Au cours du développement embryonnaire, la plupart des éléments de la plante sont mis en place. Ce processus donne lieu à un embryon mature qui possède toutes les caractéristiques d'une jeune plantule. Ces étapes se déroulent durant les premiers stades du développement et sont associées à un changement de forme, ou morphogenèse. Ces deux processus sont stéréotypés chez Arabidopsis thaliana.Au cours du développement embryonnaire, l'embryon passe d'une forme globulaire avec une symétrie radiale, à un embryon en forme de cœur avec une symétrie bilatérale. Ces changements sont basés sur des événements de croissance différentielle et de divisions cellulaires avec des orientations particulières de la surface de division dans l'embryon, des mécanismes qui sont étroitement régulés et sous le contrôle de facteurs moléculaires. Si certaines caractéristiques des stades de développement sont connues, comme le nombre de cellules ou encore des événements moléculaires, d'autres comme le changement de symétrie et l’acquisition d'une forme, qui est spécifique de l'embryon, n'ont pas encore été étudiées. Pour comprendre l'origine de la forme de cœur, une description multi-échelle et une quantification précises des changements de forme ont été réalisées. Pour cela une collection pré-existante d'image embryons fixés à différents stades du développement, a été enrichie de 47 embryons pour couvrir le développement embryonnaire précoce sur 8 générations cellulaires. Chaque embryon de la collection a été numérisé en 3D et ses cellules segmentées. À partir de ces images, une filiation cellulaire de l'embryon et des données de description de l'organisation des cellules ont été générées.L'évolution des paramètres mesurés montre un changement progressif de la forme qui démarre de manière très précoce et bien avant que des modifications morphologiques ne soient supposées. Pour suivre l'évolution de traits caractéristiques de la forme et l'attribuer à des dynamiques cellulaires particulières, des mesures sur les événements de division et de croissance cellulaire ont été calculées. Des modifications de croissances cellulaires apparaissent très précocement alors que l'embryon n'est encore que globulaire. Les caractéristiques des divisions changent également, les plans de division passent d'une orientation stéréotypée à une orientation variable. Malgré la variabilité, des comportements similaires apparaissent au cours des générations cellulaires mais également au sein des différents précurseurs des tissus et organes de l'embryon.La variabilité des divisions observées est questionnée à travers la recherche de règles simulées à l'aide d'un modèle stochastique 3D de partitionnement volumique. En testant une règle de minimisation stochastique de l'aire de la surface de partition, l'ensemble des orientations des plans de division observés ont pu être reproduites dans les formes observées et avec une répartition du volume donnée. L'hypothèse d'une règle stochastique basée sur la géométrie cellulaire et la minimisation de l'aire de la surface est envisagée, mais les générations avancées laissent entrevoir l'action progressive d'une autre contrainte sur la mise en place du plan de division. L'ensemble du phénotypage devrait définir de bonnes bases pour mieux comprendre les facteurs moléculaires qui régulent les mécanismes cellulaires de division et de croissance impliquée dans la mise en place de la forme de cœur de l'embryon. / During embryonic development, the major body plans of the plant are implemented. This process gives rise to a mature embryo which possess all the characteristics of a young seedling and is associated with a morphological change. These two processes are stereotyped in Arabidopsis thaliana embryo development.Over the developmental process, the embryo shape switches from a globular form, with a radial symmetry, to a heart form with a bilateral symmetry. These changes are based on a differential cellular growth and on particular cell division plane orientation in the embryo, mechanisms that are tightly regulated and under control of molecular factors.If a number of cellular and molecular steps are known, the evolution of the symmetry and the acquisition of the specific embryo shape have not yet been explored.To understand the origin of the heart shape, we proceed to a detailed multi-scale description and quantification of embryo shape changes during embryo stages. We completed a collection of fixed embryo images with 35 embryos distributed along the embryo development over eight cell generations. The embryos have been digitized in 3D and cell segmented. From these images, embryo cell lineages have been reconstructed and their cell organizations characterized.The evolution of parameter measurements showed a progressive change of the shape. The change has begun at an early embryo stage where morphology still look like a globular form.To correlate the morphological change and the cells events, the division and the cell growth were inferred through measurements. The cell growth behavior changed in the globular embryo. Changes in the division behavior were also observed. The division plan orientations stopped to be stereotyped. Despite the variability, similar behaviors were observed over cell generations and also among precursor of tissues and organs of the embryo.The cell division behavior has been further analyzed by a search of the realized division rules which explain observations with a stochastic model of volume partition. A division rule based on a stochastic 3D surface area minimization has reproduced all observed division plane orientations depending on the volume repartition among daughter cells. The hypothesis of a stochastic division rule based on the cell geometry with a surface area minimization of surface passing through the mother cell centroid seemed to become apparent. But divisions in older cell generations suggested a progressive action of another factor on the division plane.The overall phenotyping the embryo early development should provide a framework for the analysis of molecular factors involved in the heart shape.

