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El, Mallahi Ahmed. "Automated 3D object analysis by digital holographic microscopy." Doctoral thesis, Universite Libre de Bruxelles, 2013. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/209489.
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The main objective of this thesis is the development of new processing techniques for digital holograms. The present work is part of the HoloFlow project that intends to integrate the DHM technology for the monitoring of water quality. Different tools for an automated analysis of digital holograms have been developed to detect, refocus and classify particles in continuous fluid flows. A detailed study of the refocusing criterion permits to determine its dependencies and to quantify its robustness. An automated detection procedure has been developed to determine automatically the 3D positions of organisms flowing in the experiment volume. Two detection techniques are proposed: a usual method based on a global threshold and a new robust and generic method based on propagation matrices, allowing to considerably increase the amount of detected organisms (up to 95 %) and the reliability of the detection. To handle the case of aggregates of particles commonly encountered when working with large concentrations, a new separation procedure, based on a complete analysis of the evolution of the focus planes, has been proposed. This method allows the separation aggregates up to an overlapping area of around 80 %. These processing tools have been used to classify organisms where the use of the full interferometric information of species enables high classifier performances to be reached (higher than 93 %).<br>Doctorat en Sciences de l'ingénieur<br>info:eu-repo/semantics/nonPublished
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Degani, Ismail. "Biomedical applications of holographic microscopy." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/118494.
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Thesis: S.M. in Engineering and Management, Massachusetts Institute of Technology, System Design and Management Program, 2018.<br>This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.<br>Cataloged from student-submitted PDF version of thesis.<br>Includes bibliographical references (pages 77-79).<br>Identifying patients with aggressive cancers is a major healthcare challenge in resource-limited settings such as sub-Saharan Africa. Holographic imaging techniques have been shown to perform diagnostic screening at low cost in order to meet this clinical need, however the computational and logistical challenges involved in deploying such systems are manifold. This thesis aims to make two specific contributions to the field of point-of-care diagnostics. First, it documents the design and construction of low-cost holographic imaging hardware which can serve as a template for future research and development. Second, it presents a novel deep-learning architecture that can potentially lower the computational burden of digital holography by replacing existing image reconstruction methods. We demonstrate the effectiveness of the algorithm by reconstructing biological samples and quantifying their structural similarity relative to spatial deconvolution methods. The approaches explored in this work could enable a standalone holographic platform that is capable of efficiently performing diagnostic screening at the point of care.<br>by Ismail Degani.<br>S.M. in Engineering and Management
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Bolognesi, Guido. "Optical studies of micron-scale flows : holographic microscopy, optical trapping and superhydrophobicity." Phd thesis, Université Claude Bernard - Lyon I, 2012. http://tel.archives-ouvertes.fr/tel-00870942.
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Microfluidics is a very recent branch of science and technology. The development and the success, it has had in the last 15 years, is mainly due to the concept of lab-on-a-chip. Those miniaturized devices, integrating one or more laboratory functions, have aroused great interest among several research areas as physics, chemistry, biology and bioengineering. When a fluid is confined in a micro or nano scale structure, its behaviour is strongly affected by its interactions with the surrounding surfaces. In this context, the theme of fluid/solid slippage has been widely studied both theoretically and experimentally. Innovative technologies to enhance the surface slippage by specifically designing the solid interfaces have reportedly demonstrated to be an effective way to reduce the fluid/solid friction. To this end, superhydrophobic surfaces have increasingly attracted the interest of the scientific and technological community thanks to the large wall-slippage they present for liquid water. Though their behaviour has been extensively investigated through several theoretical and numerical methods, the experimental approaches are still indispensable to test and understand the properties of these surfaces. However, the lack of a general predicting model is also due to the fact that no one of the several existing experimental techniques has shown up as a very reliable one. Indeed, the reported measurements of slippage still depends on the specific adopted method, thwarting attempts to corroborate the proposed theoretical and numerical schemes. Therefore, it is evident that a more sensitive and effective experimental technique is still missing. This thesis began and developed inside the wider project of setting up an innovative technique to investigate the fluid-solid slippage on superhydrophobic surfaces by means of optical tweezers. Even though this project is still going on, this work reports the steps performed along the long way towards this main goal and it consists of a collection of several researches involving different scientific fields as optics, microscopy, surface science, microhydrodynamics, microfluidics and microfabrication. The researches presented in this work can be separated in two main categories: i) holographic micromanipulation and microscopy, ii) superhydrophobicity.
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Makarchuk, Stanislaw. "Measurement of cell adhesion forces by holographic microscopy." Thesis, Strasbourg, 2016. http://www.theses.fr/2016STRAE034/document.
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Les forces mécaniques, générées par la cellule jouent un rôle crucial dans l'adhésion cellulaire, qui est un processus commun à un grand nombre de lignées cellulaires. Afin de mesurer la champ des forces pendant l'adhérence cellulaire, nous utilisons la microscopie de force de traction, où la cellule adhère à la surface plane d'un substrat souple dans le plan. Les forces sont calculées à partir du champ de déplacement mesuré à l'intérieur du substrat sous la cellule. Nous avons construit le microscope, dans lequel nous utilisons des billes sphériques en polystyrène pour mesurer le champ de déplacement. Les positions des marqueurs sont obtenues en analysant I' image interférentielle des particules. Avec cette technique, nous atteignons une précision nanométrique sur le champ de déplacement des particules, ce qui nous permet d'améliorer la résolution en force de ce type de microscope. Les premières mesures ont été effectuées avec la lignée de cellules cancéreuses SW 480<br>Mechanical forces, generated by the cell plays crucial role in cell adhesion - common process for different cell lines. ln order to measure the force map during cellular adhesion, we use Traction Force Microscopy (TFM), where cell adheres to the soft substrate in 20 plane, and the forces are calculated from measured displacement field inside the substrate underneath the cell. We built the microscope, where instead of using fluorescent markers, we use spherical polystyrene beads in order to measure the displacement field. Positions of the markers are obtained by analyzing the interference pattern caused by the beads in bright-field light. With this technique, we reach nanometer accuracy of the microsphere position determination, that, respectively, influence accuracy of the calculated force field. With the microscope first measurements were performed with cancer cell line SW 480
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Flewellen, James Lewis. "Digital holographic microscopy for three-dimensional studies of bacteria." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:94ff344b-51ec-41c5-a5f8-c579e16dccd7.
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Holography has the ability to render three-dimensional information of a recorded scene by capturing both the amplitude and phase of light incident on the recording medium. The application of digital camera technology and high-speed computing means digital holograms can be analysed numerically and novel applications can be found for this technology. This thesis explores the potential for both inline and off-axis digital holographic microscopy to study the three-dimensional swimming behaviour of bacteria. A high-magnification (225x) digital holographic microscope was designed and constructed with the ability to switch easily between inline and off-axis imaging modalities. Hardware aspects, in particular the illumination source, the choice of camera and data transfer rates, were considered. Novel strategies for off-axis holography combining dark field microscopy were designed and implemented. The localisation accuracy of the inline imaging modality was assessed by studying samples of polystyrene microspheres. The microscope is sensitive to stage drift on the order of angstroms per second and can successfully localise microspheres in dilute suspensions at least 100μm from the objective specimen plane. As a simple test of the capabilities of the microscope, the diffusion coefficient of a 0.5μm microsphere was found to be isotropic and consistent with the theoretical value. Amplitude and phase image reconstructions from the off-axis modality are demonstrated. High-magnification dark field off-axis holographic microscopy is shown to be superior to inline microscopy in localising 100nm gold nanoparticles. An artifact from our method of dark-field imaging, however, restricts the depth range to 15μm. A lower-magnification (45x) configuration of the microscope was used to study the 3D swimming behaviour of wild type Escherichia coli as a qualitative demonstration of the potential for this instrument in microbiological applications.
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Lopez, Marcio André Prieto Aparicio. "Microscopia holográfica digital aplicada na análise de tecidos biológicos." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/43/43134/tde-23032013-124944/.
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Este trabalho teve como objetivo a aplicação do Microscópio Holográfico Digital para análise de amostras biológicas, por meio de imagens de parâmetros físicos e informação quantitativa de uma amostra, gerados através de hologramas digitais, o que não ocorre na holografia clássica. O processamento e análise dos hologramas digitais foi efetuada por um programa escrito por meio do software MatLab, empregando o método de Dupla Propagação. São explicados outros métodos para tratamento de hologramas digitais, presentes no programa. O método de Dupla Propagação foi discutido, destacando suas vantagens frente aos outros métodos. Foi aplicado o método de Volkov para a retirada de ambiguidade de fase. O processo de montagem do Microscópio Holográfico Digital foi descrito, por apresentar modificações em relação ao protótipo inicial adotado. Sete amostras foram analisadas no Microscópio Holográfico Digital, três de calibração e quatro para análise - sangue e solução concentrada de proteína denominada Beta2 Glicoproteína tipo I, ou Beta2-GPI. Para calibração, foram realizados testes de formação de imagem, realizando comparação em quatro microscópios descritos e explicados em funcionamento e princípio envolvidos na formação de imagens, utilizando a mesma amostra; e verificação das dimensões de uma amostra, por meio de medição usando ferramentas disponíveis no programa. Uma amostra de sangue de um indivíduo heterozigoto para Hemoglobina S (anemia falciforme) e uma amostra de sangue de um indivíduo homozigoto para hemoglobina A1 (controle normal) foram empregadas na forma de filmes líquidos secos sobre lâminas de vidro (extensão sanguínea). O uso de fixação foi avaliado com a amostra controle. Foram geradas imagens em duas e três dimensões para as amostras biológicas, reproduzindo as estruturas morfológicas de cada. Para a proteína Beta2-GPI, a análise envolveu somente imagens, sem extração de valores; apesar disso, os resultados mostraram possibilidades de aplicações em estudos futuros. Grandezas físicas foram calculadas para dois dos componentes sanguíneos (Plasma e Eritrócito), mostrando valores próximos daqueles conhecidos anteriormente. Entretanto, alguns valores foram considerados estimativas novas, por não se conhecer, até o momento, nenhum cálculo efetuado anteriormente. A análise comprovou a formação de imagens e a capacidade de mensuração oferecida pelo aparelho. Devido ao parâmetro da fase, foi possível extrair informações em três dimensões.<br>This work aimed the implementation of the Digital Holographic Microscope for the analysis of biological samples, using physical parameters images and quantitative data from a sample, both generated through digital holograms, which does not occur in Classical holography. Processing and analysis of holograms were performed by a program written using the MatLab software, applying the Double Propagation method. Other methods for the treatment of digital holograms were explained. The Double Propagation method was discussed, highlighting their advantages over other methods. The method of Volkov was applied for removing phase ambiguity. The Digital Holographic Microscope assembly process was described, because of the modifications made to the initial prototype adopted. Seven samples were analyzed in the digital holographic microscope, three of them for calibration and the other to the analysis - blood and a concentrated solution of a protein called type I Beta2 Glycoprotein, or Beta2-GPI. Calibration tests were made by observing and comparing four image microscopes, described and explained in operation and principles involved in the formation of images, using the same testing sample; and checking the dimensions of another sample through measurement, using digital tools available in the program. Hb S heterozygous (Sickle Cell disease) and Hb A1 homozygous (Control) blood samples were prepared in microscope slide glasses. Images were acquired in two and three dimensions for biological samples, reproducing their morphological structures. For Beta2-GPI, the analysis involved only images, and no values were extracted; nevertheless, the results showed potential applications in future studies. Physical quantities were calculated for two blood components (Plasma and Erythrocyte), showing values closer to those previously known. However, some values were considered new estimates, because there is no knowledge of any calculation made previously, until now, using Digital Holographic Microscopy. The analysis proved the formation of images and the measurement capacity offered by the apparatus. Due to the phase parameter, we were able to extract information in three dimensions.
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Martinez, Marrades Ariadna. "3D microscopy by holographic localization of Brownian metallic nanoparticles." Thesis, Paris 6, 2015. http://www.theses.fr/2015PA066018/document.
