This thesis describes the design of a multi-platform client-server application to access large raster data, existing and proposed ways to optimize the running speed and processing raster. The advantage of the application is an updated version of GDAL for reading most known raster format, and implementing extension for reading GeoPDF with open-source PDF rendering library. Integrating created and optimized server component into the open-source project IIPImage improves it to support more raster formats.

Transport simulation models play a crucial role in transportation planning, design, and operations, allowing for the replication of various scenarios through the incorporation of real-world data and parameters. Recently, agent-based transport models have gained prominence for their ability to simulate intricate metropolitan transport systems. These models take into account the distinct characteristics, decision-making processes, and interactions of individual agents. Among the array of agent-based transport models, MATSim stands out as a potent and adaptable tool for modeling transportation systems. A critical aspect of MATSim’s input preparation involves assigning activity location points using land use raster data. However, the characteristics of land use raster data present limitations in certain urban case studies such as Stockholm. In response, some researchers have turned their attention to buildings shapefile data, a commonly used geospatial data format. This study aims to improve the activity location assignment model by developing an evaluation workflow of model uncertainty for different geospatial input data in MATSim and empirically analyzing their impacts on simulation outcomes. Despite acknowledging data availability and activity representation limitations, the study’s results demonstrate that utilizingbuildings shapefiles as input data yields more consistent outcomes with reduced uncertainty. This suggests the promising potential of buildings shapefiles as a favorable data source for transportation modeling and planning within the studied scenarios.

West Nile virus has become a major risk to humans since its first appearance in New York City in 1999. Physicians and state health officials are interested in new and more efficient methods for monitoring disease spread and predicting future outbreaks. This study modeled habitat suitability for mosquitoes that carry West Nile virus. Habitat characteristics were used to derive risk maps for the entire state of Mississippi. Statistical significance tests yielded objective evidence for choosing among many habitat variables. Variables that were significantly correlated with diagnosed human cases for 2002 were combined in weighted linear algebraic models using a geographic information system (GIS). Road density, slope, and summer precipitation minus evaporation (P-E) were the most significant variables. GIS-based model results were compared with results from logistic regression models. The algebraic model was preferred when validated by 2003 human cases. If adopted, GIS-based risk models can help guide mosquito control efforts.

