility of using the standard telecommunication single-mode fibers as few-mode fibers (FMFs) for optical time-stretch confocal microscopy in the 1m range. It can provide sufficiently high dispersion-to-loss ratios for practical time-stretch imaging at 1 m, without the needs for high-cost specialty 1 m single mode fiber.
In addition, Coherent anti-Stokes Raman scattering (CARS) microscopy is another attractive efficient tool for label-free biochemical-specific imaging, which can bypass laborious steps of preparing and staining in routine standard histopathology. Here we further explore ultrabroadband hyperspectral multiplex (HM-CARS) to perform chemoselective histological imaging with efficient information in fingerprint region. In order to unravel the congested CARS spectra, we employ phase-retrieval algorithm based on Kramers–Kronig (KK) transform and principal component analysis (PCA) to display the key cellular structures with components distribution.
All these research efforts are aiming at improving the efficiency, from theory to implementation, for label-free bioimaging technology such as OCT and CARS. These schemes demonstrate great potential to realize powerful label-free bioimaging with high efficiency, including ultrafast 3D OCT imaging at video-rate, cost-effective optical time-stretch imaging and HM-CARS imaging with richness of biological fingerprint information.published_or_final_version
Electrical and Electronic Engineering
Doctoral
Doctor of Philosophy
3
Fung, David Cho Yau. "Visualization and analysis of gene expression in bio-molecular networks." Phd thesis, Faculty of Engineering and Information Technologies, 2010. http://hdl.handle.net/2123/9325.
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Patrick, Peter Stephen. "The development of reporter genes for in vivo imaging." Thesis, University of Cambridge, 2014. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708002.
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Dubaj, Vladimir, and n/a. "Novel optical fluorescence imaging probe for the investigation of biological function at the microscopic level." Swinburne University of Technology, 2005. http://adt.lib.swin.edu.au./public/adt-VSWT20060905.084615.
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Existing optic fibre-bundle based imaging probes have been successfully used to image
biological signals from tissue in direct contact with the probe tip (Hirano et al. 1996).
These fibre-bundle probe systems employed conventional fluorescence microscopy and
thus lacked spatial filtering or a scanned light source, two features used by laser
scanning confocal microscopes (LSCMs) to improve signal quality. Improving the
methods of imaging tissue in its natural state, deep in-vivo and at cellular resolution is
an ever-present goal in biological research. Within this study, a novel (580 μm
diameter) optic fibre-bundle direct-contact imaging probe, employing a LSCM, was
developed to allow for improved imaging of deep biological tissue in-vivo. The new
LSCM/probe system possessed a spatial resolution of 10 μm, and a temporal resolution
of 1 msec. The LSCM/probe system was compared to a previously used direct-contact
probe system that employed a conventional fluorescence microscope. Quantitative and
qualitative data indicated that the LSCM/probe system possessed superior image
contrast and quality. Furthermore, the LSCM/probe system was approximately 16 times
more effective at filtering unwanted contaminating light from regions below the
imaging plane (z-axis). The unique LSCM/probe system was applied to an exploratory
investigation of calcium activity of both glial and neuronal cells within the whisker
portion of the rat primary somatosensory cortex in-vivo. Fluorescence signals of 106
cells were recorded from 12 female Sprague Dawley rats aged between 7-8 weeks.
Fluo-3(AM) fluorophore based calcium fluctuations that coincided with 10 - 14 Hz
sinusoidal stimulation of rat whiskers for 0.5-1 second were observed in 8.5% of cells (9
of 106). Both increases and decreases in calcium levels that coincided with whisker
stimulation were observed. Of the 8.5 % of cells, 2.8% (3 cells) were categorized as
glial and 5.7% (6 cells) as neuronal, based on temporal characteristics of the observed
activity. The remaining cells (97 of 106) displayed sufficient calcium-based intensity
but no fluctuations that coincided with an applied stimulus. This was partially attributed
to electronic noise inherent in the prototype system obscuring potential very weak cell
signals. The results indicate that the novel LSCM/probe system is an advancement over
previously used systems that employed direct-contact imaging probes. The miniature
nature of the probe allows for insertion into soft tissue, like a hypodermic needle, and
provides access to a range of depths with minimal invasiveness. Furthermore, when
combined with selected dyes, the system allows for imaging of numerous forms of
activity at cellular resolution.
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Seniya, Chandrabhan. "A flexible low-cost quantitative phase imaging microscopy system for label-free imaging of multi-cellular biological samples." Thesis, University of Warwick, 2018. http://wrap.warwick.ac.uk/106451/.
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In this thesis, a flexible low-cost quantitative phase imaging microscopy (LQPIM) system for imaging both thin and thick biological phase objects in a non-contact, non-invasive, and label-free manner is reported. LQPIM optics was developed based on classical Zernike’s phase contrast approach and an additional phase shifting module to introduce user-defined phase modulations by utilising standard optical components. The phase shifting was performed using twin concentric mirrors or laser cut apertures in the arms of a Michelson interferometer where the reference mirror can be moved in / n steps (n - number of steps) with a piezoelectric transducer. Hence, the optical phase shifting modules are 10 - 15% (approximately) of the cost compared to the more widely reported modules based on spatial light modulator. In the microscope implementation reported in this thesis, a total magnification of 25x was achieved utilising relay lenses in LQPIM optics together with a standard 10x objective lens. The imaging system was simulated in MATLAB, where two-beam interference equation with varying bandwidth (1 – 250 nm), centre wavelength (450 – 650 nm) of the illumination sources and a range of previously reported phase shift algorithms (PSA) were used. The simulation results confirm that the optimum phase resolution is achievable if a broadband source of bandwidth 30 - 50 nm is used for illuminating thin (i.e. ≤ 250 nm) and thick (i.e. ≥ 1250 nm) biological samples. The four frames at 90 PSA and six plus one frames at 60 PSA offer different compromises between image acquisition time, phase resolution and out-perform other PSAs. A phase resolution of 0.382 nm and 0.317 nm was achieved using four frames at 90 and six plus one frames at 60 PSAs, respectively for the broadband illumination from a green LED. A coherent, single longitudinal mode laser source with a rotating diffuser for speckle averaging, gave 0.667 nm and 0.512 nm phase resolution using the same algorithms mentioned above. The parasitic fringes resulted in reduced resolution; hence, incoherent LED illumination was preferred. Measurements are presented over a longer optical path difference (≥ 1250 nm) than hitherto reported for a similar microscope. The given exemplar data demonstrates an ability of LQPIM system to quantify cellular and sub-cellular structures at the nanoscale in epidermis cells of Allium cepa. Key words: Quantitative phase imaging, low-cost, optical microscopy, phase imaging and phase shift imaging.
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Ho, Ka-kin, and 何家健. "Diethylenetriaminepentaacetic acid (DTPA) based lanthanide (III) complexes for bioimaging application." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B49799344.
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In this work, a series of DTPA based Ln complexes containing one or two chromophores with different degrees of conjugation were synthesized. The proton relaxivities of Gd(III) analogues were investigated as potential MRI contrast agents while the photoluminescence of Eu(III) and Tb(III) analogues were studied for their applications in optical probes for cellular imaging. Later investigation indicates that only emissions from the chromophores could be measured upon long wavelength photon excitations in the microscope. With suitable ligand design, novel dual functional imaging probes were finally synthesized and these showed good luminescence intensity and image contrast in both in-vivo and in-vitro studies.
Eight DTPA based Ln (III) complexes LnL1-L8 containing one or two chromophores which include benzene, 2-aminopyridine, 3-amino-pyridine and 4-aminopyridinewere synthesized. The syntheses, relaxometric properties, hydration numbers, quantum yields, sensitization efficiencies, brightnesses, cytotoxicities and cellular uptake properties were discussed. Those mono-substituted complexes show higher relaxivity, while the di-substituted complexes show lower relaxivity than Gd-DTPA (4.17 mM-1 s-1),a clinically used MRI contrast agent(CA).The di-substituted Tb(III)/Eu(III) analogues show lower sensitization efficiency than the mono-substituted ones in the energy transfer process. Therefore, the experimental results clearly illustrate that the complex with one chromophorein the DTPA system is a better option for being used as a MRI contrast agent and an optical probe.