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Nous présentons une nouvelle technique de microscopie stochastique basée sur un montage d'Holographie Digitale pour l'imagerie des distributions d'intensité optique. Nous montrons comment cette technique de champ lointain peut être adaptée afin d'obtenir des images de superrésolution ainsi que de champ proche. En pratique, nous imageons des nanoparticules métalliques en mouvement Brownien dans un liquide, que nous localisons ensuite dans le but de contourner la limite de diffraction. Le mouvement aléatoire des particules nous permet une exploration complète de l'échantillon. Au-delà de la simple localisation, ces marqueurs métalliques agissent comme des sondes locales du champ électromagnétique, pouvant notamment diffuser la lumière confinée vers le champ lointain. Les possibilités de cette nouvelle technique sont illustrées à travers l'imagerie de l'intensité optique d'une onde évanescente et d'une onde propagative. Grâce à des méthodes de calcul très performantes, nous sommes capables de localiser des centaines de particules par minute, avec une précision de l'ordre de 3×3×10 nm3 pour des particules immobiles. En plus de l'imagerie des distributions de champ optique, nous présentons une application combinant nos mesures superrésolues et des mesures d'électrochimie pour l'étude des processus d'oxydation de nanoparticules d'argent à proximité d'une électrode. Nos résultats ouvrent la voie à une nouvelle technique d'imagerie superrésolue, particulièrement bien adaptée à la caractérisation optique dans des milieux liquides (comme des systèmes microfluidiques), qui étaient jusqu'à présent inaccessibles par microscopie électronique ou par des microscopies à sonde locale<br>In this thesis work, we present a novel stochastic microscopy technique based on Digital Holography for the 3D mapping of optical intensity distributions. We show that this far-field, wide-field, 3D microscopy can be turned into both a superresolution and a near-field imaging technique. To do so, we use metallic nanoparticles undergoing Brownian motion as stochastic local field probes that we localize in three-dimensions in order to overcome the diffraction limit. The random motion of the particles allows for a complete exploration of the sample. Beyond simple localization, the gold markers can actually be envisaged as extremely local electromagnetic field probes, able to scatter light into the far-field. The technique we propose here is therefore a combination of the concepts of superlocalization and NSOM microscopies. The possibilities of the technique are illustrated through the 3D optical mapping of an evanescent and a propagative wave. Fast computation methods allow us to localize hundreds of particles per minute with accuracies as good as 3×3×10 nm3 for immobilized particles. In addition to optical intensity mapping, we show a particular application in electrochemistry, by coupling our high resolution images with electrochemical oxidation measurements on silver nanoparticles in solution at the vicinity of an electrode. Our results pave the way for a new subwavelength imaging technique, well adapted to optical characterization in water-based systems (such as in emerging microfluidics studies), which are mostly inaccessible to electron microscopy or local probe microscopies
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de, Leon Erich Ernesto. "Optical Design of Volume Holographic Imaging Systems for Microscopy." Diss., The University of Arizona, 2012. http://hdl.handle.net/10150/242357.
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Confocal microscopy rejects out of focus light from the object by scanning a pinhole through the object and constructing the image point by point. Volume holographic imaging (VHI) systems with bright-field illumination have been proposed as an alternative to conventional confocal type microscopes. VHI systems are an imaging modality that does not require scanning of a pinhole or a slit and thus provides video rate imaging of 3-dimensional objects. However, due to the wavelength-position degeneracy of the hologram, these systems produce less than optimal optical sectioning because the high selectivity of the volume hologram is not utilized. In this dissertation a generalized method for the design of VHI systems applied to microscopy is developed. Discussion includes the inter-relationships between the dispersive, degenerate, and depth axes of the system. Novel designs to remove the wavelength-position degeneracy and improve optical sectioning in these systems are also considered. Optimization of a fluorescence imaging system and of dual-grating confocal-rainbow designs are investigated. A ray-trace simulation that integrates the hologram diffraction efficiency and imaging results is constructed and an experimental system evaluated to demonstrate the optimization method. This results in an empirical relation between depth resolution and design tolerances. The dispersion and construction tolerances of a confocal-rainbow volume holographic imaging system are defined by the Bragg selectivity of the holograms. It is found that a broad diffraction efficiency profile of the illumination hologram with a narrow imaging hologram profile is an optimal balance between field of view, construction alignment, and depth resolution. The approach in this research is directly applicable towards imaging ovarian cells for the detection of cancer. Modeling methods, illumination design, eliminating the wavelength degeneracy of the hologram, and incorporating florescence imaging capability are emphasized in this dissertation. Results from this research may be used not only for biomedical imaging, but also for the design of volume holographic systems for both imaging and sensor applications in other fields including manufacturing (e.g. pharmaceutical), aerospace (e.g. LIDAR), and the physical sciences (e.g. climate change).
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Wu, Ning. "The use of cascaded correlation filters in holographic microscopy." Thesis, Loughborough University, 2007. https://dspace.lboro.ac.uk/2134/34156.
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Automated analysis of images collected by optical microscopes has significant potential as a straightforward and cost-effective means to screen biological samples. Depth of field restrictions, which are particularly severe in the case of high magnification and phase contrast microscopy, however, limit this approach as a means to examine more than a few nano-litres. A holographic microscope offers a solution to this problem by recording the interference between light scattered by the object field and a reference beam. In this way, all the information present in the three-dimensional scene is recorded on a single hologram without the need for mechanical scanning. A holographic microscope is thus considered as a microscope with an extended depth of field. The work presented in this thesis investigates the performance of non-linear Cascaded Correlation Filters (CCF) in two-dimensional (2D) and three-dimensional (3D) shift and rotationally invariant pattern recognition.
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Williams, Logan Andrew. "Digital Holography for Three Dimensional Tomographic and Topographic Measurements." University of Dayton / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=dayton1398436841.
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Krehl, Jonas. "Incorporating Fresnel-Propagation into Electron Holographic Tomography." Master's thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2017. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-217919.
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Tomographic electron holography combines tomography, the reconstruction of three-dimensionally resolved data from multiple measurements with different specimen orientations, with electron holography, an interferometrical method for measuring the complex wave function inside a transmission electron microscope (TEM). Due to multiple scattering and free wave propagation conventional, ray projection based, tomography does perform badly when approaching atomic resolution. This is remedied by incorporating propagation effects into the projection while maintaining linearity in the object potential. Using the Rytov approach an approximation is derived, where the logarithm of the complex wave is linear in the potential. The ray projection becomes a convolution with a Fresnel propagation kernel, which is considerably more computationally expensive. A framework for such calculations has been implemented in Python. So has a multislice electron scattering algorithm, optimised for large fields of view and high numbers of atoms for simulations of scattering at nanoparticles. The Rytov approximation gives a remarkable increase in resolution and signal quality over the conventional approach in the tested system of a tungsten disulfide nanotube. The response to noise seems to be similar as in conventional tomography, so rather benign. This comes at the downside of much longer calculation time per iteration<br>Tomographische Elektronenholographie kombiniert Tomographie, die Rekonstruktion dreidimensional aufgelößter Daten aus einem Satz von mehreren Messungen bei verschiedenen Objektorientierungen, mit Elektronenholographie, eine interferrometrische Messung der komplexen Elektronenwelle im Transmissionselektronenmikroskop (TEM). Wegen Mehrfachstreuung und Propagationseffekten erzeugt konventionelle, auf einer Strahlprojektion basierende, Tomography ernste Probleme bei Hochauflösung hin zu atomarer Auflösung. Diese sollen durch ein Modell, welches Fresnel-Propagation beinhaltet, aber weiterhin linear im Potential des Objektes ist, vermindert werden. Mit dem Rytov-Ansatz wird eine Näherung abgeleitet, wobei der Logarithmus der komplexen Welle linear im Potential ist. Die Strahlen-Projektion ist dann eine Faltung mit dem Fresnel-Propagations-Faltungskernel welche rechentechnisch wesentlich aufwendiger ist. Ein Programm-Paket für solche Rechnungen wurde in Python implementiert. Weiterhin wurde ein Multislice Algorithmus für große Gesichtsfelder und Objekte mit vielen Atomen wie Nanopartikel optimiert. Die Rytov-Näherung verbessert sowohl die Auflösung als auch die Signalqualität immens gegenüber konventioneller Tomographie, zumindest in dem getesteten System eines Wolframdisulfid-Nanoröhrchens. Das Rauschverhalten scheint ähnlich der konventionallen Tomographie zu sein, also eher gutmütig. Im Gegenzug braucht die Tomographie basierend auf der Rytov-Näherung wesentlich mehr Rechenzeit pro Iteration
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Perfetti, Claire. "Particle manipulation in minichannels for enhanced digital holographic microscopy observation." Doctoral thesis, Universite Libre de Bruxelles, 2014. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/209283.
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The development of techniques targeting the manipulation of particles of different<p>sizes - mostly in the nano to millimeter scale - when dispersed in a carrier medium, is an increasingly important topic in many fields such as biotechnology,nanotechnology, medicine, biophysics and environmental monitoring and remediation. The underlying rationale for using such techniques stands in the sometimes compelling requirements of avoiding clogging as in micro/nano channel flows, of limiting sedimentation and wall interactions in particle/cell counting, of enhancing particle-surface interaction as in bio-sensing or of facilitating characterization and sorting as in bio-physical applications. Being developed in the frame of a Belgian national project devoted to the characterization and counting of pollutant in water media by digital holographic microscopy, this thesis tackles a peculiar class of particle manipulation techniques, commonly known as Focusing. The main goal of focusing is to avoid at best wall particle interactions and sedimentation, prevalent issues for dispersions owing in micro/mini-channels especially for applications such as optical characterization and counting.<p><p>The main attention was given to two flow focusing techniques - Hydrodynamic and Acoustic Focusing - for their wide range applicability and cost effectiveness. Hydrodynamic Focusing consists in controlling the position and spreading of the sample under investigation by means of a so-called sheath flow. A low-cost, nevertheless effective, prototype has been conceived, designed, manufactured and tested. It allowed for controlling the spreading of the sample stream and achieving a focusing ratio accounting for only 4% of the original stream width.<p><p>Acoustic Focusing takes advantage of the time-averaged pressure fields induced by the creation of standing waves in channels to manipulate and focus the dispersed particles. In the frame of this thesis, several devices have been developed using square cross section glass mini-channels. Aside from the cost-effectiveness, particles where focused in a somehow unexpected but high reproducible 3D matrix-like structure. A novel numerical model has also been implemented in order to study the conditions leading to the 3D structure formation. A good agreement between experimental and numerical results was found./Ce projet de thèse portant sur la manipulation de micro-particules dans des minicanaux s'inscrit dans le développement de cellules de flux pour des applications biologiques, qui est l'une des problématiques du projet HOLOFLOW, soutenu par<p>la région de Bruxelles Capitale. Les cellules de flux doivent permettre l'observation et la reconnaissance des micro-organismes vivants dans une large gamme de dimensions (de quelques microns à 1mm) avec la microscopie holographie digitale.<p>La problématique d'observation et de manipulation des microorganismes en flux est liée au clogging (bouchage) et à la sédimentation qui limitent la durée de vie des cellules d'observation. Ce projet de thèse s'inscrit dans cette problématique et propose deux axes d'étude pour limiter l'interaction entre organismes et canaux, la focalisation hydrodynamique, basée sur le guidage de flux, et la focalisation acoustique, basée sur la manipulation des particules.<p><p>La focalisation hydrodynamique est une technique basée sur l'injection différentiée de l'échantillon à observer et d'un fluide support. La différence des vitesses d'injection des flux permet de contrôler la dispersion des particules afin d'optimiser leur observation. Dans le cadre de cette thèse, un prototype à bas-coût a été développé et construit, permettant de focaliser les particules dans un faisceau jusqu'à 4% de leur faisceau incident.<p><p>La focalisation acoustique utilise la création d'une onde acoustique stationnaire afin de regrouper les particules en suspension au centre du canal. Au cours de cette thèse, plusieurs prototypes ont été réalisés, mettant en évidence la formation de motifs tridimensionnaux. Un model numérique a été spécialement développé afin d'étudier les conditions de génération de ces motifs, et de nombreuses expériences ont été menées afin de s'assurer de leur reproductibilité. Une bonne adéquation entre la position des particules mesurée et calculée numériquement a été démontrée.<br>Doctorat en Sciences de l'ingénieur<br>info:eu-repo/semantics/nonPublished
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Abrahamsson, Anton. "Three dimensional tracking of multiple objects using digital holographic microscopy." Thesis, Umeå universitet, Institutionen för fysik, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-124722.