Planners who are involved in locational decision making often use raster-based geographic information systems (GIS) to quantify the value of land in terms of suitability or cost for a certain use. From a computational point of view, this process can be seen as a transformation of one or more sets of values associated with a grid of cells into another set of such values through a function reflecting one or more criteria. While it is generally anticipated that different transformations lead to different ‘best’ locations, little has been known on how such differences arise (or do not arise). Examples of such spatial decision problems can be easily found in the literature and many of them concern the selection of a set of cells (to which the land use under consideration is allocated) from a raster surface of suitability or cost depending on context. To facilitate GIS’s algorithmic approach, it is often assumed that the quality of the set of cells can be evaluated as a whole by the sum of their cell values. The validity of this assumption must be questioned, however, if those values are measured on a scale that does not permit arithmetic operations. Ordinal scale of measurement in Stevens’s typology is one such example. A question naturally arises: is there a more mathematically sound and consistent approach to evaluating the quality of a path when the quality of each cell of the given grid is measured on an ordinal scale? The thesis attempts to answer the questions highlighted above in the context of path planning through a series of computational experiments using a number of random landscape grids with a variety of spatial and non-spatial structures. In the first set of experiments, we generated least-cost paths on a number of cost grids transformed from the landscape grids using a variety of transformation parameters and analyzed the locations and (weighted) lengths of those paths. Results show that the same pair of terminal cells may well be connected by different least-cost paths on different cost grids though derived from the same landscape grid and that the variation among those paths is affected by how given values are distributed in the landscape grid as well as by how derived values are distributed in the cost grids. Most significantly, the variation tends to be smaller when the landscape grid contains more distinct patches of cells potentially attracting or distracting cost-saving passage or when the cost grid contains a smaller number of low-cost cells. The second set of experiments aims to compare two optimization models, minisum and minimax (or maximin) path models, which aggregate the values of the cells associated with a path using the sum function and the maximum (or minimum) function, respectively. Results suggest that the minisum path model is effective if the path search can be translated into the conventional least-cost path problem, which aims to find a path with the minimum cost-weighted length between two terminuses on a ratio-scaled raster cost surface, but the minimax (or maximin) path model is mathematically sounder if the cost values are measured on an ordinal scale and practically useful if the problem is concerned not with the minimization of cost but with the maximization of some desirable condition such as suitability. / Planerare som arbetar bland annat med att fatta beslut som hänsyftar till vissa lokaler använder ofta rasterbaserade geografiska informationssystem (GIS) för att sätta ett värde på marken med avseende på lämplighet eller kostnad för en viss användning. Ur en beräkningssynpunkt kan denna process ses som en transformation av en eller flera uppsättningar värden associerade med ett rutnät av celler till en annan uppsättning sådana värden genom en funktion som återspeglar ett eller flera kriterier. Medan det generellt förväntas att olika omvandlingar leder till olika "bästa" platser, har lite varit känt om hur sådana skillnader uppstår (eller inte uppstår). Exempel på sådana rumsliga beslutsproblem kan lätt hittas i litteraturen och många av dem handlar om valet av en uppsättning celler (som markanvändningen övervägs tilldelas) från en rasteryta av lämplighet eller kostnad beroende på kontext. För att underlätta GISs algoritmiska tillvägagångssätt antas det ofta att kvaliteten på uppsättningen av celler kan utvärderas som helhet genom summan av deras cellvärden. Giltigheten av detta antagande måste emellertid ifrågasättas om dessa värden mäts på en skala som inte tillåter aritmetiska transformationer. Användning av ordinal skala enligt Stevens typologi är ett exempel av detta. En fråga uppstår naturligt: Finns det ett mer matematiskt sunt och konsekvent tillvägagångssätt för att utvärdera kvaliteten på en rutt när kvaliteten på varje cell i det givna rutnätet mäts med ordinalskala? Avhandlingen försöker svara på ovanstående frågor i samband med ruttplanering genom en serie beräkningsexperiment med hjälp av ett antal slumpmässigt genererade landskapsnät med en rad olika rumsliga och icke-rumsliga strukturer. I den första uppsättningen experiment genererade vi minsta-kostnad rutter på ett antal kostnadsnät som transformerats från landskapsnätverket med hjälp av en mängd olika transformationsparametrar, och analyserade lägen och de (viktade) längderna för dessa rutter. Resultaten visar att samma par ändpunkter mycket väl kan vara sammanbundna med olika minsta-kostnad banor på olika kostnadsraster härledda från samma landskapsraster, och att variationen mellan dessa banor påverkas av hur givna värden fördelas i landskapsrastret såväl som av hur härledda värden fördelas i kostnadsrastret. Mest signifikant är att variationen tenderar att vara mindre när landskapsrastret innehåller mer distinkta grupper av celler som potentiellt lockar eller distraherar kostnadsbesparande passage, eller när kostnadsrastret innehåller ett mindre antal låg-kostnad celler. Den andra uppsättningen experiment syftar till att jämföra två optimeringsmodeller, minisum och minimax (eller maximin) sökmodeller, vilka sammanställer värdena för cellerna som är associerade med en sökväg med summanfunktionen respektive maximum (eller minimum) funktionen. Resultaten tyder på att minisumbanemodellen är effektiv om sökningen av sökvägen kan översättas till det konventionella minsta kostnadsproblemet, vilket syftar till att hitta en väg med den minsta kostnadsvägda längden mellan två terminaler på en ratio-skalad rasterkostyta, men minimax (eller maximin) banmodellen är matematiskt sundare om kostnadsvärdena mäts i ordinär skala och praktiskt användbar om problemet inte bara avser minimering av kostnad men samtidigt maximering av någon önskvärd egenskap såsom lämplighet. / <p>QC 20181002</p>

<p>Microwave imaging is a promising new imaging modality under research for breast cancer detection. This technique images/reconstructs the internal dielectric composition of the breasts and relies on the contrast between the dielectric properties of malignant tissues and healthy tissues to pinpoint the abnormality. Over the years, new imaging algorithms were proposed and many imaging systems were developed in accordance. However, none of the proposed systems has made it to the market.</p> <p>In this thesis, a prototype planar raster-scanning system for near-field microwave imaging is presented. This system measures the scattering parameters while scanning a 2-D plane over the imaged object (phantom) in a raster pattern. The development of this system aids significantly in our research of microwave imaging for breast cancer detection because it enables us to carry out numerous experiments and to develop and verify new imaging algorithms.</p> <p>Our contribution also lies in conducting a comprehensive study of the dynamic range of the developed system. Each source of noise/uncertainty from the system is identified and studied for the benefits of future improvements.</p> <p>Typical imaging results of phantoms with different dielectric properties are also provided to showcase the performance of the developed system.</p> / Master of Applied Science (MASc)