Another eight new mono-substituted DTPA based Ln(III) complexes LnL9-L16 containing extended conjugated chromophores were synthesized and investigated. The phenyl derivatives and naphthyl derivatives were added onto the para-position of 2-aminopyridine that was employed as the chromophore. All GdL9-L16possess one bound water molecule and show higher relaxivity than Gd-DTPA. The relaxivities at 300 MHz at 25oC are in the descending order of GdL15(5.37 mM-1s-1) > GdL16(5.23 mM-1s-1) > GdL13(5.12 mM-1s-1) > GdL14(5.06 mM-1s-1) > GdL11(4.96 mM-1s-1) > GdL12(4.83 mM-1s-1) > GdL10(4.80 mM-1s-1) > GdL9(4.50 mM-1s-1). Their quantum yields, sensitization efficiencies and brightnesses are greatly improved because of the highly conjugated chromophores. Moreover, they all showed low cytotoxicity to cells in a MTT assay and a high accumulation in cells in cellular uptake studies. However, no emission from the Eu(III) ion was detected from the Eu(III) analogues upon long wavelength photon excitation in the cell imaging studies, only the emissions from the chromophores were observed.
Two mono-substituted DTPA based Ln(III) complexes containing anthracenyl derivatives as the chromophore LnL17-L18 and two DTPA-based binuclear Ln(III) complexes LnL19-L20were synthesized and investigated. Among the four complexes, GdL18 shows the highest relaxivity (4.65 mM-1s-1) and the highest fluorescent quantum yield (2.45%).It also has low cytotoxicity to cells in MTT assay and high accumulation in cells in cellular uptake study. In addition, GdL18shows very strong binding interaction towards serum albumin, i.e. 318,400mol-1dm3for HSA and 90,200 mol-1dm3for BSA. In preliminary studies, GdL18can both give good luminescence intensity and image contrast in both in vitro cell imaging and in vivo MRI studies. Therefore, GdL18 is considered as a potential candidate for use as a dual functional MRI/optical imaging probe.published_or_final_version
Chemistry
Doctoral
Doctor of Philosophy
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Hall, David Jonathan. "The development of a near infrared time resolved imaging system and the assessment of the methodology for breast imaging." Thesis, University College London (University of London), 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.243779.
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Kujala, Naresh Gandhi Yu Ping. "Frequency domain fluorescent molecular tomography and molecular probes for small animal imaging." Diss., Columbia, Mo. : University of Missouri--Columbia, 2009. http://hdl.handle.net/10355/7021.
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Title from PDF of title page (University of Missouri--Columbia, viewed on Feb 26, 2010). The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file. Dissertation advisor: Dr. Ping Yu. Vita. Includes bibliographical references.
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Roy, Debashish. "3D Cryo-Imaging System For Whole Mouse." Case Western Reserve University School of Graduate Studies / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=case1259006676.
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Richards, Christopher I. "Dynamic dark state depletion." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/31831.
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Thesis (Ph.D)--Chemistry and Biochemistry, Georgia Institute of Technology, 2010.Committee Chair: Dickson, Robert; Committee Member: Fahrni, Christoph; Committee Member: Payne, Christine; Committee Member: Petty, Jeff; Committee Member: Srinivasarao, Mohan. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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Ma, Yun. "Photofunctional molecular materials for chemical sensing, bioimaging and electrochromic applications." HKBU Institutional Repository, 2015. https://repository.hkbu.edu.hk/etd_oa/206.
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This thesis is dedicated to developing novel photofunctional molecular materials for the applications in chemical sensing, bioimaging and electrochromic. To begin with, a brief introduction of photofunctional molecular materials and an overview of their applications in chemical sensing, bioimaging and electrochromic were presented in Chapter 1. In chapter 2, we have synthesized a series of water-soluble phosphorescent cationic iridium(III) solvato complexes (1-7) as multicolor cellular probes for imaging in living cells. All of these complexes can be dissolved in PBS. The emission of complexes can be tuned from green to red by changing the chemical structure of cyclomedtalating ligands. All complexes exhibit low cytotoxicity to living cells and exhibit cell membrane permeability and specific staining of cytoplasm. They enter the cells by the mechanism of energy-independent passive diffusion mechanisms. More importantly, complex 7 can act as a two-photon phosphorescent cellular probe, and fluorescence lifetime imaging microscopy is successfully applied for bioimaging in the presence of short-lived background fluorescence. We developed two excellent optical probes for CO2 detection in Chapter 3. The first one for the CO2 detection is a phosphorescent probe based on an iridium(III) complex with 2-phenylimidazo-[4,5-f][1,10]phenanthroline. After bubbling CO2 into the detection solution, the quenched phosphorescence by the addition of CH3COO can be recovered. Photobleaching experiment demonstrates that this phosphorescent CO2 probe shows higher photostability than some of the reported organic probes. More importantly, the time-resolved PL experiment demonstrates that this probe can be used to detect CO2 in the presence of strong background fluorescence, which improves the sensitivity and signal-to-noise ratio of the sensor in complicated media. The second one is a water-soluble fluorescent probe based on tetraphenylethene derivative. After bubbling CO2 into the detection solution, remarkable color change and fluorescence enhancement could be observed. The response of this probe to CO2 in aqueous solution is fast and the detection limit is about 2.4 × 106 M. To emphasize the practical application of this probe, a porous film was successfully fabricated by mixing the dye with sodium carboxymethyl cellulose in water, which can serve as an efficient CO2 gas sensor. More importantly, this probe exhibits low cytotoxicity towards live cells and has the ability to monitor the external CO2 concentration changes of living cells. Chapter 4 focused on the development of novel soft salt based phosphorescent probe. This type of probe consists of two oppositely charged ionic complexes with two distinguishable emission colors, which makes it a perfect candidate as a ratiometric probe. The emission color of 10 changes from blue to red with increasing pH value. 10 is cell-permeable and exhibits low cytotoxicity, and it has been successfully applied for ratiometric pH imaging with the use of confocal microscopy, demonstrating its great potential for intracellular environment monitoring. Furthermore, phosphorescence lifetime imaging experiments can detect intracellular pH variations by photoluminescence lifetime measurements, which allowed for eliminating background fluorescence and selecting long-lived phosphorescence images. Quantitative measurement of intracellular pH fluctuations caused by oxidative stress has been successfully carried out for 10 based on the pH-dependent calibration curve. A series of cationic Zn(II) complexes has been designed and synthesized in chapter 5. The photophysical properties of these Zn(II) complexes are affected by the counterions. By altering the counterions, the emission peak can be changed from 549 nm to 622 nm. Interestingly, the CIE coordinate and the emission colors can be simply tuned by adjusting the concentration of 11d in the polyether. Under an electric field of about 15 V applied onto the electrodes, the emission color of the solution of 11b-11d near the cathode changed its original emission color to sky blue. Based on this interesting electrochromic fluorescence of 11d, a quasi-solid information recording device has been successfully designed. Furthermore, data encryption has been realized by combining 1d with BODIPY, and information decoding processed has been accomplished, for the first time, by employing TPA excitation techniques, in which the large TPA cross section of 11d is differentiated from small TPA cross section of common organic dyes. Finally, Chapters 6 and 7 present the concluding remarksand the experimental details of the work described in Chapters 25
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Sanchez, Gonzalez Veronica. "Development of the cardiovascular system through the «in-vivo» imaging of FLK-1-GFP positive cells." Thesis, McGill University, 2014. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=121585.