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Naidoo, Thegaran. "Digital holographic microscopy with automated detection of red blood cells." Diss., University of Pretoria, 2017. http://hdl.handle.net/2263/61032.
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The digital in-line holographic configuration is motivated by the goal of developing a portable, cost effective sensor system for pre-screening patient blood samples. The theory of holography is explained from the foundational concepts in scalar diffraction theory all the way through to the implementation of reconstruction algorithms. Methods for the enhancement of holographic reconstructions are described. The algorithms that perform an automated count of the reconstructed objects are described and demonstrated. Simulated and experimental results are provided. Together, the lens-free holographic microscopy of micro-sized particles along with the application of image processing techniques for the automated detection and counting of objects of interest, provide a component towards realising a sensor system that can be used for pre-screening patient blood samples.<br>Dissertation (MSc)--University of Pretoria, 2017.<br>CSIR<br>Computer Science<br>MSc<br>Unrestricted
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Fernández, Meylí Valin. "Desenvolvimento da microscopia holográfica digital por reflexão para avaliação 3D de superfícies." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/3/3151/tde-04012018-105154/.
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Dentre dos procedimentos geradores de perfil óptico encontra-se a microscopia holográfica digital. Esta ferramenta interferométrica surgiu da ideia inicial proposta por D. Gabor sobre holografia, a qual permite mediante o registro da interferência de campos ópticos coerentes, guardar e extrair informações de imagens. A microscopia holográfica digital permite a análise de objetos com resoluções transversais semelhantes às obtidas por microscopia óptica, e ainda, possui a vantagem pela natureza da holografia de permitir realizar análises através do acesso a valores quantitativos de fase. Apresentam-se neste trabalho os conceitos básicos da holografia digital e da microscopia holográfica digital, com o objetivo, de introduzir o desenvolvimento de uma metodologia para a implementação da microscopia holográfica digital por reflexão para o controle dimensional de objetos e determinação da rugosidade superficial de amostras de aço. Os hologramas são obtidos mediante uma instalação óptica, que consiste em um interferômetro de Michelson por reflexão com o uso de uma lente objetiva de microscópio e uma câmera CCD sem lente. Para a reconstrução das imagens de contraste de fase são utilizadas técnicas numéricas que capacitam à microscopia holográfica digital para a supressão do termo de ordem zero, controle da resolução de pixel, desmodulação da fase óptica, determinação dos mapas de intensidades e fase, filtragem e compensação de aberrações dos hologramas obtidos. As reconstruções numéricas dos feixes objeto e referência são realizadas utilizando o método de dupla propagação. Foi desenvolvido um algoritmo que apresenta a imagem de contraste de fase com base num critério de distância a partir de um único holograma. Desta forma o programa utilizado permite a realização de medições quantitativas das dimensões dos objetos e da rugosidade superficial de amostras de aço, assim como, a representação em 3D da imagem de fase reconstruída com resultados validados através de um perfilômetro óptico 3D sem contacto modelo CCI-MP.<br>Among the procedures generating optical profile is the digital holographic microscopy. This interferometric tool arose from the initial idea proposed by D. Gabor on holography, which allows by recording the interference of coherent optical fields, save and extract information from images. Digital holographic microscopy allows the analysis of objects with transversal resolutions similar to those obtained by optical microscopy, and also has the advantage of the nature of holography to allow to perform analyzes through the access to quantitative phase values. This paper presents the basic concepts of digital holography and digital holographic microscopy, with the objective of introducing the development of a methodology for the implementation of digital holographic microscopy by reflection for the dimensional control of objects and determination of surface roughness of samples of steel. The holograms are obtained by means of an optical installation consisting of a Michelson interferometer by reflection using an objective microscope lens and a lensless CCD camera. For the reconstruction of phase contrast images, numerical techniques are used that enable digital holographic microscopy to suppress the zero-order term, control pixel resolution, optical phase demodulation, determination of intensity and phase maps, filtering and compensation of aberrations of the obtained holograms. Numerical reconstructions of the object and reference beams are performed using the double propagation method. An algorithm has been developed that presents the phase contrast image based on a distance criterion from a single hologram. In this way the program used allows the realization of quantitative measurements of the object dimensions and the surface roughness of steel samples, as well as the 3D representation of the reconstructed phase image with results validated through a 3D contactless optical profilometer model CCI- MP.
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McReynolds, Naomi. "Advanced multimodal methods in biomedicine : Raman spectroscopy and digital holographic microscopy." Thesis, University of St Andrews, 2017. http://hdl.handle.net/10023/12129.
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Moving towards label-free technologies is essential for many clinical and research applications. Raman spectroscopy is a powerful tool in the field of biomedicine for label-free cell characterisation and disease diagnosis, owing to its high chemical specificity. However, Raman scattering is a relatively weak process and can require long acquisition times, thus hampering its integration to clinical technologies. Multimodal analysis is currently pushing the boundaries in biomedicine, obtaining more information than would be possible using a single mode and overcoming any limitations specific to a single technique. Digital holographic microscopy (DHM) is a rapid and label-free quantitative phase imaging modality, providing complementary information to Raman spectroscopy, and is thus an ideal candidate for combination in a multimodal system. Firstly, this thesis explores the use of wavelength modulated Raman spectroscopy (WMRS), for the classification of immune cell subsets. Following this a multimodal approach, combining Raman spectroscopy and DHM, is demonstrated, where each technique is considered individually and in combination. The complementary modalities provide a wealth of information (both chemical and morphological) for cell characterisation, which is a step towards achieving a label-free technology for the identification of human immune cells. The suitability of WMRS to discriminate between closely related neuronal cell types is also explored. Furthermore optical spectroscopic techniques are useful for the analysis of food and beverages. The use of Raman and fluorescence spectroscopy to successfully discriminate between various whisky and extra-virgin olive oil brands is demonstrated, which may aid the detection of counterfeit or adulterated samples. The use of a compact Raman device is utilised, demonstrating the potential for in-field analysis. Finally, monodisperse and highly spherical nanoparticles are synthesised. A short study demonstrates the potential for these nanoparticles to benefit the techniques of surface enhanced Raman spectroscopy and optical trapping, by way of minimising variability.
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Kirchmann, Carl Christian, Elin Lundin, and Jakob Andrén. "A Study of Digital In-Line Holographic Microscopy for Malaria Detection." Thesis, Uppsala universitet, Institutionen för teknikvetenskaper, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-229840.
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The main purpose of the project was to create an initial lab set-up for a dig-ital in-line holographic microscope and a reconstruction algorithm. Different parameters including: light source, pin-hole size and distances pinhole-object and object-camera had to be optimized. The lab set-up is to be developed further by a master student at the University of Nairobi and then be used for malaria detection in blood samples. To acquire good enough resolution for malaria detection it has been found necessary to purchase a gray scale camera with smaller pixel size. Two dierent approaches, in this report called the on-sensor approach and the object-magnication approach, were investigated. A reconstruction algorithm anda phase recovery algorithm was implemented as well as a super resolution algorithm to improve resolution of the holograms. The on-sensor approach proved easier and cheaper to use with approximately the same results as the object-magnication method. Necessary further research and development of experimental set-up was thoroughly discussed.<br>Projketet har gått ut på att bygga en billigare och enklare metod för att identifiera malaria i blodprover. Malaria är ett stort problem i en mängd områden i världen. Flera av dessa är fattiga och kan i nuläget inte tillhandahålla den här tjänsten till sin befolkning. Förutom att dyr apparatur krävs måste även utbildad personal lägga ner mycket tid för att kolla en stor mängd blodprover för att statistiskt säkerställa om en person har malaria eller inte. Vårt mål var att bygga en labbuppställning för "Digital in line holographic microscopy" och en rekonstruktionsalgoritm som en masterstudent vid Nairobi universitet ska fortsätta utveckla. Vi kom också fram till vilken upplösning som krävdes för att kunna urskilja malaria i blodproverna. Digital in line holographic microscopy går till så att man har en ljuskälla som riktas genom ett pinnhål, ljuset som går genom pinnhålet ljuser upp det prov, blodproverna i vårt fall, man vill undersöka och det resulterande ljuset fångas på en kamera. Med kunskap om fourieroptik går det att rekonstruera den digitala bilden man fångat på kameran, innan rekonstruktion är den ett hologram vilken är svårtydd. Labbuppställningen byggdes delvis med en 3D printer. För att förbättra resultaten implementerades flera algoritmer vilka lade ihop en mängd förskjutna bilder till en bättre bild, så kallad super resolution. Vi lyckades inte komma till den upplösning som krävdes för att urskilja malaria men gjorde en grundlig förstudie och en utförlig beskrivning av det arbete som väntar den student som fortsätter med projektet. Framför allt beskrevs värden på parametrar och vilken typ av kamera som ska användas för att optimera uppställningen.
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Lahrashe, Moktar. "Atomic force microscopy of soft surface : Characterisation of holographic optical elements." Université Louis Pasteur (Strasbourg) (1971-2008), 2005. http://www.theses.fr/2005STR13046.
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Les méthodes pour la measurement des surfaces ont progressé d’une façon significative les dernières années. Elles ont été favorisées par les besoins de lithographie avancée. Le but de cette thèse est d’appliquer les techniques récemment développées au problème spécifique de l'étude de la structure de surface des réseaux holographiques. Au début de cette thèse, nous avons fait une recherche bibliographique dans le but de trouver le meilleur dispositif pour notre travail. Le dispositif choisi est un microscope à force atomique (AFM). Ce dernier est un outil permettant une mesure localisée d’une résolution sans précédent. L'AFM fournit une image des structures de surface dans une plage de quelques nanomètres à quelques centaines de micromètres. Cette flexibilité permet de réaliser une analyse quantitative de la microrugosité des surfaces avec de grande sensitivité et précision. Plusieurs exemples de réseaux holographiques enregistrés sur les plaques sont étudiés. Nous avons procédé pour chaque type de plaque à l’analyse du profil du réseau, de sa profondeur, de sa rugosité et la mesuré de le module élastique a été effectue. En outre, le sondage AFM des structures sub-surfaciques a été réalisé pour les échantillons holographiques avec la gélatine comme étant la couche supérieure. Une méthode optique complémentaire nous a servit pour obtenir des informations sur les caractéristiques global des réseaux holographiques : Indice de réfraction, modulation d'indice de réfraction, période du réseau, épaisseur de l'émulsion et absorption et pertes de dispersion ont été mesuré<br>Driven largely by the needs for advanced lithographic processes surface measurement methods have significantly advanced in the last decade. The aim of this thesis is to apply recently developed measuring techniques to the specific problem of investigating the surface structure of holographic recording gratings. At the start of thesis, search for relevant literature was given high priority, with the purpose to find the best measuring device suitable for this investigation. The device chosen was an atomic force microscope (AFM) which is a tool that enables the spatially localised measurements with unprecedented resolution. AFM provides high-resolution imaging of surface structures from few nanometres to hundreds of micrometres. This capability is useful for quantitative analysis of surface micro-roughness of technological surfaces with high sensitivity and accuracy. Various holographic gratings are studied, along with the sequence by which raw images are analysed for grating profile, profile consistency, grating depth, profile roughness and elastic modulus. In addition, AFM probing of subsurface structures has been achieved for holographic samples with gelatine - like top layers. The AFM characterisation is completed with optical characterisation of holographic gratings: i. E. The refractive index, the refractive index modulation, the groove period, the emulsion thickness and the absorption and the scattering losses are determined by this method
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Yu, Xiao. "Study of the Motility of Biological Cells by Digital Holographic Microscopy." Scholar Commons, 2014. https://scholarcommons.usf.edu/etd/5159.
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In this dissertation, I utilize digital holographic microscopy (DHM) to study the motility of biological cells. As an important feature of DHM, quantitative phase microscopy by digital holography (DH-QPM) is applied to study the cell-substrate interactions and migratory behavior of adhesive cells. The traction force exerted by biological cells is visualized as distortions in flexible substrata. Motile fibroblasts produce wrinkles when attached to a silicone rubber film. For the non-wrinkling elastic substrate polyacrylamide (PAA), surface deformation due to fibroblast adhesion and motility is visualized as tangential and vertical displacement. This surface deformation and the associated cellular traction forces are measured from phase profiles based on the degree of distortion. Intracellular fluctuations in amoeba cells are also analyzed statistically by DH-QPM. With the capacity of yielding quantitative measures directly, DH-QPM provides efficient and versatile means for quantitative analysis of cellular or intracellular motility.