Capillaroscopy is a non-invasive and safe tool which allows the evaluation of the morphology of the microcirculation. Since its recent incorporation in the 2013 American College of Rheumatology (ACR)/European League Against Rheumatism (EULAR) classification criteria for systemic sclerosis together with its assessed role to monitor disease progression, capillaroscopy became a ‘mainstream’ investigation for rheumatologists. Given its increasing use by a variety of physicians internationally both in daily practice to differentiate primary from secondary Raynaud's phenomenon, as well as in research context to predict disease progression and monitor treatment effects, standardisation in capillaroscopic image acquisition and analysis seems paramount. To step forward to this need, experts in the field of capillaroscopy/microcirculation provide in this very consensus paper their view on image acquisition and analysis, different capillaroscopic techniques, normal and abnormal capillaroscopic characteristics and their meaning, scoring systems and reliability of image acquisition and interpretation. / Revisión por pares

Machine learning has been utilized in bio-imaging in recent years, however as it is relatively new and evolving, some researchers who wish to utilize machine learning tools have limited access because of a lack of programming knowledge. In electron microscopy (EM), immunogold labeling is commonly used to identify the target proteins, however the manual annotation of the gold particles in the images is a time-consuming and laborious process. Conventional image processing tools could provide semi-automated annotation, but those require that users make manual adjustments for every step of the analysis. To create a new high-throughput image analysis tool for immuno-EM, I developed a deep learning pipeline that was designed to deliver a completely automated annotation of immunogold particles in EM images. The program was made accessible for users without prior programming experience and was also expanded to be used on different types of immuno-EM images. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2020. / FAU Electronic Theses and Dissertations Collection

Packed bed combustors burn fairly large solid fuel particles within confining walls, with air supplied from below the grate. As combustion occurs and particles are consumed, fresh particles are fed onto the bed so the level is kept roughly constant. Packed bed combustion is used for wood and biomass combustion in small-scale power plants, wood waste combustion in pulp and paper plants, and trash incineration. The structure of a packed bed is very important to the combustion process and can be defined by particle shape and size, sphericity, particle overlap (decreasing area availability) and chiefly by void fraction. Void fraction has already been proven of great influence in packed beds – it is raised to the third power in the pressure loss equation, and it can also affect heat and mass transfer and surface reaction rates. This thesis presents results of several experimental combustion tests that were performed in a packed bed combustor, using commercial spruce lumber particles of parallelepipedal geometry as fuel. At the end of each test the bed contents were removed, taking care to preserve their structure, and fixed with liquefied wax. The solidified bed was then cut into circular cross sections at different heights of the bed, and photographs of the cross sections were taken so the local void fraction could be estimated using image analysis. The bed sampling led to the discovery that, surprisingly, the actual bulk void fraction in the combustor, which is the average of local void fraction measurements, is less than that of the unburnt particles, varying from 19% to 30% in decrease in void fraction depending on the particle type used. Local measurements allowed the development of an empirical linear equation model to represent the variation of void fraction with height above the grate. Each combustion test had measurements of gas volume fractions and temperatures at different heights above the bed grate to be compared with the results of a numerical model simulation. The numerical model used in this work is an existing numerical model of all the relevant processes in packed bed combustion. Previously, the numerical model had assumed the void fraction to be constant and equal to that of the unburnt fuel, since no information on local variation was available, and the packing geometry remained self-similar as particles are consumed. Three models for void fraction were then compared in the combustion model: a constant void equal to that of the unburnt particles, the empirical linear fit of void fraction with height, and a constant void equal to the measured bulk void fraction. Maximum temperatures were higher using the unburnt fuel void fraction because of a thicker oxidation zone, whereas the void fraction model iii based on experiments generated a thicker reduction zone and therefore higher CO concentrations. CO concentrations were experimentally measured and agreed quite well with the CO concentration from the model. Local void fraction differences had the most impact in the diffusion-controlled zone, as shown by comparing the empirical void model and the measured bulk void fraction. How lowering the void fraction can increase gas velocities, heat and mass transfer coefficients, and burning rates is also discussed in this work.