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The mouse Flk-1 gene encodes for vascular endothelial growth factor receptor 2 (VEGFR-2), the receptor for vascular endothelial growth factor A (VEGF-A). This gene is essential for the development of the vascular system. In the early embryo, Flk-1 expression marks angioblasts and subsequent endothelial cells. Flk-1-/- embryos die at E8.5-9.5 and fail to develop the blood island, endocardium, dorsal aortae, intersomitic vessels, and capillaries. This gene product is required for endothelial cell development as well as for primitive and definitive erythrocyte differentiation. Flk-1-/- cells locate to the amnion, where it is not normally expressed. It is accepted that FLK-1 positive cells contribute to the formation of the endocardium as well as the embryonic vasculature and the extraembryonic yolk sac vasculature; however, the origins of these individual populations remain unknown. We hypothesize FLK-1 positive cells contributing to different lineages originate from different areas and behave differently; therefore, the aim of this project is to identify the origins of endothelial progenitors and study their behavior during their contribution to the cardiovascular system.Live-imaging microscopy analysis allows temporal and spatial observation of natural processes. Using the Flk-1-GFP mouse reporter line, heterozygous and homozygous embryos were used to live-image embryos from E7.5 to E8.5. The origins of endothelial cells forming the cardiovascular system were retrospectively identified with the use of software programs. The process of formation was then compared to that of Flk-1GFP/GFP mutant embryos.Live-imaging analysis of embryos during the streak stages showed the appearance of Flk-1- GFP+ cells laterally to the primitive streak. These cells then expanded embryonically and extraembryonically. During the head-fold stages, embryos showed a small population of Flk-1-GFP positive cells actively migrating from the embryonic-extraembryonic boundary into the embryonic region to form the dorsal aortae. During the migration, the cells aggregated and luminal structures were formed. The embryonic dorsal aortae form as these small luminal structures aggregated, lined laterally to the embryo midline. We also identified that endocardium progenitors originate from a region more anterior than dorsal aortae angioblasts. The majority of Flk-1-GFP+ cells in the extraembryonic region become part of the yolk sac vasculature. Flk-1GFP/GFP embryos appeared normal during the streak stages; however, during the head-fold stages, Flk-1-GFP+ cells showed lack of migration and failed to form vascular structures. The cells were located within the amnion, the base of the allantois, the cardiac mesoderm, and the extraembryonic region. The heart tube formed although the endocardium was absent. These data show the origins and contribution of Flk-1-GFP cells during gastrulation. Moreover, Flk-1 was found to be dispensable for the migration of mesodermal cell from the primitive streak and essential for angioblast migrationLe gène murin Flk-1 code pour le récepteur 2 du facteur de croissance endothélial vasculaire (VEGFR-2), récepteur au facteur de croissance endothélial vasculaire A (VEGF-A). Ce gène est essentiel au développement du syolk sactème cardiovasculaire. Au stade initial du développement de l'embryon, Flk-1 est exprimé sur les angioblastes, et sur les cellules endothéliales qui en sont issues. Chez les embryons Flk1-/- on constate la mort à E8.5-9.5, et l'absence de développement des îlots vasculaires, de l'endocarde, de l'aorte dorsale, des vaisseaux intersomitiques et des capillaires. Le produit de ce gène est nécessaire au développement des cellules endothéliales, ainsi qu'à la différenciation primitive et définitive des érythrocytes. Les cellules Flk1-/- sont localisées, de manière normale, dans l'amnios. Il est admis que les cellules exprimant Flk-1 contribuent à la formation de l'endocarde, ainsi qu'à la vascularisation de l'embryon et de la vésicule vitelline; cependent, les origines de ces populations cellulaires individuelles restent inconnues. L'hypothèse émise est que les cellules exprimant Flk-1, à l'origine de différentes lignées cellulaires, proviennent de différentes régions et ont un comportement différent; le but de ce projet est donc d'identifier l'origine des progéniteurs endothéliaux et d'étudier leur comportement contributif au développement du système cardiovasculaire. L'analyse en videomicroscopie permet une observation temporelle et spatiale de processus naturels. Des embryons issus de la lignée murine Flk-1-GFP, hétérozygotes ou homozygotes, ont été observés en videomicroscopie de E7.5 à E8.5 pour visualiser la formation du système cardiovasculaire. Les origines des cellules endothéliales formant le système cardiovasculaire ont été rétrospectivement identifiées à l'aide de logiciels. Le processus de formation a été comparé à celui d'embryons mutés Flk-1GFP/GFP. L'analyse en videomicroscopie des embryons durant les étapes séquentielles du développement a montré que les cellules Flk-1-GFP+ apparaissent latéralement sur la ligne primitive. Ces cellules se répartissent ensuite dans les régions embryonnaires et extra-embryonnaires. Au cours de "head-fold stage" on a observé l'apparition d'une petite population de cellules Flk-1-GFP+, migrant de la frontière entre les régions embryonnaire et extra-embryonnaire dans la région embryonnaire pour former l'aorte dorsale. Durant cette migration, les cellules s'agrègent et initient la formation luminale. L'aorte dorsale embryonnaire se forme à mesure que ces petites structures luminales s'agrègent et s'alignent dans la région embryonnaire, formant une structure tubulaire distincte. Nous avons également pu identifier que les progéniteurs endocardiaux sont localisés dans une zone plus antérieure que les angioblastes de l'aorte dorsale. La majorité des cellules Flk-1-GFP+ de la région extra-embryonnaire forme la vascularisation de la vésicule vitelline. Les embryons Flk-1GFP/GFP sont apparus normaux au cours des étapes séquentielles, cependant, durant les étapes "head-fold", ni la migration ni les structures vasculaires n'ont été observées. Les cellules ont été localisées à l'intérieur de l'amnios, de l'allantoïde, du mésoderme cardiaque et de la région extra-embryonnaire. Le tube cardiaque s'est formé malgré l'absence de l'endocarde. Ces données montrent les origines des cellules exprimant Flk-1-GFP et leur contribution dans la gastrulation; de plus, il a été montré que Flk-1 est indispensable à la migration des cellules du mésoderme de la ligne primitive ainsi qu'à la migration des angioblastes.
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Malkusch, Sebastian [Verfasser], Mike [Akademischer Betreuer] Heilemann, and Martin [Akademischer Betreuer] Grininger. "Imaging-systems for localization-based super-resolution light-microscopy in physical biology : design and applications / Sebastian Malkusch. Gutachter: Mike Heilemann ; Martin Grininger." Frankfurt am Main : Univ.-Bibliothek Frankfurt am Main, 2014. http://d-nb.info/1060097966/34.
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Ogden, Melinda Anne. "Two-photon total internal reflection microscopy for imaging live cells with high background fluorescence." Thesis, Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/34786.
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Fluorescence microscopy allows for spatial and temporal resolution of systems which are inherently fluorescent or which can be selectively labeled with fluorescent molecules. Temporal resolution is crucial for imaging real time processes in living samples. A common problem in fluorescence microscopy of biological samples is autofluorescence, fluorescence inherent to the system, which interferes with detection of fluorescence of interest by decreasing the signal to noise ratio.
Two current methods for improved imaging against autofluorescence are two-photon excitation and total internal reflection microscopy. Two-photon excitation occurs when two longer wavelength photons are absorbed quasi-simultaneously by a single fluorophore. For this to take place there must be a photon density on the order of 1030 photons/(cm2)(s), which is achieved through use of a femtosecond pulsed laser and a high magnification microscope objective. Two-photon excitation then only occurs at the focal spot, significantly reducing the focal volume and therefore background autofluorescence.
The second method, total internal reflection, is based on evanescent wave excitation, which decreases exponentially in intensity away from the imaging surface. This allows for excitation of a thin (~200 nm) slice of a sample. Since only a narrow region of interest is excited, an optical slice can be imaged, decreasing excitation of out-of-focus autofluorescence, and increasing the signal to noise ratio.
By coupling total internal reflection with two-photon excitation, an entire cell can be imaged while still maintaining the use of lower energy photons to irradiate the sample and achieve two-photon excitation along the length traveled by the evanescent wave. This system allows for more sensitive detection of fluorescence of interest from biological systems as a result of a significant decrease in excitation volume and therefore a decrease in autofluorescence signal. In the two-photon total internal reflection microscopy setup detailed in this work, an excitation area of 20 μm by 30 μm is achieved, and used to image FITC-stained actin filaments in BS-C-1 cells
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del, Risco Norrlid Lilián. "Modeling the Performance of a Hybrid Pixel Detector for Digital X-ray Imaging." Doctoral thesis, Uppsala University, Department of Nuclear and Particle Physics, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4545.
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The development of digital detectors for X-ray imaging in medical diagnostics receives an increasing amount of attention. The detector under development at the Department of Radiation Sciences at Uppsala University is a hybrid pixel detector, which consists of a semiconductor sensor mounted onto a readout chip. The readout chip is capable of performing photon counting and has an externally adjustable threshold.