Three-dimensional profiling and tracking by DHM enable label-free and quantitative analysis of the characteristics and dynamic processes of objects, since DHM can record real-time data for micro-scale objects and produce a single hologram containing all the information about their three-dimensional structure. Here, I utilize DHM to visualize suspended microspheres and microfibers in three dimensions, and record the four-dimensional trajectories of free-swimming cells in the absence of mechanical focus adjustment. The displacement of microfibers due to interactions with cells in three spatial dimensions is measured as a function of time at sub-second and micrometer levels in a direct and straightforward manner. It has thus been shown that DHM is a highly efficient and versatile means for quantitative tracking and analysis of cell motility.
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Fung, Jerome. "Measuring the 3D Dynamics of Multiple Colloidal Particles with Digital Holographic Microscopy." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:11200.
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We discuss digital holographic microscopy (DHM), a 3D imaging technique capable of measuring the positions of micron-sized colloidal particles with nanometer precision and sub-millisecond temporal resolution. We use exact electromagnetic scattering solutions to model holograms of multiple colloidal spheres. While the Lorenz-Mie solution for scattering by isolated spheres has previously been used to model digital holograms, we apply for the first time an exact multisphere superposition scattering model that is capable of modeling holograms from spheres that are sufficiently close together to exhibit optical coupling.<br>Physics
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Nguyen, Minh-Chau. "Chemistry of individual nanoparticles : 3D tracking by holographic microscopy and dynamic spectroscopy." Thesis, Université de Paris (2019-....), 2019. http://www.theses.fr/2019UNIP7196.
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Dans ce travail, nous avons développé un système de spectroscopie dynamique utilisant l'holographie afin de surmonter cette difficulté. Notre stratégie est de localiser la nanoparticule en 3D et en temps réel grâce à l’holographie, et d’utiliser la position mesurée afin d’asservir le mouvement de la zone de collection du spectromètre. Notre système est donc constitué de deux parties principales: un microscope holographique pour le suivi 3D de la nanoparticule et un système optique adaptatif pour le déplacement de la zone de mesure spectroscopique. Après validation, ce système a été appliqué à l’étude du changement spectral de nanoparticules soumises à un échange galvanique. Dans cette réaction, un métal (Ag) est réduit et dissous pour être remplacé par un métal plus noble (Au) présent en solution sous forme ionique. Pour appréhender ce type de réaction la solution d’ions Au3+ est produite par voie électrochimique. Ceci permet le contrôle du déclenchement de la modification profonde de la particule qui s’accompagne d’une modification de son spectre de diffusion, et nous a permis de suivre la cinétique de la réaction. Par ailleurs, le suivi holographique de la trajectoire permet une mesure du rayon hydrodynamique de la particule, donc de l’évolution de son volume. Ces mesures indépendantes fournissent un tableau complet et cohérent du déroulement de la réaction<br>In this work, we developed a holography-based dynamic spectroscopy system in order to localize the nanoparticle in 3D and in real time, and use this position to move the spectroscopic measurement zone. Therefore, it consists of two main parts: an off-axis holographic microscope for 3D nanoparticle localization, and (ii) an adaptive optical system to position the spectral collection zone in 3D. Using this system, we monitored nanoparticles undergoing a galvanic exchange, i.e. a redox reaction in which a metal (Ag) is reduced and dissolved, to be replaced by a more noble metal (Au) present in ionic form in the solution. This change in the particle composition is here triggered by an electrochemical generation of the Au3+ ions solution. It induces a dynamic spectral shift which provides a first insight into the kinetics of the reaction. In addition, 3D particle tracking provides a measurement of the hydrodynamic radius of the particle, which affects Brownian motion. Together, these independent measurements give a relatively complete and coherent picture of the transformation undergone by these nanoparticles
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Rosová, Kateřina. "Justážní kolimátor pro Fluorescenční holografický mikroskop." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2018. http://www.nusl.cz/ntk/nusl-392837.
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For the proper function of the Fluorescence olographic microscope, it is necessary to adjust all the optical components of the microscope. Furthermore, the precise adjustment is the very critical condition for proper imaging of the Coherence-controlled holographic microscope. Therefore, it is necessary to create a sight collimator for these microscopes for their adjustment. The fluorescence holographic microscope is based on an interference and holographic principles, whose history is mentioned in the theoretical part of the thesis. The existing state of the art of laser sight collimators and their use in practice is also mentioned. The optical and mechanical design of the laser sight collimator and its realization are described in the next part of the thesis. The software for detecting the black sight cross was created for the use of the laser sight collimator in practice. The software is necessary to evaluate the correctness of the alignment of the adjusted microscope. The descriptions of the adjustment procedures for the laser sight collimator and for the Fluorescence holographic microscope are mentioned in the last part of the thesis. These procedures are necessary for proper manipulation and use with the proposed laser sight collimator.
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Khmaladze, Alexander. "Three-dimensional microscopy by laser scanning and multi-wavelength digital holography." [Tampa, Fla] : University of South Florida, 2008. http://purl.fcla.edu/usf/dc/et/SFE0002638.
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Týč, Matěj. "Trojrozměrná rekonstrukce obrazu v digitální holografické mikroskopii." Doctoral thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2015. http://www.nusl.cz/ntk/nusl-234389.
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This thesis deals with the topic of 3D image processing for digital holographic microscopy - numerical refocusing. This method allows to perform mathematically accurate defocus correction on image of a sample captured away from the sample plane and it was applicable only for images that were made made using coherent illumination source. It has been generalized to a form in which it is also applicable to devices that use incoherent (non-monochromatic or extended) illumination sources. Another presented achievement concerns hologram processing. The advanced hologram processing method enables obtaining more data mainly concerning precision of quantities from one hologram — normally, one would have to capture multiple holograms to get those. Both methods have been verified experimentally.
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Ash, William Mason III. "Total Internal Reflection Holographic Microscopy (TIRHM) for Quantitative Phase Characterization of Cell-Substrate Adhesion." Scholar Commons, 2010. https://scholarcommons.usf.edu/etd/1564.
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Total Internal Reflection Holographic Microscopy (TIRHM) combines near-field microscopy with digital holography to produce a new form of near-field phase microscopy. Using a prism in TIR as a near-field imager, the presence of microscopic organisms, cell-substrate interfaces, and adhesions, causes relative refractive index (RRI) and frustrated TIR (f-TIR) to modulate the object beam's evanescent wave phase front. Quantitative phase images of test specimens such as Amoeba proteus, Dictyostelium Discoideum and cells such as SKOV-3 ovarian cancer and 3T3 fibroblasts are produced without the need to introduce stains or fluorophores. The angular spectrum method of digital holography to compensate for tilt anamorphism due to the inclined TIR plane is also discussed.
The results of this work conclusively demonstrate, for the first time, the integration of near-field microscopy with digital holography. The cellular images presented show a correlation between the physical extent of the Amoeba proteus plasma membrane and the adhesions that are quantitatively profiled by phase cross-sectioning of the holographic images obtained by digital holography. With its ability to quantitatively characterise cellular adhesion and motility, it is anticipated that TIRHM can be a tool for characterizing and combating cancer metastasis, as well as improving our understanding of morphogenesis and embryogenesis itself.
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Boussemaere, Luc. "Investigating off-axis digital holographic microscopy with a source of partial spatial coherence as a real-time sensor for cell cultures." Doctoral thesis, Universite Libre de Bruxelles, 2015. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/209086.
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Bio-pharmaceutical industry is a vast growing market and recent recommendations of the Food and Drug Administration have put a large emphasis on the characterization of biological processes and models. As a consequence, there is a high incentive on developing modern sensors in order to more accurately monitor and control processes. In that way, Digital Holographic Microscopy (DHM) presents unique features thanks to the refocusing and quantitative phase contrast imaging capabilities. In this thesis we investigate the usage of DHM to monitor yeast cultures that are often used in both the bio-pharmaceutical and bread industries and lay the basis of a methodological framework for the study of in-line cell cultures in the context of process control. We begin with a description of Digital Holography and the microscopy setup used in the thesis as well as a detailed explanation of the image processing required to extract the holographic data and its implementation on GPU with some speed execution figures given for three popular programming paradigms. We then describe the flow setup used and infer the limitations on the dynamic range of the technique due to both Poisson statistics and overlapping phenomena. Finally, we describe an algorithm that extracts the cells position, count and morphological information such as the size, aspect ratio, circularity and refraction index. Some experimental results are presented for yeasts before drawing a general overview of the technology and its dependencies. We further end with some conclusions concerning the technology and a brief comparison with existing competitors.<br>Doctorat en Sciences de l'ingénieur<br>info:eu-repo/semantics/nonPublished
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Mann, Christopher J. "Quantiative biological microsocopy by digital holography." Scholar Commons, 2006. http://scholarcommons.usf.edu/etd/2614.
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In this dissertation, improved techniques in digital holography, that have produced high-resolution, high-fidelity images, are discussed. In particular, the angular spectrum method of calculating holographic optical field is noted to have several advantages over the more commonly used Fresnel transformation or Huygens convolution method. It is observed that spurious noise and interference components can be tightly controlled through the analysis and filtering of the angular spectrum. In the angular spectrum method, the reconstruction distance does not have a lower limit, and the off-axis angle between the object and reference waves can be lower than that of the Fresnel requirement, while still allowing the zero-order background to be cleanly separated. Holographic phase images are largely immune from the coherent noise commonly found in amplitude images. With the use of a miniature pulsed laser, the resulting images have 0.5um diffraction-limited lateral resolution and the phase profile is accurate to about several nanometers of optical path length. Samples such as ovarian cancer cells (SKOV-3) and mouse-embryo fibroblast cells have been imaged. These images display intra-cellular and intra-nuclear organelles with clarity and quantitative accuracy. This technique clearly exceeds currently available methods in phase-contrast opticalmicroscopy in both resolution and detail and provides a new modality for imaging morphology of cellular and intracellular structures that is not currently available. Furthermore, we also demonstrate that phase imaging digital holographic movies provide a novel method of non-invasive quantitative viewing of living cells and other objects. This technique is shown to have significant advantages over conventional microscopy.
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Ugele, Matthias [Verfasser], Oliver [Akademischer Betreuer] Friedrich, and Oliver [Gutachter] Friedrich. "High-throughput hematology analysis with digital holographic microscopy / Matthias Ugele ; Gutachter: Oliver Friedrich ; Betreuer: Oliver Friedrich." Erlangen : Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 2019. http://d-nb.info/1190892278/34.
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Grosse, Doris [Verfasser], Martin [Gutachter] Hofmann, and Thomas [Gutachter] Mussenbrock. "Topographic measurements using digital holographic microscopy combined with photorefractive single-shot holography / Doris Grosse ; Gutachter: Martin Hofmann, Thomas Mussenbrock ; Fakultät für Elektrotechnik und Informationstechnik." Bochum : Ruhr-Universität Bochum, 2014. http://d-nb.info/1214440932/34.
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Flasseur, Olivier. "Object detection and characterization from faint signals in images : applications in astronomy and microscopy." Thesis, Lyon, 2019. http://www.theses.fr/2019LYSES042.
