Background: Single ventricle congenital heart defects with cyanotic mixing between systemic and pulmonary circulations afflict 2 per 1000 live births. Following the atriopulmonary connection proposed by Fontan and Baudet in 1971, the present procedure is the total cavopulmonary connection (TCPC), where the superior vena cava (SVC) and inferior vena cava (IVC) are sutured to the left pulmonary artery (LPA) and right pulmonary artery (RPA). However, surgeon preference dictates the implementation of the extra-cardiac and intra-atrial varieties of the TCPC. Overall efficiency and hemodynamic advantage of the competing methodologies have not been determined. Hypothesis: It is hypothesized that an understanding of the experimental fluid dynamic differences between various Fontan surgical methodologies in the TCPC allows for power loss evaluation toward improved surgical planning and design. Methods: Toward such analysis, a previously developed data processing methodology is applied to create an anatomic database of single ventricle patients from in vivo magnetic resonance imaging (MRI) to examine the gamut of TCPC anatomies. From stereolithographic models of representative cases, pressure and flow data are used to quantify control volume power loss to measure overall efficiency. particle image velocimetry (PIV) is employed to detail flow structures in the vasculature. Results are validated with dye injection flow visualization and 3-D phase contrast magnetic resonance imaging (PC-MRI) velocimetry, highlighting flow phenomena that cannot be captured with in vivo MRI due to prohibitively long scanning times. Preliminary results illustrate the variation of control volume power loss over several TCPC anatomies with varying flow conditions, the application of PIV, and validation approaches with 3-D PC-MRI velocimetry. Data from control volume power loss evaluation demonstrate a correlation with TCPC anatomy, providing added clinical knowledge of optimal TCPC design. Findings from PIV and 3-D PC-MRI velocimetry reveal a means for quantitatively comparing flow structure. Dye injection flow visualization offers qualitative insight into limitations of the selected velocimetry techniques.

This dissertation deals with customised image analysis tools in cancer research. In the field of biomedical sciences, mathematical imaging has become crucial in order to account for advancements in technical equipment and data storage by sound mathematical methods that can process and analyse imaging data in an automated way. This thesis contributes to the development of such mathematically sound imaging models in four ways: (i) automated cell segmentation and tracking. In cancer drug development, time-lapse light microscopy experiments are conducted for performance validation. The aim is to monitor behaviour of cells in cultures that have previously been treated with chemotherapy drugs, since atypical duration and outcome of mitosis, the process of cell division, can be an indicator of successfully working drugs. As an imaging modality we focus on phase contrast microscopy, hence avoiding phototoxicity and influence on cell behaviour. As a drawback, the common halo- and shade-off effect impede image analysis. We present a novel workflow uniting both automated mitotic cell detection with the Hough transform and subsequent cell tracking by a tailor-made level-set method in order to obtain statistics on length of mitosis and cell fates. The proposed image analysis pipeline is deployed in a MATLAB software package called MitosisAnalyser. For the detection of mitotic cells we use the circular Hough transform. This concept is investigated further in the framework of image regularisation in the general context of imaging inverse problems, in which circular objects should be enhanced, (ii) exploiting sparsity of first-order derivatives in combination with the linear circular Hough transform operation. Furthermore, (iii) we present a new unified higher-order derivative-type regularisation functional enforcing sparsity of a vector field related to an image to be reconstructed using curl, divergence and shear operators. The model is able to interpolate between well-known regularisers such as total generalised variation and infimal convolution total variation. Finally, (iv) we demonstrate how we can learn sparsity promoting parametrised regularisers via quotient minimisation, which can be motivated by generalised Eigenproblems. Learning approaches have recently become very popular in the field of inverse problems. However, the majority aims at fitting models to favourable training data, whereas we incorporate knowledge about both fit and misfit data. We present results resembling behaviour of well-established derivative-based sparse regularisers, introduce novel families of non-derivative-based regularisers and extend this framework to classification problems.