A simulation tool for the detector and a model applying the linear-systems transfer theory to X-ray hybrid pixel detectors have been developed. Also a characterization of the readout chip has been done. In order to estimate the potential of the detector for diagnostic radiology, we investigate the image quality using the spatial frequency dependent detective quantum efficiency (DQE). By means of the detector simulations, the influence of threshold setting, noise sources, level of exposure and charge sharing on the DQE have been studied. By means of the linear-systems theory, a single analytical expression is provided to obtain the DQE of a hybrid pixel detector.
The method developed in this thesis will make it possible to optimize a detector design according to a particular medical application. It will also permit modifications and new features to be included without having to construct a full detector system.
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Cosette, Jérémie. "Design and optimization of small animal non-invasive imaging approaches for evaluating the effects of innovative treatments of Primary Central Nervous System Lymphomas." Thesis, Paris 5, 2014. http://www.theses.fr/2014PA05T069/document.
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Pas de résumé en françaisPrimary central nervous system lymphomas (PCNSL) are very aggressive malignancies with poor survival rate even with treatments (survival median is 44 months). This disease affects immune cells (lymphocytes) and forms diffuse and non-surgically removable tumor in the central nervous system. High-dose chemotherapy and radiotherapy are the common treatments with severe side effects. New therapeutic approaches are required for increasing treatment efficiency. We focused on primary intraocular lymphomas (PIOL) and primary cerebral lymphomas (PCL), which are subtypes of PCNSL. PIOL and PCL cells have a high propensity to migrate and form metastases in the brain and in the controlateral eye in the case of PIOL, and in the eye in the PCL case. However, metastatic dissemation mechanisms remain unclear. The objective of the present work was to study the effects of innovative treatments of B-cell lymphoma on primary tumor, on metastases, and on circulating tumor cells in PIOL and PCL immunocompetent syngeneic murine models of lymphomas using non-invasive in vivo imaging methods. We studied the effects of Ublituximab, a glycoengineered anti-CD20 monoclonal antibody (mAb), and CpG-ODN, a TLR-9 agonist, in mouse models. We showed that Ublituximab exhibits significant anti-tumor effect in PIOL and PCL, while CpG showed significant anti-tumor effect in PCL. We monitored the tumor burden and metastases using innovating non-invasive optical imaging or cell detection methods: bioluminescence imaging (BLI) and in vivo flow cytometer (IVFC). BLI was used to locate metastasis and to quantify tumor burden. We indeed developed a bioluminescence-based tumor burden quantification method that reduces user-dependence, allows comparisons between experiments, reveals statistical relevance, and which is easy to use. An IVFC device was set up to investigate the role of circulating tumor cells (CTCs) in PIOL and PCL. This fluorescence-based technique allows detection of CTCs by analyzing the cells flowing in blood vessels. However we had to overcome the problem of autofluorescence and tissue absorption. Two approaches were studied in parallel: a elaborating new cell line expressing far red fluorescent proteins, modulating the excitation light of an IVFC device to give the cell a unique signature therefore enhancing sensitivity, increasing signal to noise ratio. The modulated excitation IVFC allowed us to calculate the velocity of cells, and infer their position in blood vessel phantoms. The analysis of treatment effects on tumor burden, metastases and CTCs in PIOL and PCL could help understanding lymphoma metastatic dissemination and contribute to treatment follow-up, thus allowing design of new therapeutic approaches with increased efficacy
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Aluoch, Austin Ochieng. "Metal enhanced detection of salivary proteins, Bacillus globigii and novel reagents for bioimaging & sensing." Diss., Online access via UMI:, 2007.
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Lontoc-Roy, Melinda. "Three-dimensional visualization in situ and complexity analysis of crop root systems using CT scan data : a primer." Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=82282.
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The importance of root systems for soil-based resource acquisition by plants has long motivated researchers to quantify the complexity of root system structures. However, most of those studies proceeded from 2-D spatial data, and thus lacked the relevance of a 3-D analysis. In this project, helical CT scanning was applied to study root systems with an unprecedented level of accuracy, using non-destructive and non-invasive 3-D imaging that allowed for a spatio-temporal analysis. The appropriate CT scan parameters and configuration were determined for root systems of maize seedlings grown in sand and loamy sand. It was found that the soil conditions allowing for better visualization were sand before watering and loamy sand after watering. Root systems were CT scanned and visualized either at a single moment in time or repeatedly on successive days. Complexity analysis was performed by estimating the fractal dimension on skeletonized 3-D images of root systems.
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Lorbeer, Christina [Verfasser]. "Optical imaging techniques for the study of cellular properties in developing neural systems / Christina Lorbeer." Hannover : Bibliothek der Tierärztlichen Hochschule Hannover, 2017. http://d-nb.info/1150304545/34.
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Davis, Katie S. "Use of a Towed Camera System along the west Florida shelf: A Case Study of the Florida Middle Grounds Benthic Marine Communities." Scholar Commons, 2018. https://scholarcommons.usf.edu/etd/7494.
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As technologies advance the study of ocean dynamics, new approaches to vexing problems of scale and process are becoming more widely available. Originally conceived as a tool primarily for indexing the abundance of near-bottom fishes, the Camera-based Assessment and Survey System (C-BASS) may also be an effective tool for monitoring benthic invertebrate resources vulnerable to natural and anthropogenic perturbations, and for characterizing the composition of benthic communities to inform spatial management. Using still images derived from the C-BASS video of benthic transects within the Florida Middle Grounds, I documented the abundance of benthic habitat-forming functional groups—sponges, algae, and corals—and noted taxa that were present in a SCUBA and ROV study conducted a decade earlier. Images were pre-processed using MATLAB computer programming language to correct for light attenuation and scattering in seawater at depth, and examined using ImageJ software and Coral Point Count software or rapid visual assessment methodology to assess image quality and percent cover, respectively. Exploratory data analysis (dissimilarity profile) delineated five habitat types in the northern Florida Middle Grounds, and discriminating benthic cover was identified using similarity percentage analysis: soft corals, fleshy macroalgae, low-relief algae, encrusted rubble, and sand. Hard corals and sponges represented relatively low area cover. A canonical analysis of principle components of in situ environmental measurements, chlorophyll a, turbidity, salinity, slope, and depth highlighted the association of the sand habitat type with greater depths and least amount of slope. Fleshy macroalgae were associated with greater slope, which reflected its presence in transitional areas between sand and reef. Soft coral habitat type was correlated with shallower depths, but also to lower temperature and lower salinity, highlighting the limitations of one-time environmental measurements to the condition of that time and space. A distance-based redundancy analysis of fish species abundance revealed that sponges, soft corals, and hard corals explained some of the variation of Holocentridae spp., angelfishes, and porgy, and that gray snapper appeared to associate with higher measurements of chlorophyll a. A comparison of C-BASS measurements with a coincidental stationary camera survey revealed that a slight shift in view, either from the seafloor to the water column, or from two slightly different positions in the water column, can obscure or reveal benthic cover to varying degrees, suggesting that more imaging could provide more complete representations of the benthic cover. Continued surveys of the benthic composition of the west Florida shelf could elucidate the range of environmental conditions and facilitate further investigations into the fish species associations with biotic cover in these benthic communities.
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Setlur, Nagesh Swetadri Vasan. "Improved imaging for x-ray guided interventions| A high resolution detector system and patient dose reduction technique." Thesis, State University of New York at Buffalo, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3613101.
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Over the past couple of decades there has been tremendous advancements in the field of medicine and engineering technology. Increases in the level of integration between these two branches of science has led to better understanding of physiology and anatomy of a living organism, thus allowing for better understanding of diseases along with their cures and treatments. The work presented in this dissertation aims at improving the imaging aspects of x-ray image guided interventions with endovascular image guided intervention as the primary area of application.
Minimally invasive treatments for neurovascular conditions such as aneurysms, stenosis, etc involve guidance of catheters to the treatment area, and deployment of treatment devices such as stents, coils, balloons, etc, all under x-ray image guidance. The features in these device are in the order of a few 10 µm's to a few 100 µm's and hence demand higher resolution imaging than the current state of the art flat panel detector. To address this issue three high resolution x-ray cameras were developed. The Micro Angiography Fluoroscope (MAF) based on a Charge Coupled Device (MAF-CCD), the MAF based on Complementary Metal Oxide Semiconductors (MAF-CMOS) and the Solid State X-ray Image Intensifier based on Electron Multiplying CCDs. The construction details along with performance evaluations are presented. The MAF-CCD was successfully used in a few interventions on human patient to treat neurovascular conditions, primarily aneurysm. Images acquired by the MAF-CCD during these procedures are presented.