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La détection et la caractérisation d’objets dans des images à faible rapport signal sur bruit est un problème courant dans de nombreux domaines tels que l’astronomie ou la microscopie. En astronomie, la détection des exoplanètes et leur caractérisation par imagerie directe depuis la Terre sont des sujets de recherche très actifs. Une étoile cible et son environnement proche (abritant potentiellement des exoplanètes) sont observés sur de courtes poses. En microscopie, l’holographie en ligne est une méthode de choix pour caractériser à faibles coûts les objets microscopiques. Basée sur l’enregistrement d’un hologramme, elle permet une mise au point numérique dans n’importe quel plan du volume 3-D imagé. Dans ces deux applications cibles, le problème est rendu difficile par le faible contraste entre les objets et le fond non stationnaire des images enregistrées.Dans cette thèse, nous proposons un algorithme non-supervisé dédié à la détection et à la caractérisation d’exoplanètes par une modélisation statistique des fluctuations du fond. Cette méthode est basée sur une modélisation de la distribution statistique des données à une échelle locale de patchs, capturant ainsi leur covariances spatiales. Testé sur plusieurs jeux de données de l’imageur haut-contraste SPHERE opérant au Très Grand Télescope Européen, cet algorithme atteint de meilleures performances que les méthodes de l’état de l’art. En particulier, les cartes de détection produites sont stationnaires et statistiquement fondées. La détection des exoplanètes peut ainsi être effectuée à probabilité de fausse alarme contrôlée. L’estimation de la distribution d’énergie spectrale des sources détectées est également non biaisée. L’utilisation d’un modèle statistique permet également de déduire des précisions photométriques et astrométriques fiables. Ce cadre méthodologique est ensuite adapté pour la détection de motifs spatialement étendus tels que les motifs de diffraction rencontrés en microscopie holographique qui sont également dominés par un fond non-stationnaire. Nous proposons aussi des approches robustes basées sur des stratégies de pondération afin de réduire l’influence des nombreuses valeurs aberrantes présentes sur les données réelles. Nous montrons sur des vidéos holographiques que les méthodes de pondération proposées permettent d’atteindre un compromis biais/variance. En astronomie, la robustesse améliore les performances de détection, en particulier à courtes séparations angulaires, où les fuites stellaires dominent. Les algorithmes développés sont également adaptés pour tirer parti de la diversité spectrale des données en plus de leur diversité temporelle, améliorant ainsi leurs performances de détection et de caractérisation. Tous les algorithmes développés sont totalement non-supervisés: les paramètres de pondération et/ou de régularisation sont estimés directement à partir des données. Au-delà des applications considérées en astronomie et en microscopie, les méthodes de traitement du signal introduites dans cette thèse sont générales et pourraient être appliquées à d’autres problèmes de détection et d’estimation<br>Detecting and characterizing objects in images in the low signal-to-noise ratio regime is a critical issue in many areas such as astronomy or microscopy. In astronomy, the detection of exoplanets and their characterization by direct imaging from the Earth is a hot topic. A target star and its close environment (hosting potential exoplanets) are observed on short exposures. In microscopy, in-line holography is a cost-effective method for characterizing microscopic objects. Based on the recording of a hologram, it allows a digital focusing in any plane of the imaged 3-D volume. In these two fields, the object detection problem is made difficult by the low contrast between the objects and the nonstationary background of the recorded images.In this thesis, we propose an unsupervised exoplanet detection and characterization algorithm based on the statistical modeling of background fluctuations. The method, based on a modeling of the statistical distribution of patches, captures their spatial covariances. It reaches a performance superior to state-of-the-art techniques on several datasets of the European high-contrast imager SPHERE operating at the Very Large Telescope. It produces statistically grounded and spatially-stationary detection maps in which detections can be performed at a constant probability of false alarm. It also produces photometrically unbiased spectral energy distributions of the detected sources. The use of a statistical model of the data leads to reliable photometric and astrometric accuracies. This methodological framework can be adapted to the detection of spatially-extended patterns in strong structured background, such as the diffraction patterns in holographic microscopy. We also propose robust approaches based on weighting strategies to reduce the influence of the numerous outliers present in real data. We show on holographic videos that the proposed weighting approach achieves a bias/variance tradeoff. In astronomy, the robustness improves the performance of our detection method in particular at close separations where the stellar residuals dominate. Our algorithms are adapted to benefit from the possible spectral diversity of the data, which improves the detection and characterization performance. All the algorithms developed are unsupervised: weighting and/or regularization parameters are estimated in a data-driven fashion. Beyond the applications in astronomy and microscopy, the signal processing methodologies introduced are general and could be applied to other detection and estimation problems
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Farré, Flaquer Arnau. "Momentum measurements of single-beam traps and quantitative holographic experiments: two sides of the same coin." Doctoral thesis, Universitat de Barcelona, 2012. http://hdl.handle.net/10803/83665.
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After an intense development of optical tweezers as a biophysical tool during the last decades, quantitative experiments in living cells have not found in this technique its best ally, due, in part, to the lack of a reliable method to measure forces in complex environments. The attempts to overcome this problem either require complicated in situ calibrations, which make their use impossible in the study of dynamic processes, or they are inaccurate. Using a different approach, Steven Smith at Carlos Bustamante’s lab at the University of Berkeley developed a method based on the direct measurement of the momentum change of the trapping beam. However, its diffusion has been modest mainly because it requires a counter-propagating optical trapping system, which is difficult to implement and combine with other techniques. Although it has not been used for this purpose yet, it seems a more suitable method for in vivo experiments since the measurement depends only on some properties of the sensor apparatus but not on the experiment itself.
On the other hand, the use of holographic optical tweezers in molecular biology experiments involving force and position measurements is still far from established. The existence of different effects associated to the use of spatial light modulators to create the optical traps has restricted their use.
In this thesis, I present the work that I carried out in the Optical Trapping Lab – Grup de Biofotònica at the University of Barcelona related to these two subjects. During these years, I have focused on the implementation of the force detection method based on the conservation of the light momentum in single-beam optical traps, and on the analysis of several aspects of holographic tweezers oriented to their use in quantitative experiments.
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Findejsová, Anna. "Rekonstrukční metody v holografické mikroskopii." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2019. http://www.nusl.cz/ntk/nusl-400998.
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This master’s thesis focuses on the image reconstruction from holographic microscope. The first part of the thesis summarizes problems of holography, describes its principle and application particularly in live cell biology. In the second part the description of several methods used for off-axis hologram reconstruction is provided. The last part describes the implementation of the basic step in holographic reconstruction – the elimination of autocorrelation and twin image – and then also the reconstruction of 3D information of the sample.
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Vašíček, David. "Fluorescenční zobrazovací techniky v multimodálním holografickém mikroskopu." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2014. http://www.nusl.cz/ntk/nusl-231466.
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The diploma thesis deals with the registration of images taken with the multimodal holographic microscope (MHM). The summary covers the fluorescent and holographic microscopy, and the multimodal holographic microscope combining both these microscopy types. Every pair of the images needs to be aligned in order to gain new information by combining both image types. The thesis contains an algorithm that registers images by phase correlation as well as a process created in MATLAB in accordance with the algorithm. The most important procedure parameters’ influence on the registration success is described and the results are annotated.
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Samaan, Julien. "Étude et applications de l'imagerie sans lentille par diffraction cohérente." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLS557/document.
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Ce mémoire est dédié à l’imagerie par diffraction cohérente. Dans un premier temps, nous présentons la conception et à la mise en oeuvre expérimentale d’un système d’imagerie compact fonctionnant sur ce principe. Il est composé d’unediode UV (λ = 400 nm), d’une caméra CCD, et d’une plate-forme pour placer l’échantillon à observer. Le faisceau cohérent issu de la diode éclaire l’échantillon, et la figure de diffraction est enregistrée par la caméra. La rétro-propagation du champ détecté permet, en principe, de déterminer le profil de l’échantillon. Néanmoins, la phase du champ, perdue lors de la détection, nous contraint à employer desméthodes de « reconstruction de la phase », cette quantité étant nécessaire à l’opération d’inversion. Plusieurs techniques ont été utilisées. L’holographie par Transformée de Fourier, par exemple, est une méthode déterministe qui consiste à utiliser une référence circulaire (ou rectangulaire) gravée à côté de l’échantillon. La phase est encodée dans la figure de diffraction, sous la forme de franges d’interférences issues de l’objet et de la référence. Une simple Transformée de Fourier du signal permet alors de retrouver le profil de l’échantillon. Uneméthode itérative a également été mise en oeuvre, basée sur un jeu de contraintes dans les espaces réel et réciproque. En particulier, l’objet éclairé doit être « isolé », i.e. plus petit que le faisceau incident. Bien que cette méthode soit non-déterministe, nous verrons toutefois qu’elle est plus robuste et permet d’obtenir de meilleures résolutions spatiales qu’en holographie. Cette étude est un point de départ à l’observation d’objets tridimensionnels. Nous présentons une première méthode déterministe, basée sur l’holographie par Transformée de Fourier. Pour ce faire, une « pupille holographique » est utilisée et sert de support à une première reconstruction 2D du champ. Celui-ci est ensuite rétro-propagé vers l’échantillon placé à proximité, afin de réaliser une mise au point entièrement numérique de ce dernier. La contrainte « d’isolation » de l’objet est alors levée par l’utilisation de cette pupille. Avec cette méthode, le champ latéral est toutefoislimité par le diamètre de la pupille. Pour l’observation d’échantillons plus larges, la technique d’holographie « en ligne » a également été exploitée. Elle consiste à éclairer l’objet avec une onde sphérique et à enregistrer les franges d’interférences (ou « hologramme »). Une rétro-propagation est ensuite effectuée pour faire la mise au point sur l’échantillon. Le caractère divergent du faisceau permet de disposer d’un champ latéral de plusieurs millimètres. Le problème de « l’image jumelle », inhérent à cette configuration, est résolu via unalgorithme itératif couplé à la rétro-propagation. Des reconstructions tridimensionnelles ont été effectuées sur divers échantillons, avec cesdeux méthodes — reconstruction pupillaire et holographie en ligne. Pour chacune d’entre elles, des interfaces de reconstruction ont été mises au point et fonctionnent pendant la détection, afin d’observer l’objet en temps réel. Nous disposons alors d’un prototype d’imagerie sans lentille compact et complet. Enfin, nous présentons l’application d’une technique de reconstruction de la phase, appelée LIFT (pour LInearized Focal plane Technique), appliquée à un analyseur de front d’onde Shack-Hartmann. Usuellement, de tels capteurs ont une résolution spatiale limitée par le pas des micro-lentilles : seules les pentes locales (tip/tilt) sont déterminées. Le LIFT consiste à déterminer la phase à l’échelle de chaque micro-lentille, en exploitant le profil du spot correspondant. Des matrices d’interaction sont calculées afin de linéariser la relation entre l’espace réel (micro-lentilles) et l’espace réciproque (matrice CCD), et une boucle itérative permet d’étendre cedomaine de linéarité. Un gain de résolution spatiale de l’ordre de 3, au niveau de chaque micro-lentille, est attendu avec cette technique<br>This dissertation is dedicated to coherent diffractive imaging. Firstly, we present the conception and experimental implementation of a compact imaging system, working on this principle. It is made of an UV laser diode (λ = 400 nm), a CCD camera,and a platform to place the sample. The coherent beam coming from the diode illuminates the sample, and the diffraction pattern is recorded by the camera. Back-propagating the detected field should allow, in principle, to derive the sample’s profile. Nevertheless, the field’s phase, lost during the detection, forces us to use “phase retrieval” methods, this quantity being necessary to the inversion process. Several techniques have been used for that purpose. Fourier Transform Holography (FTH), for example, is a deterministic method thatconsists in using a circular reference, closely drilled nearby the sample. The phase is encoded in the diffraction pattern, in the form of interference fringes coming from the object and the reference. Then, a simple inverse Fourier Transform of the signal leads the profile of the sample. An iterative method has also been implemented, based on a set of constraints in the real and reciprocal spaces. In particular, the illuminated object must be “isolated”, i.e. smaller than the incident beam. Although this method is non-deterministic, we will see thatit is more robust and gives better resolutions than the holographic cases. This study is the starting point of three-dimensional imaging. We present a first deterministic method, based on FTH. For this purpose, a “holographic pupil” is used and serves as a support for a first 2D reconstruction of the field. The latter is then back-propagated towards the sample closely placed, in order to realize an entirely numerical focusing on it. The “isolation constraint” is then removed by the use of this pupil. However, with this method, the field of view is limitedby the pupil’s diameter. In order to observe larger samples, the “in-line holography” technique has been exploited as well. It consists in illuminating the object with a spherical wave and recording the interference fringes (or “hologram”). A back-propagation is made after the fact in order to do the focusing on the sample. The divergent nature of the beam allows for reaching several millimeters for the lateral field of view. The “twin image problem”, inherent to this configuration, is solved via an iterative algorithm coupled to the back-propagation process. Three-dimensional reconstructions have been made on varied samples, with these two methods — pupil reconstruction and in-line holography. In both cases, reconstruction interfaces have been implemented and work during the detection, in order to observe the object in real time. We then have a compact and complete lens-less imaging prototype. Finally, we present the application of a phase retrievaltechnique, named LIFT (LInearized Focal plane Technique), applied to a Shack-Hartmann wavefront sensor. Usually, such sensors have a spatial resolution that is limited by the micro-lenses size : only the local slopes, i.e. tip and tilt, are retrieved. The LIFT consists in determining the phase at the scale of each micro-lens, by exploiting the corresponding spot profile. Interaction matrices are calculated in order to linearize the relation between the real space (micro-lenses) and the reciprocal space (CCD chip), and an iterative loop allows for increasing this linearity domain. With this technique, a gain in spatial resolution by a factor 3 is expected
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Kropáč, Vlastimil. "Vláknový osvětlovací modul pro mikroskopii." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2020. http://www.nusl.cz/ntk/nusl-417106.