L’histologie virtuelle est un domaine qui suscite un intérêt de recherche croissant. Nous nous intéressons à une de ces techniques en particulier via l’imagerie de contraste de phase par rayonnement synchrotron. Cette imagerie nous permet d’observer des cerveaux de souris intacts avec une résolution spatiale de 8µm isotropique, soit une résolution similaire à celle d’une histologie optique classique mais sans endommager les tissus par des colorations ou des marquages spécifiques. Ces travaux de thèse sont organisés autour de trois grands axes. Un premier axe présente l’instrumentation photonique qui permet l’obtention du contraste de phase et le paramétrage original qui est proposé pour l’acquisition d’échantillons biologiques de composition hétérogène. Un second axe présente différents traitements d’images développés pour des tâches informationnelles précises telles que l’optimisation de la visualisation, la détection d’agrégats cellulaires et la tractographie de structures fibreuses. Enfin, une application biomédicale de ces traitements est proposée via la détection et la quantification de nanoparticules d’oxyde de fer dans un modèle expérimental d’accident vasculaire cérébral. / Virtual histology is a field of investigation with growing interest in the commmunity of bioimage analysis. We focus on one of these techniques with the phase contrast tomography using synchrotron radiation. This technique allows us to visualize mice brains with no impact and with a spatial resolution of 8µm isotropically, which is a resolution similar to the one obtained with classic optical histology but without damaging samples with specific dyeing. This thesis is organized along three main axes. The first one presents photonic instrumentation which gives us access to the phase information and the original setting of a reconstruction parameter for the acquisition of biological heterogeneous samples. A second axis shows several image processing developed in order to address different informational tasks such as visual optimization, cellular aggregates detection or fiber tractography. Eventually, a biomedical application of these process is proposed by adressing detection and quantification of iron oxide nanoparticles in an experimental model of stroke.

Orientador: Carlos Manuel Giles Antunez de Mayolo / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin / Made available in DSpace on 2018-08-28T08:31:04Z (GMT). No. of bitstreams: 1 Lussani_FernandoCesar1985-_D.pdf: 17433522 bytes, checksum: 73b3d625a81aa4bef21c60e28b981e0e (MD5) Previous issue date: 2015 / Resumo: O escopo desta tese foi o estudo, implementação, caracterização e aplicação das técnicas de imagens de raios X por contraste de fase e contraste de espalhamento. Este trabalho inicialmente descreve a formação das imagens por contraste de fase pelo método da propagação. Apresenta simulações de primeiros princípios para esta técnica comparando estes com a literatura. Em seguida reporta o desenvolvimento da instrumentação para uma estação experimental de microtomografias de raios X bem como os métodos de processamento de dados para reconstruções tomográficas. Microtomografias com alta resolução foram obtidas e são apresentadas com o intuito de caracterizar a instrumentação e suas aplicações. Essa técnica de instrumentação foi aplicada, em particular, no estudo da histomorfometria óssea em ratos Sprague-Dawley com o objetivo de quantificar os efeitos da dieta alimentar na estrutura óssea trabecular e compacta. Argumenta-se que ocorre uma ligeira tendência a diferenciação nesses tecidos em função da dieta alimentar. Além disso, neste trabalho foi implementado, caracterizado e aplicado a técnica de imagens harmônicas por espalhamento em amostras biológicas, detecção de fraturas e espalhamento anisotrópico. Também são descritos os esforços na melhoria da qualidade sinal-ruído dessa técnica / Abstract: The main scope of this work was the study, implementation, characterization and application of x-ray phase contrast and scattering constrast imaging techniques. First we describe the production of phase constrast images and early attempts to simulate phase contrast phenomena following the known literature. We also report efforts toward development of an experimental x-ray microtomography station as well as imaging processing techniques for tomography reconstruction. We present results on high resolution x-ray microtomography. This technique was applied in the study of Sprague-Dawley bone morphometric properties aiming quantification of high-fat diet effects on compact and trabecular bone structuture. It is argued about a tendency to differentiation on these tissues according to the diet. We also implemented, characterized and applied harmonic scattering imaging in biological samples, fracture detection and anisotropic scattering describing efforts to enhance signal to noise ratio in this technique / Doutorado / Física / Doutor em Ciências / 142800/2010-4 / CNPQ

No description available.