There is an upsurge of research interest on Ni-based superalloys additively manufactured (AM) in aerospace sectors. However, achieving the accuracy and quality of the AM part is a challenging task because it is a process of adding material layer by layer with different process parameters. Hence, defects can be observed, and these defects have a detrimental effect on the mechanical properties of the material. Also, AM materials commonly portray a columnar grain structure which also makes it difficult to determine the average grain size because while using the commonly used intercept method, the grain boundaries do not intercept to the test line appropriately. It is important to measure the defects and grain size before performing mechanical testing on the material. Defect measurement and grain size measurements are usually measured manually which results in longer lead time. This work is addressed towards testing recipes in the automated image analysis software to optimize the lead time with good accuracy. Haynes 282, a γ' strengthened superalloy is used in this work. It was assumed that 1,5mm of material from the surface will be machined away so defects had to be measured in this region of interest. The image analysis tools used to test its potentials are MIPAR and ImageJ. Initially, five images in MIPAR and Image J were tested keeping the manual measurements as a benchmark. From this part, it was concluded that metallography and image quality play an important role in the automated measurement. Also, basic Image J software cannot give the measurements of lack of fusion in terms of caliper diameter (longest measurable diameter). Hence, MIPAR was chosen for the application because it was more promising. In the next part, 15 samples were used with manual measurements from a stitched sample and batch processing with MIPAR. The total caliper diameter results were plotted to compare manual measurements and MIPAR. It was observed that scratches were measured as lack of fusion defects at few instances by MIPAR which were further refined using a post-processing function. The defect density results were plotted and compared as well. Due to the difference in calculation of region of interest, the difference in results was observed.To perform the grain size measurement, Haynes 282 was used in HIP and heat treated condition, achieving equiaxed grains. The etchant should be appropriate to reveal the grains. Hence four different etchants were used in this study hydrogen peroxide+HCl, Kallings (electro etch), Kallings (swab) and diluted oxalic acid. This measurement was performed on the material which was cut along the build direction as well as 90º to the growth direction. Since there is no standard for additively manufactured material yet, the results were tested with hall-petch equation to be convinced of the results obtained. It was observed that MIPAR recipe portrayed good results. The results of manual measurements and MIPAR measurements were plotted and compared. It was observed that Hydrogen peroxide and Kallings (swab) showed the grains evidently but twin boundaries were revealed as well. MIPAR calculated the twin boundaries as grains so it over calculated than manual measurements. Kallings (electro etch) and diluted oxalic acid did not reveal the grains so it was difficult for MIPAR to identify the grains.

Traditional sand analysis is labor and cost-intensive, entailing specialized equipment and operators trained in geological analysis. Even a small step to automate part of the traditional geological methods could substantially improve the speed of such research while removing chances of human error. Digital image analysis techniques and computer vision have been well developed and applied in various fields but rarely explored for sand analysis. This research explores capabilities of remote sensing digital image analysis techniques, such as object-based image analysis (OBIA), machine learning, digital image analysis, and photogrammetry to automate or semi-automate the traditional sand analysis procedure. Here presented is a framework combining OBIA and machine learning classification of microscope imagery for use with unconsolidated terrigenous beach sand samples. Five machine learning classifiers (RF, DT, SVM, k-NN, and ANN) are used to model mineral composition from images of ten terrigenous beach sand samples. Digital image analysis and photogrammetric techniques are applied and evaluated for use to characterize sand grain size and grain circularity (given as a digital proxy for traditional grain sphericity). A new segmentation process is also introduced, where pixel-level SLICO superpixel segmentation is followed by spectral difference segmentation and further levels of superpixel segmentation at the object-level. Previous methods of multi-resolution and superpixel segmentation at the object level do not provide the level of detail necessary to yield optimal sand grain-sized segments. In this proposed framework, the DT and RF classifiers provide the best estimations of mineral content of all classifiers tested compared to traditional compositional analysis. Average grain size approximated from photogrammetric procedures is comparable to traditional sieving methods, having an RMSE below 0.05%. The framework proposed here reduces the number of trained personnel needed to perform sand-related research. It requires minimal sand sample preparation and minimizes user-error that is typically introduced during traditional sand analysis. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2020. / FAU Electronic Theses and Dissertations Collection