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This diploma thesis describes the design of the illumination system for a Coherence--Controlled Holographic Microscope (CCHM). The theoretical part mentions the history of microscopy, the principle of holography and individual types of interference microscopy. To get closer to the topic, individual light sources and an overview of current illumination systems are mentioned. The diploma thesis also describes the procedure of designing a fiber-optic illumination module for microscopy from optical design through design of construction to the last step, which is assembly and testing of the module.
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Kvasnica, Lukáš. "Řízení optického stolku interferenčního mikroskopu na základě obrazové fáze." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2008. http://www.nusl.cz/ntk/nusl-228199.
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Digital holographic microscopy is an interferometric imaging technique, the principle of which is the off-axis image plane holography. The principle of this technique enables to reconstruct both the image intensity and the image phase from the output interferencesignal. The reconstruction can be carried out on the basis of a single image plane hologram. This leads to the possibility of a realtime image reconstruction. The speed of the reconstruction depends on the detection and the computing process. The aim of this diploma thesis is to develop user software for the control of the detection camera and for the image plane hologram reconstruction. The effort was to achieve the highest number of image reconstructions per time unit, with the maximum utilization of the data transfer between the camera and the computer.The next aim of this thesis is the stabilization of the optical table position. The method of stabilization is based on the image phase information, which is used for the control loop feedback between reconstructed image phase and the piezoelectric actuator placed inside of the optical table. Experimental results, which prove the functionality of the stabilization, are presented.
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Telliez, Cécile. "Advanced optical microscopy for spatially and temporally precise deep brain interrogation." Electronic Thesis or Diss., Sorbonne université, 2024. http://www.theses.fr/2024SORUS041.
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Dans le domaine des neurosciences, l'avènement des outils optogénétiques sensibles à la lumière a ouvert de nouvelles opportunités pour contrôler précisément l'activité neuronale et étudier le fonctionnement cérébral optiquement. En optique, cela a motivé le développement de diverses stratégies d'illumination et de collecte de la lumière pour imager l'activité neuronale et la manipuler avec une précision spatiotemporelle élevée. En particulier, les approches de mise en forme de la lumière, telles que l'holographie générée par ordinateur combinée à la focalisation temporelle, ont permis de cibler des neurones individuels ou des groupes de neurones avec une grande précision temporelle et une précision spatiale proche de la cellule unique, dans des espaces volumétriques de centaines de microns. Cette précision est cruciale pour obtenir des informations critiques sur le code neuronal et établir des connexions entre l'activité neuronale, le comportement et la perception à une échelle fine. Malgré ces avancées, des défis persistent pour permettre des investigations cérébrales complexes, notamment en ce qui concerne le contrôle de vastes populations de cellules avec une précision spatiotemporelle élevée en profondeur. Pendant ma thèse, j'ai particulièrement concentré mes efforts sur ces défis et développé de nouvelles stratégies optiques de mise en forme de la lumière visant à (i) étendre le nombre de neurones excitables, (ii) améliorer la résolution temporelle et (iii) augmenter la profondeur de pénétration de l'investigation optogénétique multi-photonique ciblée et basée sur la modulation de phase de la lumière.Initialement, j'ai concentré mes efforts sur le développement d'un système optique ultra-rapide à deux photons (2P) (FLiT), où un modulateur spatial de lumière et un miroir galvanométrique sont couplés pour permettre la commutation à un taux de kHz de motifs d'illumination précis spatialement sur l'échantillon. Cela sert deux objectifs principaux. Premièrement, cela permet d'ajuster optiquement le temps d'excitation relatif de cellules distinctes avec une résolution temporelle d'environ un ordre de grandeur supérieur par rapport aux méthodes précédentes. Deuxièmement, FLiT permet de cibler un ensemble donné de cellules en réduisant le budget de puissance d'excitation d'un facteur 4-5, tout en minimisant l'élévation thermique induite par la lumière. Pour pousser cette approche encore plus loin, j'ai ensuite modifié la conception optique originale en incluant une unité de de-scan (deFLiT), ce qui a permis d'élargir le nombre d'hologrammes utilisables et d'augmenter encore davantage le gain de puissance et la précision temporelle du FLiT conventionnel.Dans la deuxième phase de la thèse, je me suis concentré sur un système holographique à trois photons (3P) pour mener des expériences d'optogénétique plus profondément à l'intérieur du cerveau. J'ai conçu et construit le système, puis je l'ai validé en photo-activant diverses opsines et en induisant leur activation à haute fréquence dans les neurones ciblés sous un régime d'excitation à 3P que j'ai également vérifié. Par rapport aux systèmes holographiques à deux photons précédents, cette approche permettra d'étendre les investigations entièrement optiques à des régions plus profondes du cerveau.Ces nouvelles stratégies seront importantes pour étudier les circuits neuronaux avec une stimulation optogénétique rapide et précise à travers de vastes ensembles neuronaux en profondeur<br>In the field of neuroscience, the advent of light-sensitive optogenetic tools has opened new opportunities for precisely controlling neuronal activity and study brain functioning optically. In optics, this has motivated the development of various light-delivery and collection strategies to functionally image and manipulate neural activity with high spatiotemporal precision. Particularly, light-shaping approaches, such as Computer-Generated Holography combined with Temporal Focusing, have enabled temporally precise targeting of individual neurons or clusters with near single-cell accuracy within volumetric spaces of hundreds of microns. This precision is crucial to get critical insights into the neural code and establishing connections between neural activity with behavior and perception at fine scale. Despite these advancements, challenges persist in enabling complex brain investigations, especially when it comes to control vast populations of cells with high spatiotemporal precision in depth. During my thesis, I particularly focused on those challenges and developed new light-shaping optical strategies aiming at (i) expanding the number of excitable neurons, (ii) improving temporal resolution and (iii) increasing the penetration depth of cell-targeted multiphoton optogenetic investigation based on phase-modulation light-targeting.Initially, I concentrated on developing an ultra-fast two-photon (2P) optical system (FLiT), where a multiplexing LC-SLM and a galvanometric mirror are coupled to allow kHz-rate switching of spatially precise illumination patterns on the sample. This serves two primary purposes. Firstly, it enables to optically tune the relative spiking time of distinct cells with a temporal resolution of about one order of magnitude higher compared to previous methods. Secondly, FLiT allows targeting a given ensemble of cells by reducing the excitation power budget by a 4-5 factor, while minimizing light-induced thermal rise. To push forward this approach, I further modified the original optical design by including a de-scan unit (deFLiT) which enabled to enlarge the number of usable holograms and increase even further the power gain and temporal precision of conventional FLiT .In the second phase of the thesis, I focused on a three-photon (3P) holographic system to conduct optogenetics experiments deeper inside the brain. I designed and built the system and I then validated it by photo-activating various opsins and driving high-rate firing in targeted neurons under a verified 3PE regime. Compared to previous holographic 2P-photon systems, this approach will enable the extension of all-optical investigations to deeper brain regions.These new strategies will be important for studying neuronal circuits with rapid and precise optogenetic stimulation across large neuronal ensembles in depth
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Ukropcová, Iveta. "Automatizovaný bioreaktor pro kultivaci živých buněk." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2020. http://www.nusl.cz/ntk/nusl-417105.
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Control of cultivation conditions in the~live cell imaging extends the possibilities of biological experiments and makes the experimental results more reliable. In order to change the~cultivation conditions in a controlled manner and increase the reproducibility of the experiments, it is necessary to reduce the amount of manual operations and replace them with automated procedures. Therefore, the concept of a new automated culture device (bioreactor) was created. This device controls the exchange of medium in the observation chamber, ensures the circulation and exchange of the atmosphere and controls its composition. The bioreactor is intended for use in the Laboratory of Experimental Biophotonics. This laboratory is equipped with coherence-controlled holographic microscope (CCHM), which uses quantitative phase imaging (QPI) method. Thus, the bioreactor is adapted to the current requirements of this laboratory and optical elements of the bioreactor meet the requirements of the QPI method. This text specifies the cultivation conditions of the living cells and summarizes, how the conditions could be controlled in the live cell microscopy. Next some commercially available culture devices are described and assessed, whether they are convenient for the~use in Laboratory of Experimental Biophotonics. The crucial part of the thesis is the~design, construction and testing of the new bioreactor.
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Říha, René. "Využití metody FDTD k modelování zobrazování v biofotonice." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2020. http://www.nusl.cz/ntk/nusl-417154.
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This thesis deals with the problem of practical application of FDTD technique for simulation of image formation in coherence controlled holographic microscope. Various ways for obtaining scattering matrices are explored in detail and the optimal technique based on a rigorous calculation of the far field is proposed. The scattering matrix, containing information about the observed sample, is subsequently used in analytic calculation of holographic signal; two levels of approximation of pupil function are also evaluated. The results are compared with a traditional approach based on Rytov approximation resulting in specification of the parameter domain where the approximation is applicable. Based on the simulations of the microscope, the dependence of axial resolution on apertures of the objective and the condenser and sensitivity of the signal to changes of refractive index of the sample is also studied.
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Vodičková, Marie. "Měření indexu lomu a morfometrie živých buněk pomocí koherencí řízeného holografického mikroskopu." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2018. http://www.nusl.cz/ntk/nusl-392854.
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This master’s thesis deals with the design of methodology for measurement of refractive index and thickness of living cells by coherence-controlled holographic microscope. The theoretical part summarises the holographic microscopy and its development at IPE FME BUT in Brno. The thesis focuses on the multimodal holographic microscope, its description, the principle, the procedure of work and data processing. Confocal microscopy is also described, which serves to compare the acquired values with the proposed methodology. The last part of the theoretical part deals with the testing of statistical hypotheses, which is needed for the processing of measured data. Experiments were designed for the verification of methodology for determination of the refractive index and cell thickness. The experimental part of the thesis deals with the sample preparation and measurement. The procedure and results of the proposed experiments and their evaluation follows.
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Denneulin, Thibaud. "Holographie électronique en champ sombre : une technique fiable pour mesurer des déformations dans les dispositifs de la microélectronique." Phd thesis, Université de Grenoble, 2012. http://tel.archives-ouvertes.fr/tel-00844107.
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Les contraintes font maintenant partie des " boosters " de la microélectronique au même titre que le SOI (silicium sur isolant) ou le couple grille métallique / diélectrique haute permittivité. Appliquer une contrainte au niveau du canal des transistors MOSFETs (transistors à effet de champ à structure métal-oxyde-semiconducteur) permet d'augmenter de façon significative la mobilité des porteurs de charge. Il y a par conséquent un besoin de caractériser les déformations induites par ces contraintes à l'échelle nanométrique. L'holographie électronique en champ sombre est une technique de MET (Microscopie Électronique en Transmission) inventée en 2008 qui permet d'effectuer des cartographies quantitatives de déformation avec une résolution spatiale nanométrique et un champ de vue micrométrique. Dans cette thèse, la technique a été développée sur le microscope Titan du CEA. Différentes expériences ont été réalisées afin d'optimiser la préparation d'échantillon, les conditions d'illumination, d'acquisition et de reconstruction des hologrammes. La sensibilité et la justesse de mesure de la technique ont été évaluées en caractérisant des couches minces épitaxiées de Si_{1-x}Ge_{x}/Si et en effectuant des comparaisons avec des simulations mécaniques par éléments finis. Par la suite, la technique a été appliquée à la caractérisation de réseaux recuits de SiGe(C)/Si utilisés dans la conception de nouveaux transistors multi-canaux ou multi-fils. L'influence des phénomènes de relaxation, tels que l'interdiffusion du Ge et la formation des clusters de β-SiC a été étudiée. Enfin, l'holographie en champ sombre a été appliquée sur des transistors pMOS placés en déformation uniaxiale par des films stresseurs de SiN et des sources/drains de SiGe. Les mesures ont notamment permis de vérifier l'additivité des deux procédés de déformation.