Phase-contrast imaging (PCI) is a modality of medical x-ray imaging that can solve one of the main limitations with conventional attenuation-based imaging: the imaging of materials with low attenuation coefficients, such as soft tissues. A modality of PCI, Propagation-based phase-contrast imaging (PBI), was used in this project. This method does not require any optical elements than those used in the conventional imaging; it does, however, require more processing compared to other kinds of PCI. In addition to the reduced image quality, the required image reconstruction process, with PCI, also requires several manual adjustments, which in turn results in a lot of time consuming. In order to achieve that, a simple iterative image reconstruction method that combines Simultaneous Iterative Reconstruction Technique (SIRT) and propagation-based phase-contrast imaging was developed. The proposed method was compared with another commonly used phase-retrieval method, Paganin's algorithm. The obtained results showed higher resolution and reduced blur artefacts compared with Paganin's method. The developed method also appeared to be less sensitive to error in the input parameters, such as the attenuation coefficient, but also more time-consumption than the non-iterative Paganin's method, due to the higher data processing. / Faskontrastavbildning är en ny medicinsk röntgenavbildningsteknik, som har utvecklats för att ge bättre kontrast än konventionell röntgenavbildning, särskilt för objekt med låg attenuationskoefficient, såsom mjuk vävnad. I detta projekt användes s.k. propagationsbaserad faskonstrantavbildning, som är en av de enkla metoder som möjliggör faskontrastavbildningen, utan extra optiska element än det som ingår i en konventionell avbildning. Metoden kräver dock mer avancerad bildbehandling. Två av de huvudsakliga problemen som oftast uppstår vid faskontrastavbildning är minskad bildkvalité efter den väsentliga bildrekonstruktionen, samt att den är tidskrävande p.g.a. manuella justeringar som måste göras. I det här projektet implementerades en enkel metod baserad på en kombination av den iterativa algoritmen för bildrekonstruktion, Simultaneous Iterative Reconstruction Technique (SIRT), med propagationsbaserad faskonstrantavbildning. Resultaten jämfördes med en annan fasåterhämtningsmetod, som är välkänd och ofta används inom detta område, Paganinsmetod. Efter jämförelsen konstaterades att upplösningen blev högre och artefakter som suddighet reducerades. Det noterades också att den utvecklade metoden var mindre känslig för manuell inmatning av parametern för attenuationskoefficient. Metoden visade sig dock vara mer tidskrävande än Paganin-metoden.

Semiconductors are used in many electronic applications, for example diodes, solar cells and transistors. Typically, semiconductors are inorganic materials, such as silicon and gallium arsenide, but lately more research and development has been devoted to organic semiconductors, for example semiconducting polymers. One of the reasons is that polymers can be customized, to a greater extent than inorganic semiconductors, to create a material with desired properties. Often, two polymers are blended to obtain the desired function, but two polymers do not usually result in an even blend. Instead they tend to separate from each other to varying degrees. The morphology of the blend affects the material properties, for example how efficiently it can convert electricity to light. In this project, thin films consisting of polymer blends were examined using microscopy techniques for the purpose of increasing our understanding of the morphology of such blends. One goal was to investigate whether a technique called correlative light and electron microscopy can be useful for examining the morphology of these films. In correlative light and electron microscopy, a light microscope and an electron microscope are used in the same location in order to be able to correlate the information from the two microscopes. The second goal was to learn about the morphology of the thin films using various microscopy techniques. The polymers used were Super Yellow and poly(ethylene oxide) with large molecular weight. Super Yellow is a semiconducting and light-emitting polymer while poly(ethylene oxide) is an isolating and non-emitting polymer that can crystallize. In the blend films, large, seemingly crystalline structures appeared. The structures could be up to 1 mm in the lateral direction, while the films were only approximately 170 nm thick. These structures could grow after the films had dried and their shapes were similar to those of poly(ethylene oxide) crystals. Consequently, there is reason to believe that it is the poly(ethylene oxide) that makes up the seemingly crystalline structures, but the structures also emitted more light than the rest of the film, and Raman spectroscopy showed that there was Super Yellow in the same location as the crystals. Among the microscopy techniques used, phase contrast microscopy was particularly interesting. This method visualizes differences in optical path length and was useful for studying polymer blends when the polymers have different indices of refraction. Correlating light and electron microscopy showed that there was a pronounced topographical difference between the seemingly crystalline regions and the rest of the thin film. Light microscopy has a limited resolution due to diffraction, but as long as the resolution of the light microscope is sufficient for seeing phase separation, correlative light and electron microscopy turned out to be a good method for studying the morphology of thin films of polymer blends. / Halvledare är viktiga för många elektroniska ändamål eftersom de kan användas till exempelvis dioder, solceller och transistorer. Traditionellt används inorganiska halvledande material som kisel eller galliumarsenid, men på senare tid har allt mer forskning och utveckling inriktat sig mot organiska (kolbaserade) halvledare, såsom halvledande polymerer, bland annat eftersom det i högre utsträckning går att skräddarsy de organiska materialen så att de får önskvärda egenskaper. Ofta blandas två polymerer med varandra för att skapa ett material med nya egenskaper som är önskvärda, men två polymerer brukar inte blandas jämnt utan tenderar att separera från varandra i olika utsträckning. Hur blandningen ser ut (morfologin) påverkar materialets egenskaper, till exempel hur effektivt det omvandlar ström till ljus. Med syfte att öka förståelsen för hur morfologin ser ut hos en blandning av två polymerer, har detta projekt gått ut på att undersöka tunna filmer av polymer-blandningar med hjälp av mikroskopiska tekniker. Ett delmål var att ta reda på om en teknik som heter korrelativ ljus- och elektronmikroskopi är en bra metod för att undersöka morfologin hos dessa filmer. Vid korrelativ ljus- och elektronmikroskopi används både ett ljusmikroskop och ett elektronmikroskop på samma plats för att kunna korrelera informationen som de båda mikroskopen ger. Det andra delmålet var att undersöka vad de olika mikroskopi-teknikerna kan säga om morfologin hos de tunna filmerna. De polymerer som använts är Super Yellow och poly(etylenoxid) med hög molekylmassa. Super Yellow är en oordnad halvledande och ljusemitterande polymer medan poly(etylenoxid) är en isolerande och icke-emitterande polymer som kan kristallisera. I de blandade filmerna uppstod stora kristall-liknande strukturer som kunde vara upp emot 1 mm breda trots att filmerna bara var ungefär 170 nm tunna. Dessa strukturer kunde växa fram efter det att filmerna redan hade torkat och påminde i form om kristaller som kan bildas av poly(etylenoxid). Det finns alltså skäl att tro att det är poly(etylenoxid) som kristalliserats, men de kristall-liknande strukturerna visade sig emittera mer ljus än vad resten av filmen gjorde, och Raman-spektroskopi visade att det även fanns Super Yellow på samma plats som kristallerna. Bland de mikroskopitekniker som testades utmärker sig faskontrastmikroskopi, som visar skillnader i den optiska vägskillnaden (det vill säga faktisk vägskillnad multiplicerat med brytningsindex). Det visade sig vara en intressant teknik för att studera polymerblandningar när de båda polymererna har olika brytningsindex. Genom att korrelera ljus- och elektronmikroskopi visade det sig att det fanns en tydlig skillnad i struktur mellan de kristall-liknande områdena och resten av den tunna filmen. Ljusmikroskopi har begränsad upplösning på grund av ett fenomen som heter diffraktion, men så länge som ljusmikroskopets upplösning är tillräcklig för att se fasseparation visade det sig att korrelativ ljus- och elektronmikroskopi är en bra metod för att studera morfologin hos tunna filmer av polymerblandningar.