A software platform CAPIDS was previously developed to facilitate the use of the high resolution MAF-CCD in a clinical environment. In this work the platform was modified to be used with any camera. The upgrades to CAPIDS, along with parallel programming including both the Graphics Processing Unit (GPU) and Central Processing Unit (CPU) are presented.
With increasing use of x-ray guidance for minimally invasive interventions, a major cause of concern is that of prolonged exposure to x-ray radiation that can cause biological damage to the patient. Hence during x-ray guided procedures necessary steps must be taken to minimize the dose to the patient. In this work a novel dose reduction technique, using a combination of Region of Interest (ROI) fluoroscopy to reduce dose along with spatially different temporal filtering to restore image quality is presented.
Finally a novel ROI imaging technique for biplane imaging in interventional suites, combining the use of high resolution detector along with dose reduction technique using ROI fluoroscopy with spatially different temporal filtering is presented.
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KIZILIRMAK, CISE. "L’ORIGINE DELL’ETEROGENEITÀ DINAMICA DI NF-KB: DALLE CELLULE QUASI-IDENTICHE ALLA SEGNALAZIONE INFIAMMATORIA PARACRINA." Doctoral thesis, Università Vita-Salute San Raffaele, 2022. http://hdl.handle.net/20.500.11768/133065.
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Il fattore nucleare kappa B (NF-kB) è un fattore di trascrizione cruciale nella risposta della cellula agli stimoli infiammatori poiché controlla l'espressione di chemochine e citochine chiave. NF-kB stesso è attivato da molte di queste molecole, e questa attivazione è mediata in larga misura dalle sue dinamiche di localizzazione nucleare. La dinamica di NF-kB è fondamentale per la corretta espressione dei suoi geni bersaglio, tuttavia può anche essere altamente eterogenea in diversi tipi cellulari e persino all'interno di popolazioni omogenee. L’origine di tale variabilità dinamica non è chiara. D'altra parte, in un tessuto la segnalazione paracrina implica che le cellule ricevano diversi segnali che possono attivare NF-kB a seconda della loro posizione rispetto alle sorgenti. La risposta dinamica NF-kB risultante potrebbe essere eterogenea e tuttavia potrebbe anche contenere informazioni spaziotemporali, ma questa possibilità non è stata adeguatamente esplorata.
Per ottenere informazioni sull’origine dell'eterogeneità delle dinamiche di NF-kB abbiamo isolato più popolazioni clonali a partire da una popolazione omogenea di fibroblasti GFP-NF-kB e abbiamo scoperto che ciascuna ha una dinamica di localizzazione nucleare di NF-kB diversa quando sono stimolate con la citochina fattore di necrosi tumorale alfa (TNF-a). Ci siamo concentrati su tre popolazioni clonali che mostrano risposte oscillatorie, persistenti e deboli al TNF-a, rispettivamente, e abbiamo scoperto che hanno differenze piccole ma significative nell'espressione dei geni appartenenti al circuito regolatorio NF-kB che spiegano queste differenze dinamiche. Invece, per caratterizzare le dinamiche eterogenee di NF-kB che potrebbero insorgere nella segnalazione infiammatoria paracrina, abbiamo sviluppato modelli in vitro nei quali possiamo osservare la dinamica di NF-kB per cellule che ricevono segnali da due tipi di “mittenti”: cellule RAW 264.7 e una versione ingegnerizzata dei nostri fibroblasti GFP-NF-kB che secernono TNF-a istantaneamente dopo l'induzione. Abbiamo scoperto che le singole cellule utilizzano l'attivazione spaziotemporale di NF-kB per codificare la posizione e la forza dei segnali di pericolo, anche con un certo grado di eterogeneità. Inoltre, questa dinamica spaziotemporale è influita dal fatto che le cellule diventano meno rispondenti allo stimolo dovuto alla secrezione basale di citochine da parte dei mittenti, che si traduce in una risposta moderata a livello di popolazione che dipende dalla posizione anche in situazioni di alta secrezione di citochine infiammatorie.
Nel complesso, i nostri risultati mostrano che parte dell'eterogeneità della popolazione sull'attivazione di NF-kB potrebbe emergere nei tessuti come risultato dell'interazione di diversi livelli di regolazione: in primo luogo, a causa di piccole variazioni nei livelli di espressione dei geni del circuito regolatorio di NF-kB tra le cellule e secondo, a seconda del contesto spazio-temporale. Il nostro studio ha fornito ulteriori approfondimenti su come l'infiammazione si sviluppa attraverso dinamiche eterogenee di NF-kB nello spazio e nel tempo e potenzialmente contribuirà a far luce su come le risposte immunitarie complesse sono coordinate in condizioni fisiologiche e patologiche.Nuclear factor kappa B (NF-kB) is a master transcription factor in the cell’s response to inflammatory stimuli as it controls the expression of key chemokines and cytokines. NF-kB itself is activated by many of these molecules, largely mediated by its nuclear localization dynamics. NF-kB dynamics is fundamental for proper target gene expression, however it can also be highly heterogeneous in different cell types and even within homogeneous populations. The source of such dynamic variability is unclear. On the other hand, in a tissue paracrine signaling implies that cells receive different NF-kB activating signals depending on their position relative to the sources. The resulting NF-kB dynamic response might be also heterogeneous and yet might also carry spatiotemporal information, but this has not been properly characterized. To gain insights on the source of heterogeneity of NF-kB dynamics we isolated multiple clonal populations of a homogenous GFP-NF-kB fibroblast population and found that each has a robustly distinct NF-kB nuclear localization dynamics upon stimulation with tumor necrosis factor alpha (TNF-a). We focused on three clonal populations displaying oscillatory, persistent, and weak responses to TNF-a and found that they have small but significant differences in the expression of genes belonging to the NF-kB regulatory circuit. To characterize the heterogeneous NF-kB dynamics that might arise in paracrine inflammatory signaling, we developed in vitro sender receiver models where we can image the dynamics of NF-kB receiving signals from two senders: RAW 264.7 cells and an engineered version of our GFP-NF-kB fibroblasts that secrete TNF-a instantaneously upon induction. We found that single cells use spatiotemporal NF-kB activation to encode location and strength of the danger signals, even with a certain degree of heterogeneity. Furthermore, this spatiotemporal dynamics is shaped by an anti-priming effect due to the basal secretion of cytokines by the senders, which results in a moderate spatially-dependent population-level response to strong cytokine secretion. Overall, our results show that part of populational heterogeneity on NF-kB activation might emerge in tissue as a result of the interaction of many layers: first, due to small variations in the expression levels of genes of the NF-kB regulatory circuit between cells and second, depending on the spatiotemporal context. Our study has provided additional insights on how inflammation develops through heterogeneous dynamics of NF-kB in space and time and will potentially contribute to shed light on how complex immune responses are coordinated in healthy and pathological conditions.
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Spaw, Alexandra J. "Fetal Developmental Anatomy of the Human Cardiovascular and Central Nervous Systems Using Lugol’s Iodine Staining and Micro-Computed Tomography." Ohio University Honors Tutorial College / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=ouhonors1398950897.
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Kinyanjui, Sophia Nduta. "Biological Applications of a Strongly Luminescent Platinum (II) Complex in Reactive Oxygen Species Scavenging and Hypoxia Imaging in Caenorhabditis elegans." Thesis, University of North Texas, 2015. https://digital.library.unt.edu/ark:/67531/metadc822774/.