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Babocký, Jiří. "Příprava a charakterizace nanostruktur s funkčními vlastnostmi v oblasti plazmoniky." Doctoral thesis, Vysoké učení technické v Brně. CEITEC VUT, 2020. http://www.nusl.cz/ntk/nusl-432891.
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Tato dizertční práce se zabývá výrbou a charakterizací plasmonických nanostruktur. Její první část začíná krátkým úvodem do plasmoniky s navazujícím přehledem metod, které jsou v dnešní době nejčastěji používány k výrobě a charakterizaci plasmonických nanostruktur. Druhá část se pak zaměřuje na samotný výzkum, který byl v rámci PhD studia realizován. Cílem prvních experimentů bylo prozkouat možnosti použití elektronové litografie za variabilního tlaku v procesní komoře pro výrobu plasmonických nanostruktur na nevodivých substrátech jako je např. sklo. Jelikož se jedná o materiály, které jsou velice často používány k přípravě plasmonických struktur pacujících v oblasti viditelného světla. Druhá sekce pak diskutuje některé specifické aspekty přípravy plasmonických mikrostruktur elektronovou litografií pro THz oblast. Poslední část se pak zaměřuje na funkční vlastnosti plasmonických nanostruktur, převážně pak na kvantitativní charakterizaci fáze dalekého pole indukovaného plasmonickými nanostrukturami a jejich aplikacemi v oblasti optických metapovrchů - uměle připravených povrchů, které mohou být použity jako planární optické komponenty. Práce demonstruje a diskutuje různé experimentální přístupy použití mimoosové holografické mikroskopie pro jejich charakterizaci.
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Ďuriš, Miroslav. "Zobrazení objektu v rozptylujícím prostředí kombinací signálu balistických a rozptýlených fotonů v koherencí řízeném holografickém mikroskopu." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2018. http://www.nusl.cz/ntk/nusl-392845.
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Diplomová práca sa zaoberá kvantitatívnym fázovým zobrazovaním objektov umiestnených za rozptyľujúcim prostredím v koherenciou riadenom holografickom mikroskope. Tento mikroskop umožnuje zobrazovať s úplne nekoherentným osvetlením vzorky, čo vyvoláva efekt koherenčnej brány. Koherenčná brána je veľmi dôležitá vlastnosť zobrazovacieho systému umožňujúca separáciu balistických a rozptýlených fotónov, jej dôkladnému vysvetleniu je venovaná značná časť práce. Ďalej sú prezentované základy teórie zobrazenia v koherenciou riadenom holografickom mikroskope. Tie sú využité v závere práce pri interpretácii experimentálnych výsledkov. Cieľom práce je navrhnúť metódu pre pozorovanie fázových objektov v rozptyľujúcich prostrediach a experimentálne túto metódu overiť. Na základe analytických výsledkov a predchádzajúceho výskumu je navrhnutá nová metóda, ktorá je ďalej overovaná pomocou rôzne komplexných vzoriek. Je založená na zázname viacerých obrazov s rôznym posunutím referenčného poľa. Každý posun korešponduje so zobrazovaním pomocou inej skupiny fotónov. Je možné vytvoriť syntetický obraz so zlepšenou kvalitou sčítaním jednotlivých obrazov získaných z interferencie balistických alebo rozptýlených fotónov. Experimenty s rôzne komplexnými vzorkami poskytujú náhľad na obmedzenia prezentovanej metódy.
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Sládková, Lucia. "Možnosti trojrozměrného zobrazování v transmisním holografickém mikroskopu." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2013. http://www.nusl.cz/ntk/nusl-230610.
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Digital holographic microscopy (DHM) is noninvasive method for obtaining images even from samples with low contrast. Nowadays DHM design makes it possible to illuminate sample by broad light source, halogene lamp. Broad light source is displayed in the front focal plane of condensor in such way, that Köhler illumination is achieved. Each point of the source corresponds to a plane wave in image field of objective, which illuminates the whole field of view, but from different direction. Position of the point determines the direction of illumination. In this reason, the microscope enables so reconstruct not only intensity, but also phase of object wave. New designed and constructed interchangeable pinhole aperture modify broad light illumination by rotation around the optical axis. Aperture is placed eccentrically considering the optical axis of microscope. Incidence of light beam on a sample would be under defined angle. After the reconstruction of taken phase images from individual angles of illumination should be possible to obtain three-dimensional structure of the sample.
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Andersen, Ingrid Marie. "2D and 3D quantitative TEM mapping of CoNi nanowires." Thesis, Toulouse 3, 2020. http://www.theses.fr/2020TOU30205.
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Les nanofils magnétiques constituent un domaine de recherche en plein essor. De section cylindrique, ils permettent la propagation des parois de domaines magnétiques à très grandes vitesses et des interactions fortes avec les ondes de spin, ce qui les rend particulièrement intéressants pour le développement de futurs composants de la spintronique. L'objectif de ce travail de thèse est de fournir une analyse quantitative et qualitative complète de la configuration magnétique locale dans des nanofils magnétiques cylindriques d'alliage CoNi à anisotropie magnétocristalline perpendiculaire en utilisant les techniques d'imagerie magnétique avancées de la microscopie électronique à transmission (MET), principalement axées sur l'holographie électronique (HE). Une étude corrélative entre les propriétés structurales, les variations locales de composition et les configurations magnétiques de ces nanofils a été réalisée. De plus, les configurations tridimensionnelles (3D) complexes des domaines et des parois magnétiques ont été analysées par tomographie holographique de champ vectoriel (THCV) afin d'obtenir les trois composantes de l'induction magnétique. Enfin, un protocole a été développé pour étudier in situ par microscopie de Lorentz la configuration magnétique de ces nanofils lors de l'injection d'impulsions de courant. La première partie de ce travail est focalisée sur la corrélation des configurations magnétiques de nanofils individuels de CoNi avec les propriétés structurales et chimiques locales. L'orientation de la phase cristalline a été cartographiée en diffraction électronique par précession et combinée à des mesures de composition par spectroscopie de perte d'énergie des électrons. Les résultats révèlent une coexistence de grains de phase cfc et de phase hcp, cette dernière présente sa direction cristallographique c orientée presque perpendiculairement à l'axe du nanofil. Cette coexistence de phases cristallographiques est à l'origine de variations localisées et abruptes de la configuration magnétique. Deux nanofil configurations principales ont été observées : une chaîne d'états transversaux par rapport à l'axe du, de type vortex, et un état longitudinal. Nous avons observé que les états transversaux sont liés à la phase hcp possédant une forte anisotropie magnétocristalline perpendiculaire, ce que confirment les simulations micromagnétiques. Une autre partie de ce travail concerne l'étude de la structure magnétique 3D des domaines et des parois de domaines dans la phase hcp. Cette étude a été menée pour des états rémanents différents en fonction de l'application d'un champ de saturation perpendiculaire et parallèle à l'axe du nanofil. Les mesures ont été réalisées par la méthode THCV afin d'extraire les trois composantes de l'induction magnétique et reconstruire en 3D la configuration magnétique locale du nanofil. Les résultats montrent une stabilisation d'une chaîne de vortex dans le cas d'une saturation perpendiculaire, et des états d'enroulement longitudinaux séparés par des parois de domaine transversales après l'application d'un champ externe parallèle à l'axe du fils. La dernière partie du manuscrit présente les résultats obtenus en microscopie de Lorentz in situ démontrant la possibilité de manipuler les parois des domaines magnétiques d'un nanofil de CoNi par injection d'impulsions électriques. Cette preuve de concept est considérée comme le précurseur des observations in situ de la dynamique des parois de domaines en EH. Un protocole précis, axé sur les étapes cruciales de préparation des échantillons et les développements à poursuivre pour réaliser ces expériences délicates, est détaillé<br>Cylindrical magnetic nanowires (NWs) are currently subjects of high interest due to fast domain wall velocities and interaction with spin-waves, which are considered interesting qualities for developing future spintronic devices. This thesis aims to provide a wholesome quantitative and qualitative analysis of the local magnetic configuration in cylindrical Co-rich CoNi NWs with perpendicular magnetocrystalline anisotropy using state-of-the-art transmission electron microscopy (TEM) magnetic imaging techniques, mainly focused on two-dimensional (2D) and three-dimensional (3D) electron holography (EH). A correlative study between the NW's texture, modulation in composition, and magnetic configuration has been conducted. Further, the complex 3D nature of the domain and domain wall configurations have been analyzed using holographic vector field electron tomography (VFET) to retrieve all three components of the magnetic induction. Finally, I have successfully manipulated the magnetic configuration observed by Lorentz microscopy in Fresnel mode by the in situ injection of a current pulse. A TEM study comparing the magnetic configuration to the local NW structure was performed on single NWs. The crystal phase analysis was done by precession electron diffraction assisted automated crystal orientation mapping in the TEM combined with compositional analysis by scanning-TEM (STEM) electron energy loss spectroscopy (EELS) for a detailed correlation with the sample's magnetic configuration. The results reveal a coexistence of fcc grains and hcp phase with its c-axis oriented close to perpendicular to the wire axis in the same NW, which is identified as the origin of drastic local changes in the magnetic configuration. Two main configurations are observed in the NW region: a chain of transversal vortex-like states and a longitudinal curling state. The chain or vortices are linked to the hcp grain with the perpendicular magnetocrystalline anisotropy, as confirmed by micromagnetic simulations. The 3D magnetic structure of the domains and domain walls observed in the hcp grain of the NWs has been studied for two different remnant states: after the application of a saturation field perpendicular (i) and parallel (ii) to the NW axis. The measurements were done using state-of-the-art holographic VFET to extract all three components of the magnetic induction in the sample, as well as a 3D reconstruction of the volume from the measured electric potentials, giving insight into the local morphology of the NW. The results show a stabilization of a vortex chain in the case of perpendicular saturation, but longitudinal curling states separated by transversal domain walls after applying a parallel external field. Finally, preliminary Lorentz microscopy results are presented, documenting the manipulation of magnetic domain walls by the in situ injection of electrical pulses on a single cylindrical CoNi nanowire contacted by focused ion beam induced deposition. This is believed to be the forerunner for quantitative electrical measurements and in situ observations of domain wall dynamics using EH at the CEMES. A detailed protocol focusing on the crucial steps and challenges ahead for such a delicate experiment is presented, together with suggestions for future work to continue the developments
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Corman, Ramona. "2D/3D lensless imaging : prototype and applications." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASS042.