This thesis presents a new optical imaging technique which measures the structure of objects without the use of lenses. Termed diffraction-contrast imaging (DCI), the method retrieves the object structure from a Fresnel diffraction pattern of the object, using a deconvolution algorithm. DCI is particularly adept at imaging highly transparent objects and this is demonstrated by retrieving the structure of an almost transparent cloud of laser-cooled atoms. Applied to transparent Bose-Einstein condensates, DCI should allow the non-destructive imaging of the condensate while requiring only the minimum possible apparatus of a light source and a detector. (For complete abstract open document)

No description available.

ransmitted-light coherence-controlled holographic microscope (CCHM) based on an off-axis achromatic and space-invariant interferometer with a diffractive beamsplitter has been designed, constructed and tested. It is capable to image objects illuminated by light sources of arbitrary degree of temporal and spatial coherence. Off-axis image-plane hologram is recorded and the image complex amplitude (intensity and phase) is reconstructed numerically using fast Fourier transform algorithms. Phase image represents the optical path difference between the object and the reference arms caused by presence of an object. Therefore, it is a quantitative phase contrast image. Intensity image is confocal-like. Optical sectioning effect induced by an extended, spatial incoherent light source is equivalent to a conventional confocal image. CCHM is therefore capable to image objects under a diffusive layer or immersed in a turbid media. Spatial and temporal incoherence of illumination makes the optical sectioning effect stronger compared to a confocal imaging process. Object wave reconstruction from the only one recorded interference pattern ensures high resistance to vibrations and medium or ambience fluctuations. The frame rate is not limited by any component of the optical setup. Only the detector and computer speeds limit the frame rate. CCHM therefore allows observation of rapidly varying phenomena. CCHM makes the ex-post numerical refocusing possible within the coherence volume. Coherence degree of the light source in CCHM can be adapted to the object and to the required image properties. More coherent illumination provides wider range of numerical refocusing. On the other hand, a lower degree of coherence makes the optical sectioning stronger, i.e. the optical sections are thiner, it reduces coherence-noise and it makes it possible to separate the ballistic light. In addition to the ballistic light separation, CCHM enables us to separate the diffused light. Multi-colour-light