INTRODUCTION: Ebola virus (EBOV) is a highly infectious and often lethal filovirus that causes hemorrhagic fever, with a reported case fatality rate of 40-90%. There are currently no Food and Drug Administration (FDA) approved medical countermeasures (MCMs) for EBOV. Non-human primates (NHPs) remain the gold standard animal model for EBOV research as they most accurately recapitulate human disease. OBJECTIVE: This study aimed to characterize the temporal viral pathogenesis of EBOV in the liver of infected rhesus macaques using routine histopathology, multiplex immunohistochemistry (mIHC) and multiplex fluorescent In Situ Hybridization (mFISH), refined by digital pathology (DP) and image analysis (DIA). METHODS: 21 FFPE liver sections from EBOV-infected rhesus macaques were examined microscopically (Uninfected controls n=3; 3 DPE n=3; 4 DPE n=3; 5 DPE n=3; 6 DPE n=3; Terminal n=6). Tissues were stained with H&E and PTAH for histopathological scoring. Three serial sections were fluorescently immunolabeled or hybridized under three independent conditions (1.EBOV VP35, Tissue Factor, CD68; 2.EBOV VP35, Heppar, Myeloperoxidase (MPO); 3.EBOV VP35, IL-6, ISG-15). Slides were digitized by a Vectra PolarisTM fluorescent whole slide scanner and DIA was conducted using HaloTM image analysis software. Statistical analysis was conducted using GraphPad PrismTM 8.0. RESULTS: Comparing peracute (3-4 DPE) to acute (5-6 DPE) and terminal (6-8 DPE) EBOV infection, there is a statistically significant (p < 0.05) increase in hepatic inflammation and fibrin thrombi, correlating with an absolute increase in macrophages (CD68), neutrophils (MPO), and total % of Tissue Factor in the liver. There is also a significant increase in the severity of necrosis, which correlates with a decrease in Heppar. While there was significant colocalization of VP35 and CD68 starting at 4 DPE, there was only rare colocalization of VP35 with Heppar, even in terminal animals. Similar to mIHC, progressive and statistically significant differences were observed in gene expression when comparing peracute to acute and terminal EBOV infection. IL-6 predominated within periportal fibrovascular compartments, but also colocalized within cells concurrently expressing EBOV VP35. EBOV VP35 expression was observed within histiocytes, endothelial cells, and less commonly hepatocytes. ISG-15 expression was observed in periportal regions and in proximity to cells expressing EBOV VP35, but colocalization within EBOV VP35 expressing cells was an extremely rare event. CONCLUSION: Qualitative tools are well suited for confirming virulence and viral tissue tropism, but do little to build on our current understanding of disease. Using DIA in partnership with mIHC and mFISH, this study quantified statistically significant temporal changes in the immunoreactivity and hybridization of host and viral biomarkers that have previously been linked to the pathogenesis of EBOV. Taken together, these tools have enabled us to characterize minute changes that reflect magnitudes of biological variability simply not feasible to detect with the human eye. Furthermore, spatial context has refined our current understanding of differential gene expression of EBOV, which has the potential to aid in development of host-directed therapies. The establishment of these benchmarks will serve as a guide for the validation of cross-institutional EBOV animal models.

abstract: Non-Destructive Testing (NDT) is a branch of scientific methods and techniques used to evaluate the defects and irregularities in engineering materials. These methods conduct testing without destroying or altering material’s structure and functionality. Most of these defects are subsurface making them difficult to detect and access. SONIC INFRARED (IR) is a relatively new and emerging vibrothermography method under the category of NDT methods. This is a fast NDT inspection method that uses an ultrasonic generator to pass an ultrasonic pulse through the test specimen which results in a temperature variation in the test specimen. The temperature increase around the area of the defect is more because of frictional heating due to the vibration of the specimen. This temperature variation can be observed using a thermal camera. In this research study, the temperature variation in the composite laminate during the SONIC IR experimentation using an infrared thermal camera. These recorded data are used to determine the location, dimension and depth of defects through SONIC IR NDT method using existing defect detection algorithms. Probability of detection analysis is used to determine the probability of detection under specific experimental conditions for two different types of composite laminates. Lastly, the effect of the process parameters such as number of pulses, pulse duration and time delay between pulses of this technique on the detectability and probability of detection is studied in detail. / Dissertation/Thesis / Masters Thesis Mechanical Engineering 2019

京都大学 / 0048 / 新制・課程博士 / 博士(情報学) / 甲第20738号 / 情博第652号 / 新制||情||112(附属図書館) / 京都大学大学院情報学研究科社会情報学専攻 / (主査)教授 黒田 知宏, 教授 大手 信人, 教授 松田 哲也 / 学位規則第4条第1項該当 / Doctor of Informatics / Kyoto University / DFAM

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