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L’imagerie biologique a réalisé des progrès significatifs durant les dernières décennies. Les récentes innovations portent sur la manipulation et la visualisation de cellules uniques avec une résolution spatiale de l’ordre du nanomètre. Une technologie d’imagerie récente, l’imagerie «sans lentille », est particulièrement prometteuse car elle combine une bonne résolution spatiale, un champ de vision étendu, une simplicité d’utilisation, un coût abordable et la possibilité de travailler sur des échantillons exempts de marqueurs spécifiques. En imagerie sans lentille, le système optique classiquement utilisé pour constituer l’image de l’échantillon est remplacé par des algorithmes informatiques qui s’appuient sur les propriétés de cohérence spatiale de la lumière. Dans cette thèse, deux approches différentes de microscopie sans lentille sont considérées : l’holographie numérique en ligne et l’holographie par transformée de Fourier.Deux prototypes d’imagerie, construits selon ces principes, sont présentés. Ils offrent une résolution de l’ordre du micron, ainsi que la possibilité de retrouver les informations relatives à l’amplitude spatiale et à la phase du champ optique. Cela permet la réalisation de reconstructions pseudo-3D d’objets volumétriques à partir d’un unique hologramme. Les deux dispositifs ont d’abord été caractérisés avec des échantillons de référence. Par la suite, des expériences d’applications ont été testées pour estimer la capacité des dispositifs à répondre à des problématiques concrètes dans le domaine de la biologie, grâce à la haute résolution, l’imagerie en temps réel et la reconstruction 3D.L’objectif de cette thèse est également de développer une nouvelle plateforme qui intègre, dans une puce microfluidique, d’une part un système permettant la manipulation de cellules par diélectrophorèse, et d’autre part un masque optique pour la visualisation des cellules par imagerie sans lentille. Le principe de fonctionnement est basé sur le déplacement des cellules en milieu liquide et la séparation des cellules dans le champ de vision du microscope en utilisant un champ électrique induit par des électrodes spécifiques. Le masque optique permet de définir le champ de vision du microscope et de créer les faisceaux de référence nécessaires pour l’imagerie par holographie par transformée de Fourier. Le principal avantage de ce système électro-optique pour l’imagerie cellulaire réside dans sa capacité à fournir une plateforme d’imagerie compacte qui regroupe précision et sensibilité. Les champs d’applications de cette plateforme sont variés. Une application concrète qui découle immédiatement des premières expériences présentées dans ce manuscrit serait l’analyse du comportement des cellules et de leurs modifications morphologiques lors d’un processus électrochimique de diélectrophorèse.L’un des challenges majeurs dans le domaine de la microscopie est de réduire les coûts de fabrication. Les deux types de microscopes sans lentille présentés dans cette thèse visent à introduire dans le monde scientifique des outils d’imagerie permettant d’obtenir une haute résolution à un faible coût et sans marquage. Par ailleurs, la puce microfluidique est une première démonstration de plateforme intégrée pour l’analyse des cellules en temps réel dans un dispositif de type « Lab-on-a-chip »<br>Biological imaging has made tremendous progresses these last decades. The latest developments concern manipulating and imaging single cells with nanometer spatial resolutions. A recent category of imaging techniques, called lensless microscopy, are very promising because they combine very good spatial resolutions in a large field-of-view, simplicity of use and low cost, while operating on label free samples. In this thesis two different lensless approaches are considered: digital in-line holography (DILH) and Fourier transform holography (FTH). In lensless imaging, the usual optical system used to form the sample’s image are remove and replace by numerical algorithms using the light spatial coherence properties.Two imaging prototypes, built on these principles, are presented. They offer (sub ) micrometer scale resolutions, and offer the possibility to retrieve both spatial amplitude and phase information of the optical field. This allows to achieve pseudo-3D reconstruction of volumetric objects from a single 2D hologram. Both devices were first characterized with reference samples. In a second step, real applications, relevant to selected biological problems, were performed to assess the devices’ performances towards high resolution, real time imaging and 3D.This thesis objective is also to develop a new platform directly integrating in a single chip a microfluidics system for biological cell handling by dielectrophoresis and an optical mask for cell visualization by lensless microscopy. Its working principle is based on cell transport in a liquid media by microfluidics, cell separation in the microscope field of view by the electric field induced by specific electrodes, and simultaneous cell imaging by Fourier Transform Holography. The main advantage of such coupled electro-optical system for cell imaging and analysis are the improved control, the precision and sensitivity regarding cell morphology all together merged in a compact imaging platform. The capability of the platform can be extended to analysis of cells’ behavior and morphologic deviation during the electrochemical processes of DEP.A major challenge in microscopy field is to reduce the production costs. The two types of lensless microscopy presented in this thesis aims to introduce new imaging tools that allows scientists to obtain low-cost high-resolution images in label-free conditions. Additionally, the microfluidics chip is a first demonstration of a new integrated platform for cell live analysis into a single Lab-on-a-chip device
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Kubátová, Eva. "Konfokální modul pro koherencí řízený holografický mikroskop." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2020. http://www.nusl.cz/ntk/nusl-417063.
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The Coherence Controlled Holographic Microscope (CCHM) was developed at BUT Brno for a quantitative phase imaging of living cells. Nowadays it ocurres that its imaging properties are enhanced by the use of additional modules. In the present the microscope is equipped with the epifluorescence module, which allows observation of fluorescently marked living cells. This thesis is going to follow up on the development of this module and is going to extend its options by confocal imaging. The disadvantage of current multi-channel confocal microscopes is a mechanical rotation of the Nipkow discs, which causes undesired mechanical vibrations. That is why in this thesis it is replaced by Digital Micromirror Device. With its use was developed optical system of the whole confocal model, whose correct funcion was simulated in optical CAD. The experimentally verified prototype serves to test the imaging properties. On this basis is designed an application idea of the fluorescence confocal module, which will be possible to connect to the CCHM microscope.
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Brodoline, Alexey. "Holographie numérique appliquée à l’imagerie 3D rapide de la circulation sanguine chez le poisson-zèbre." Thesis, Montpellier, 2018. http://www.theses.fr/2018MONTS058/document.
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Nous présentons dans ce manuscrit une technique d’imagerie basée sur l’holographie numérique. Elle permet d’imager en 3D et dans le temps la circulation sanguine chez une larve de poisson-zèbre. L’information 3D est acquise en une seule image de la caméra, ce qui permet de suivre le mouvement des globules rouges dans le système vasculaire. Nous évoquerons dans un premier temps les techniques de bio-imagerie et d’imagerie du flux sanguin traditionnelles, puis nous rappellerons les principes de l’holographie. Ensuite, nous décrirons la méthode d’imagerie que nous avons développée et les résultats expérimentaux obtenus. Nous compléterons, en présentant les différentes améliorations que nous avons apportées à la technique. Enfin, nous discuterons brièvement de l’application du compressed sensing à l’imagerie de la circulation sanguine dans le poisson-zèbre<br>In this manuscript, we present an imaging technique based on digital holography.It enables to image in 3D and in time the blood circulation in a zebrafish larva. The 3D information is acquired in a single frame of the camera, which makes possible to track the movement of red blood cells in the vascular system. We will first discuss the traditional techniques of bio and blood flow imaging, then we will remind the principles of holography. Afterwards, we will describe the imaging method we developed and the experimental results obtained. We will then present the improvements that have been made to the technique. Finally, we will briefly discuss the application of the compressed sensing to the blood flow imaging in zebrafish
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Schockaert, Cédric. "Three dimensional object analysis and tracking by digital holography microscopy." Doctoral thesis, Universite Libre de Bruxelles, 2007. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210718.
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Digital Holography Microscopy (DHM) is a new 3D measurement technique that exists since Charge Coupled Devices (or CCD cameras) allow to record numerically high resolution images. That opens a new door to the theory of holography discovered in 1949 by Gabor: the door that masked the world of digital hologram processing. A hologram is a usual image but that contains the complex amplitude of the light coded into intensities recorded by the camera. The complex amplitude of the light can be seen as the combination of the energy information (squared amplitude modulus) with the information of the propagation angle of the light (phase of the amplitude) for each point of the image. When the hologram is digital, this dual information associated with a diffractive model of the light propagation permits to numerically investigate back and front planes to the recorded plane of the imaging system. We understand that 3D information can be recorded by a CCD camera and the acquisition rate of this volume information is only limited by the acquisition rate of the unique camera. For each digital hologram, the numerical investigation of front and back regions to the recorded plane is a tool to numerically refocus objects appearing unfocused in the original plane acquired by the CCD.<p>This thesis aims to develop general and robust algorithms that are devoted to automate the analysis process in the 3D space and in time of objects present in a volume studied by a specific imaging system that permits to record holograms. Indeed, the manual processing of a huge amount of holograms is not realistic and has to be automated by software implementing precise algorithms. In this thesis, the imaging system that records holograms is a Mach-Zehnder interferometer working in transmission and studied objects are either of biological nature (crystals, vesicles, cancer cells) or latex particles. We propose and test focus criteria, based on an identical focus metric, for both amplitude and phase objects. These criteria allow the determination of the best focus plane of an object when the numerical investigation is performed. The precision of the best focus plane is lower than the depth of field of the microscope. From this refocus theory, we develop object detection algorithms that build a synthetic image where objects are bright on a dark background. This detection map of objects is the first step to a fully automatic analysis of objects present in one hologram. The combination of the detection algorithm and the focus criteria allow the precise measurement of the 3D position of the objects, and of other relevant characteristics like the object surface in its focus plane, or its convexity or whatever. These extra relevant measures are carried out with a segmentation algorithm adapted to the studied objects of this thesis (opaque objects, and transparent objects in a uniform refractive index environment). The last algorithm investigated in this research work is the data association in time of objects from hologram to hologram in order to extract 3D trajectories by using the predictive Kalman filtering theory. <p>These algorithms are the abstract bricks of two software: DHM Object Detection and Analysis software, and Kalman Tracking software. The first software is designed for both opaque and transparent objects. The term object is not defined by one other characteristic in this work, and as a consequence, the developed algorithms are very general and can be applied on various objects studied in transmission by DHM. The tracking software is adapted to the dynamic applications of the thesis, which are flows of objects. Performance and results are exposed in a specific chapter. <p><br>Doctorat en sciences appliquées<br>info:eu-repo/semantics/nonPublished
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Ferreira, Merilyn Santos. "Microscopia interferométrica holográfica para a caracterização de microtransdutores." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/3/3140/tde-14122014-111144/.
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A finalidade deste trabalho é aplicar a técnica de holografia em cristais fotorrefrativos para o estudo de propriedades mecânicas de microdispositivos, garantindo ainda a obtenção de uma geometria de arranjo holográfico simples e compacto. Foram feitas a análise de vibração e a análise de deformação de microdispositivos por meio da interferometria de média temporal e de dupla exposição, respectivamente. Como fontes de luz, foram utilizados diodos laser emitindo em 660nm, e um He-Ne laser emitindo em 632,8nm. Como meio fotorrefrativo de registro holográfico foi utilizado o cristal Bi12TiO20, (BTO) da família das selenitas. Foi proposto um arranjo óptico de holografia de reflexão do tipo Denisiuk, e a este arranjo foi adicionado um conjunto de lentes objetiva e ocular para formar uma configuração de microscópio composto, com o objetivo de obterem-se imagens holográficas de objetos de dimensões microscópicas. A gravação e a reconstrução do holograma se deram simultaneamente, devido à associação do cristal fotorrefrativo a uma câmera CMOS. Desta maneira, a observação dos hologramas foi feita em tempo real. Foram feitas, inicialmente, imagens de dupla exposição de piezorresistores MEMS (microelectromechanical systems), de geometria reduzida (2,96 x 0,6 mm2), e de dispositivos CMUT (Capacitive Micromachined Ultrasonic Transducers) com 640m de diâmetro. Através desta técnica foi possível medir deslocamentos de 0,33m a 4,3m. Foram obtidos também interferogramas de média temporal de cerâmicas e transdutores piezoelétricos, porém, iluminando apenas pequenas regiões destes objetos. Estas imagens mostraram qualidade razoável, indicando que é possível aplicar a técnica de interferometria em média temporal para objetos com amplitude de vibração entre 0,12m e 1,7m. Para investigar as potencialidades microscópicas foram feitas imagens de padrões de teste de resolução, onde foi possível visualizar estruturas com geometrias entre 2mm e 20m.<br>The aim of this work is to apply photorefractive crystals holography technique for the study of mechanical properties of micro-devices; it ensures obtaining a simple and compact geometry of holographic setup. Vibration and deformation analyses of micro-devices were performed using time average and double exposure interferometry, respectively. As light sources, it was used diode lasers emitting at 660nm, and He-Ne laser emitting at 632.8nm. As photorefractive holographic recording medium was used Bi12TiO20 (BTO) crystal, family of selenites. An optical setup of Denisiuk-type reflection holography was proposed, and this setup was added a set of objective and eyepiece lenses to form a compound microscope configuration, in order to obtain holographic images of objects with microscopic dimensions. Recording and reconstruction of the hologram occurred simultaneously, due to the combination of the photorefractive crystal to a CMOS camera. Thus, holograms observation occurs in real time. It was initially performed double exposure images of MEMS (microelectromechanical systems) piezoresistors, with reduced geometry (2.96 x 0.6 mm2), and CMUT (capacitive micromachined ultrasonic transducers) devices with 640m diameter. By this technique was possible measure displacements of 0.33m to 4.3m. Time average interferograms of Ceramics and piezoelectric transducers were also obtained, however, it illuminating only small regions of these objects. These images showed reasonable quality, indicating that it is possible apply the time average technique for objects with vibration amplitude between 0.12m e 1.7m. In order to investigate the microscopic potentialities images of resolution test chart were done, where it was possible to visualize structures with geometries between 20 m and 2mm.