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Phosphorescent transition metal complexes make up an important group of compounds that continues to attract intense research owing to their intrinsic bioimaging applications that arise from bright emissions, relatively long excited state lifetimes, and large stokes shifts. Now for biomaging assay a model organism is required which must meet certain criteria for practical applications. The organism needs to be small, with a high turn-over of progeny (high fecundity), a short lifecycle, and low maintenance and assay costs. Our model organism C. elegans met all the criteria. The ideal phosphor has low toxicity in the model organism. In this work the strongly phosphorescent platinum (II) pyrophosphito-complex was tested for biological applications as a potential in vivo hypoxia sensor. The suitability of the phosphor was derived from its water solubility, bright phosphorescence at room temperature, and long excited state lifetime (~ 10 µs). The applications branched off to include testing of C. elegans survival when treated with the phosphor, which included lifespan and fecundity assays, toxicity assays including the determination of the LC50, and recovery after paraquat poisoning. Quenching experiments were performed using some well knows oxygen derivatives, and the quenching mechanisms were derived from Stern-Volmer plots. Reaction stoichiometries were derived from Job plots, while percent scavenging (or antioxidant) activities were determined graphically. The high photochemical reactivity of the complex was clearly manifested in these reactions.
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Gorishek, Emma Lee. "Laser Ablation Inductively Coupled Plasma Mass Spectrometry and Raman Spectroscopy Imaging of Biological Tissues." Thesis, University of North Texas, 2016. https://digital.library.unt.edu/ark:/67531/metadc849725/.
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Laser Ablation Inductively coupled plasma mass spectrometry (LA-ICP-MS) and Raman spectroscopy are both powerful imaging techniques. Their applications are numerous and extremely potential in the field of biology. In order to improve upon LA-ICP-MS an in-house built cold cell was developed and its effectiveness studied by imaging Brassica napus seeds. To further apply LA-ICP-MS and Raman imaging to the field of entomology a prong gilled mayfly (Ephemeroptera: Leptophlebiidae) from the Róbalo River, located on Navarino Island in Chile, was studied. Analysis of both samples showcased LA-ICP-MS and Raman spectroscopy as effective instruments for imaging trace elements and larger molecules in biological samples respectively.
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Chen, Huiyi. "System-Wide Studies of Gene Expression in Escherichia coli by Fluorescence Microscopy and High Throughput Sequencing." Thesis, Harvard University, 2011. http://dissertations.umi.com/gsas.harvard:10044.
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Gene expression is a fundamental process in the cell and is made up of two parts – the information flow from DNA to RNA, and from RNA to protein. Here, we examined specific sub-processes in Escherichia coli gene expression using newly available tools that permit genome-wide analysis. We begin our studies measuring mRNA and protein abundances in single cells by single-molecule fluorescence microscopy, and then focus our attention to studying RNA generation and degradation by high throughput sequencing. The details of the dynamics of gene expression can be observed from fluctuations in mRNA and protein copy numbers in a cell over time, or the variations in copy numbers in an isogenic cell population. We constructed a yellow fluorescent fusion protein library in E. coli and measured protein and mRNA abundances in single cells. At below ten proteins per cell, a simple model of gene expression is sufficient to explain the observed distributions. At higher expression levels, the distributions are dominated by extrinsic noise, which is the systematic heterogeneity between cells. Unlike proteins which can be stable over many hours, mRNA is made and degraded on the order of minutes in E. coli. To measure the dynamics of RNA generation and degradation, we developed a protocol using high throughput sequencing to measure steady-state RNA abundances, RNA polymerase elongation rates and RNA degradation rates simultaneously with high nucleotide-resolution genome-wide. Our data shows that RNA has similar lifetime at all positions throughout the length of the transcript. We also find that our polymerase elongation rates measured in vivo on a chromosome are generally slower than rates measured on plasmids by other groups. Studying nascent RNA will allow further understanding of RNA generation and degradation. To this end, we have developed a labeling protocol with a nucleoside analog that is compatible with high throughput sequencing.
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Smith, Aaron. "Vertex model approaches to epithelial tissues in developmental systems." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:4d19f232-764c-4e27-bca9-d2ede0ec2db9.
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The purpose of this thesis is to develop a vertex model framework that can be used to perform computational experiments related to the dynamics of epithelial tissues in developmental systems. We focus on three example systems: the Drosophila wing imaginal disc, the Drosophila epidermis and the visceral endoderm of the mouse embryo. Within these systems, key questions pertaining to size-control mechanisms and coordination of cell migration remain unanswered and are amenable to computational testing. The vertex model presented here builds upon existing frameworks in three key ways. Firstly, we include novel force terms, representing, for example, the reaction of a cell to being compressed and its shape becoming distorted during a highly dynamic process such as cell migration. Secondly, we incorporate a model of diffusing morphogenetic growth factors within the vertex framework, using an arbitrary Lagrangian-Eulerian formulation of the diffusion equation and solving with the finite-element method (FEM). Finally, we implement the vertex model on the surface of an ellipsoid, in order to simulate cell migration in the mouse embryo. Throughout this thesis, we validate our model by running simple simulations. We demonstrate convergence properties of the FEM scheme and discuss how the time taken to solve the system scales with tissue size. The model is applied to biological systems and its utility demonstrated in several contexts. We show that when growth is dependent on morphogen concentration in the Drosophila wing disc, proliferation occurs preferentially in regions of high concentration. In the Drosophila epidermis, we show that a recently proposed mechanism of compartment size-control, in which a growth-factor is released in limited amounts, is viable. Finally, we examine the phenomenon of rosettes in the mouse embryo, which occur when five or more cells meet at a common vertex. We show, by running simulations both with and without rosettes, that they are crucial facilitators of ordered migration, and are thus critical in the patterning of the early embryo.
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Lewark, Erick A. "Automated techniques in anthropometry using a three dimensional laser scanner." Ohio : Ohio University, 1998. http://www.ohiolink.edu/etd/view.cgi?ohiou1176485676.
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Fortun, Denis. "Aggregation framework and patch-based representation for optical flow." Thesis, Rennes 1, 2014. http://www.theses.fr/2014REN1S093/document.
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Nous nous intéressons dans cette thèse au problème de l'estimation dense du mouvement dans des séquences d'images, également désigné sous le terme de flot optique. Les approches usuelles exploitent une paramétrisation locale ou une régularisation globale du champ de déplacement. Nous explorons plusieurs façons de combiner ces deux stratégies, pour surmonter leurs limitations respectives. Nous nous plaçons dans un premier temps dans un cadre variationnel global, et considérons un filtrage local du terme de données. Nous proposons un filtrage spatialement adaptatif, optimisé conjointement au mouvement, pour empêcher le sur-lissage induit par le filtrage spatialement constant. Dans une seconde partie, nous proposons un cadre générique d'agrégation pour l'estimation du flot optique. Sous sa forme générale, il consiste en une estimation locale de candidats de mouvements, suivie de leur combinaison à l'étape d'agrégation avec un modèle global. Ce schéma permet une estimation efficace des grands déplacements et des discontinuités de mouvement. Nous développons également une méthode générique de gestion des occultations. Notre méthode est validée par une analyse expérimentale conséquente sur des bases de données de référence en vision par ordinateur. Nous démontrons la supériorité de notre méthode par rapport à l'état de l'art sur les séquences présentant de grands déplacements. La dernière partie de la thèse est consacrée à l'adaptation des approches précédentes à des problématiques d'imagerie biologique. Les changements locaux importants d'intensité observés en imagerie de fluorescence sont estimés et compensé par une adaptation de notre schéma d'agrégation. Nous proposons également une méthode variationnelle avec filtrage local dédiée au cas de mouvements diffusifs de particulesThis thesis is concerned with dense motion estimation in image sequences, also known as optical flow. Usual approaches exploit either local parametrization or global regularization of the motion field. We explore several ways to combine these two strategies, to overcome their respective limitations. We first address the problem in a global variational framework, and consider local filtering of the data term. We design a spatially adaptive filtering optimized jointly with motion, to prevent over-smoothing induced by the spatially constant approach. In a second part, we propose a generic two-step aggregation framework for optical flow estimation. The most general form is a local computation of motion candidates, combined in the aggregation step through a global model. Large displacements and motion discontinuities are efficiently recovered with this scheme. We also develop a generic exemplar-based occlusion handling to deal with large displacements. Our method is validated with extensive experiments in computer vision benchmarks. We demonstrate the superiority of our method over state-of-the-art on sequences with large displacements. Finally, we adapt the previous methods to biological imaging issues. Estimation and compensation of large local intensity changes frequently occurring in fluorescence imaging are efficiently estimated and compensated with an adaptation of our aggregation framework. We also propose a variational method with local filtering dedicated to the case of diffusive motion of particles
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Caesar, Nicole O. "An evaluation of the Along Track Reef Imaging System (ATRIS) for efficient reef monitoring and rapid groundtruthing of EAARL Lidar." [Tampa, Fla] : University of South Florida, 2006. http://purl.fcla.edu/usf/dc/et/SFE0001483.
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Tirier, Stephan Marius [Verfasser], and Roland [Akademischer Betreuer] Eils. "Dissecting tumor cell heterogeneity in 3D cell culture systems by combining imaging and next generation sequencing technologies / Stephan Marius Tirier ; Betreuer: Roland Eils." Heidelberg : Universitätsbibliothek Heidelberg, 2018. http://d-nb.info/1198484292/34.
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Poon, Chien Sing. "Early Assessment of Burn Severity in Human Tissue with Multi-Wavelength Spatial Frequency Domain Imaging." Wright State University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=wright1484582176416423.
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Zhang, Yu. "Inverse opal scaffolds and photoacoustic microscopy for regenerative medicine." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/50231.
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This research centers on the fabrication, characterization, and engineering of inverse
opal scaffolds, a novel class of three-dimensional (3D) porous scaffolds made of
biocompatible and biodegradable polymers, for applications in tissue engineering and
regenerative medicine. The unique features of an inverse opal scaffold include a highly
ordered array of pores, uniform and finely tunable pore sizes, high interconnectivity, and
great reproducibility.
The first part of this work focuses on the fabrication and functionalization of inverse
opal scaffolds based on poly(D,L-lactic-co-glycolic acid) (PLGA), a biodegradable
material approved by the U.S. Food and Drug Administration (FDA). The advantages of
the PLGA inverse opal scaffolds are also demonstrated by comparing with their
counterparts with spherical but non-uniform pores and poor interconnectivity.
The second part of this work shows two examples where the PLGA inverse opal
scaffolds were successfully used as a well-defined system to investigate the effect of pore
size of a 3D porous scaffold on the behavior of cell and tissue growth. Specifically, I
have demonstrated that i) the differentiation of progenitor cells in vitro was dependent on
the pore size of PLGA-based scaffolds and the behavior of the cells was determined by
the size of individual pores where the cells resided in, and ii) the neovascularization
process in vivo could be directly manipulated by controlling a combination of pore and
window sizes when they were applied to a mouse model.
The last part of this work deals with the novel application of photoacoustic
microscopy (PAM), a volumetric imaging modality recently developed, to tissue
engineering and regenerative medicine, in the context of non-invasive imaging and
quantification of cells and tissues grown in PLGA inverse opal scaffolds, both in vitro
and in vivo. Furthermore, the capability of PAM to monitor and quantitatively analyze
the degradation of the scaffolds themselves was also demonstrated.
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Braman, Nathaniel. "Novel Radiomics and Deep Learning Approaches Targeting the Tumor Environment to Predict Response to Chemotherapy." Case Western Reserve University School of Graduate Studies / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=case1586546527544791.
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Hawthorne, Alicia Lynn. "The Development and Regeneration of the Serotonergic System." Case Western Reserve University School of Graduate Studies / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=case1264027000.
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Flanagan, Shawn D. "Neurological Basis of Persistent Functional Deficits after Traumatic Musculoskeletal Injury." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1469031876.
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Luo, Yuan. "Novel Biomedical Imaging Systems." Diss., The University of Arizona, 2008. http://hdl.handle.net/10150/193907.
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The overall purpose of the dissertation is to design and develop novel optical imaging systems that require minimal or no mechanical scanning to reduce the acquisition time for extracting image data from biological tissue samples. Two imaging modalities have been focused upon: a parallel optical coherence tomography (POCT) system and a volume holographic imaging system (VHIS). Optical coherence tomography (OCT) is a coherent imaging technique, which shows great promise in biomedical applications. A POCT system is a novel technology that replaces mechanically transverse scanning in the lateral direction with electronic scanning. This will reduce the time required to acquire image data. In this system an array with multiple reduced diameter (15μm) single mode fibers (SMFs) is required to obtain an image in the transverse direction. Each fiber in the array is configured in an interferometer and is used to image one pixel in the transverse direction. A VHIS is based on volume holographic gratings acting as Bragg filters in conjunction with conventional optical imaging components to form a spatial-spectral imaging system. The high angular selectivity of the VHIS can be used to obtain two-dimensional image information from objects without the need for mechanical scanning. In addition, the high wavelength selectivity of the VHIS can provide spectral information of a specific area of the object that is being observed. Multiple sections of the object are projected using multiplexed holographic gratings in the same volume of the Phenanthrenquinone- (PQ-) doped Poly (methyl methacrylate) (PMMA) recording material.
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Hofer, Sonja. "Imaging development and plasticity in the mouse visual system." Diss., [S.l.] : [s.n.], 2006. http://edoc.ub.uni-muenchen.de/archive/00005846.
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He, Jiang. "Fluorescence Imaging of Virus-Host Cell Interaction and Super-Resolution Imaging of Neuronal Cytoskeleton." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:26718714.
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To study biological molecules, pathways and processes, fluorescence microscope has become an indispensable tool in modern biology. The major advantages of using fluorescence microscope include its ability to achieve molecule-specific visualization for targets of interest, and the compatibility of live cell imaging. With the advent of super-resolution imaging techniques, fluorescent microscope, for the first time, allows researchers to study biological processes on the nanometer scale. In this dissertation, I present the application of fluorescence imaging to characterize the role of host factors in influenza virus infection, and super-resolution imaging to study the developmental mechanism and prevalence of a periodic membrane skeleton in neurons.
In Chapter 2 and 3, my colleagues and I studied the role of CD81 and COPI complex, two host factors identified in large-scale screens, for influenza infection. We found that CD81 regulates two distinct steps during influenza infection cycle: virus uncoating during entry and virus budding during egress. Depleting CD81 led to a significant defect in viral uncoating and viral gene replication during entry, while during virus egress, CD81 depletion resulted in virions that failed to detach from the plasma membrane and a marked decrease in progeny virus production. For COPI complexes, we found that COPI plays a direct role in viral membrane protein expression and assembly post-viral entry.
In Chapter 4 and 5, we used super-resolution imaging to study the developmental mechanism and prevalence of a newly discovered periodic membrane skeleton in axons, formed by actin, spectrin and associated molecules. We found that the periodic membrane skeleton is highly prevalent in different neuronal types. It forms early during neuronal development, and originates from regions closer to the cell body and propagates toward the distal ends of axons. The lattice structure further matures by recruiting additional molecular components and appears to be highly stable once formed. The local concentration of βII spectrin is a key determinant for the formation of this periodic membrane skeleton. In addition, we identified ankyrin B as a critical molecular component for the polarized distribution of βII spectrin in neurites.Biology, Molecular and Cellular
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Ertürk, Ali. "In vivo imaging of the degenerating and regenerating nervous system." Diss., lmu, 2008. http://nbn-resolving.de/urn:nbn:de:bvb:19-81821.
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WOOD, LYNNETTE. "RESTORATION FOR SAMPLED IMAGING SYSTEMS." Diss., The University of Arizona, 1986. http://hdl.handle.net/10150/183994.
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Digital image restoration requires some knowledge of the degradation phenomena in order to attempt an inversion of that degradation. Typically, degradations which are included in the restoration process are those resulting from the optics and electronics of the imaging device. Occasionally, blurring caused by an intervening atmosphere, uniform motion or defocused optics is also included. Recently it has been shown that sampling, the conversion of the continuous output of an imaging system to a discrete array, further degrades or blurs the image. Thus, incorporating sampling effects into the restoration should improve the quality of the restored image. The system transfer function (the Fourier transform of the point spread function), was derived for the Landset Multi-Spectral Scanner and Thematic Mapper systems. Sampling effects were included, along with the relevant optical, instantaneous field of view and electronic filter data, in the system analysis. Using the system transfer function, a least squares (Wiener) filter was then derived. A Wiener filter requires the ratio of the power spectra of the scene and noise, which is often, for simplicity, assumed to be a constant over frequency. The restoration method used here includes models for the power spectra which are based on the study of several different types of Landsat scenes. The Wiener filter is then inverse Fourier transformed to find a restoration filter which is spatially windowed to suppress ringing. Qualitative and quantitative evaluations are made of the restored imagery. Comparisons are made to the approaches taken by other investigators, in particular, to one who has had success restoring the same type of imagery. It is found that the restoration method used here compares favorably with this previous work.
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Benjamin, David Colin. "Intravital imaging of metastasis in zebrafish." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/117867.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2018.DVD-ROM contains: movies/videos.
Cataloged from PDF version of thesis.
Includes bibliographical references.
Metastasis is the cause of the overwhelming majority of cancer deaths. However, it remains a poorly understood process. The events at the metastatic site are especially poorly comprehended. These events are dynamic and so require intravital imaging to investigate. However, the intravital imaging of these events in mice is challenging. Sites of metastasis are often in vital organs that are inaccessible to microscopy without surgical intervention. Furthermore, circulating tumor cells are rare and are involved in many transient interactions adding to the challenge. The development of a line of zebrafish, Casper, that is transparent throughout its life suggested that zebrafish might be a powerful system for intravital imaging. I first developed novel injection and imaging techniques to study metastasis through intravital imaging in adult zebrafish. I then followed individual ZMEL1 zebrafish melanoma cells at the metastatic site over the course of two weeks as they grew from single disseminated tumor cells into macroscopic metastases. From these studies, I characterized the steps of metastasis at the metastatic site for this cell line. I also utilized transparent zebrafish embryos to uncover a new role for the oncogene YAP during metastasis. I observed that the over-expression of a Hippo-insensitive mutant of YAP (YAP-AA) promoted brain metastasis following intravenous in zebrafish embryos. I determined that YAP-AA was promoting tumor cell dispersal throughout the embryo by allowing tumor cells to escape the first capillary bed they encounter. Following intravenous injection, control cells lodge in blood vessels in the tail and cease their travel through circulation. However, YAP-AA cells are able to move through these vessels, re-enter circulation and travel to other organs, such as the brain. These observations represent a new mechanism by which tumor cells can increase their dissemination throughout an animal.
by David Colin Benjamin.
Ph. D.
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Wang, Lulu. "Virtual imaging system." Click here to access this resource online, 2009. http://hdl.handle.net/10292/668.
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The main purpose of this research project was to implement a combination of computer graphics and processing to generate displays that will aid in the visualization of the colour rendering properties of a range of light sources, including the new generation of high-output LEDs (light emitting diodes) that are becoming widely adopted in general lighting service. The CIE (International Commission on Illumination) has developed a colour appearance model CIECAM02 for use in colour imaging and colour management, and this model is utilized in this work. This thesis describes the design and construction of a computer-based model that can be used as a research tool for the simulation and demonstration of the colour rendering properties of various artificial light sources. It is a comprehensive study of the colour models and measurement procedures currently in use in the lighting industry, as recommended by the CIE. This research project focused on the display of a set of surface colour patches as if they were illuminated by a specific light source, and the simultaneous display of two such sets to demonstrate the surface colour differences arising from the use of the two different light sources. A VIS (virtual imaging system) has been developed to display the colour properties of a series of test colour samples under different light sources. This thesis describes the computer models developed for the representation and display of surface colours in general, and colour rendering in particular. The designed system computes and displays the colour of each sample from a knowledge of the light-source spectrum and the spectral reflectance of each surface. It can simultaneously display the colours resulting from illumination by two different sources. In addition, the system computes the colour appearance differences for two sets of colours using the CIECAM02 colour appearance model. Subjective and objective tests were taken to validate the computed results. The VIS has been designed and implemented. It also has been tested by 21 observers and we believe that it will be a powerful research tool for the lighting industry, especially in relation to colour rendering.
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Sukhija, Ruchi. "Document imaging application." CSUSB ScholarWorks, 2007. https://scholarworks.lib.csusb.edu/etd-project/3217.
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The purpose of this project was to develop a document imaging application. By scanning the documents into an electronic repository, medical staff will be able to more easily store and locate these records. To make the application user friendly and facilitate staff access to patient medical records, the application is wed-based and uses the Oracle Application Server to implement a multitiered model.
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Feller, Alex J. "Instrument systems for imaging spectro-polarimetry." Göttingen Cuvillier, 2007. http://d-nb.info/988229595/04.
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Feller, Alex Jean. "Instrument systems for imaging spectro-polarimetry /." Göttingen : Cuvillier, 2008. http://d-nb.info/988229595/04.
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Blackband, S. J. "NMR imaging of liquid-solid systems." Thesis, University of Nottingham, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.356019.
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Phan, Long N. 1976. "Automated rapid thermal imaging systems technology." Thesis, Massachusetts Institute of Technology, 2012. http://hdl.handle.net/1721.1/75664.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2012.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 266-276).
A major source of energy savings occurs on the thermal envelop of buildings, which amounts to approximately 10% of annual energy usage in the United States. To pursue these savings, energy auditors use closed loop energy auditing processes that include infrared thermography inspection as an important tool to assess deficiencies and identify hot thermal gradients. This process is prohibitively expensive and time consuming. I propose fundamentally changing this approach by designing, developing, and deploying an Automated Rapid Thermal Imaging Systems Technology (ARTIST) which is capable of street level drive-by scanning in real-time. I am doing for thermal imaging what Google Earth did for visual imaging. I am mapping the world's temperature, window by window, house by house, street by street, city by city, and country by country. In doing so, I will be able to provide detailed information on where and how we are wasting energy, providing the information needed for sound economic and environmental energy policies and identifying what corrective measures can and should be taken. The fundamental contributions of this thesis relates to the ARTIST. This thesis will focus on the following topics: * Multi-camera synthetic aperture imaging system * 3D Radiometry * Non-radiometric infrared camera calibration techniques * Image enhancement algorithms - Hyper Resolution o Kinetic Super Resolution - Thermal Signature Identification - Low-Light Signal-to-Noise Enhancement using KSR
by Long N. Phan.
Ph.D.
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Whitcombe, Michael James. "Red-sensitive imaging systems for holography." Thesis, Royal Holloway, University of London, 1987. http://repository.royalholloway.ac.uk/items/93c5198a-27d2-4c1d-ba1b-744bdc04fac0/1/.
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The primary objective of the work described in this thesis was to devise a red-sensitive photoresist imaging process for use in the replication of diffraction optics. In the introduction the chemistry of conventional photopolymer systems and photoresists used for holographic recording and the fabrication of diffraction gratings and diffracting optical elements is reviewed. The limitations of commercially available photoresist systems, particularly for applications requiring the use of red light are discussed. A polymer system has been investigated which could be imaged by photochemically generated free radicals, followed by a simple aqueous development procedure as required by the original specification. The polymer chosen for study was a copolymer of methyl methacrylate, methacrylic acid and 2-hydroxyethyl methacrylate. This was derivatized using methacryloyl chloride or methacrylic anhydride in order to introduce cross-linkable units to the polymer backbone. Polymers have been characterized by a number of techniques and the effect of varying composition on aqueous base solubility has been thoroughly studied. Various methods of derivatization have been employed. The ease of imaging has been found to be very sensitive to both the composition of the polymer and the extent of functionalization. High quality images have been obtained from this polymer using an organic solvent developer. Imaging experiments have been carried out on thin films of the photopolymer coated on glass using phenylazotriphenylmethane (PATM) as photoinitiator. Good images of 100 lines permillimetre (1 mm-1) have been recorded by contact printing. Interferometry has been used to demonstrate that interference patterns having 600 and 1200 1 mm-1 can be recorded using this polymer with PATM as initiator, exposed to an argon ion laser operating at 458nm. A number of two component photoredox initiator systems have been investigated, the light absorbing species of such systems being a dye such as methylene blue or certain cyanine dyes. The second component of these initiators may be an aryl sulphinate salt, a 1,3-diketone or some alkyl sulphides. The red light-initiated phatopolymerization of acrylamide has been demonstrated using some of these initiators and a low resolution photopolymer image has been recorded using Azure A and perinaphth-1,3-indandione as the photoinitiator system. This polymer can, in principle, produce images over a wide range of wavelengths depending on the nature of the initiator used.