Among the central constituents of the innate immune system are macrophages, which are known for phagocytosis or ‘eating’ foreign particles or pathogens. Macrophages express several cell-surface proteins including transmembrane and membrane-anchored receptors, which play a vital role in their response to pathogenic stimuli. The plasma membrane is a highly fluid and dynamic environment, which facilitates the diffusion of lipids and proteins within the plane of the membrane. This study aims to measure the lateral diffusion of two types of plasma membrane receptors on macrophages, toll-like receptor II (TLR2) and cluster of differentiation 14 (CD14), to answer three main research questions: 1) Which type of fluorescence-based microscopy techniques is best suited for measuring the lateral diffusion of TLR2 and CD14 on macrophage plasma membrane? 2) Does culturing macrophages on different surface topographies impact the diffusion of TLR2 in the plasma membrane and its pro-inflammatory response, along with morphological changes? 3) Does aging alter the lateral diffusion of TLR2 in the plasma membrane of macrophages? To date, a variety of fluorescence-based methods have been developed to study the dynamics of cell membrane constituents. These techniques are based on either ensemble or single particle measurements. We have used single particle tracking methods to track the mobility of fluorescently labeled membrane receptors on murine bone marrow-derived macrophages. Total internal reflection fluorescence microscopy (TIRF) was used to visualize and capture the dynamics in live cells. Using a custom routine algorithm we detected, localized, and tracked the particles to calculate their diffusion coefficient, extracted from the mean-squared displacement as the most common measure of diffusion. We also measured the diffusion coefficient using an ensemble-based technique known as Raster Image Correlation Spectroscopy (RICS) with a confocal laser-scanning microscope. The use of confocal eliminates the out-of-focus signal and enables measurements that are confined to a narrow plane in the cell. Also, the ability of RICS to separate the slow and immobile fractions of particles makes it possible to detect heterogeneities in diffusion. To our knowledge, this is the first study that has utilized both SPT and RICS to directly compare receptors’ diffusion in different membrane sections. Moreover, this is the first study that has examined the diffusion of receptors on macrophages adhered to different surface topographies, and the first that has investigated the receptors’ diffusion in young and old macrophages. / Thesis / Doctor of Philosophy (PhD) / The immune system is highly dependent on a specialized subset of white blood cells known as macrophages that are capable of clearing damaged and dead cells as well as a wide range of invading micro-organisms. Specific receptor proteins present on the membrane of macrophages are involved in the recognition of particles and subsequent signaling to recruit other immune cells or to promote healing and wound repair. To date, a variety of fluorescence-based microscopy methods have been used to study the dynamics of cell membrane components. The mobility of several membrane receptors in macrophages has been studied using microscopy techniques, which have provided valuable insights into their function. However, there is still insufficient information about the behavior of two key receptors (TLR2 and CD14) that participate in signaling in response to bacterial products. This thesis aims to answer three major questions with regard to receptor mobility (i.e., diffusion) within macrophage membrane: 1) Which type of fluorescence-based microscopy technique is more suitable for measuring the mobility of TLR2 and CD14 receptors on macrophage membranes? 2) What is the impact of different surface topographies on TLR2 diffusion in adhered macrophages, as well as cell shape, and the ability of macrophages to internalize particles? 3) Does aging alter TLR2 mobility in the membrane of macrophages? The following chapters provide detailed answers to these questions. In brief, we have demonstrated that TLR2 and CD14 diffusion measurements in adhered macrophages highly depend on the membrane section chosen. In addition, our results show that micro- and nanostructured surface topographies alter the shape of adhered macrophages and yield higher bacteria internalization, while the diffusion of TLR2 is not changed. When comparing macrophages derived from young and old mice, we find similar diffusion rate of TLR2 in macrophages of the two age groups.

As population increases and urbanization occurs, watershed management will be critical in the protection of water resources in North Central Texas. By 2040, Denton County will nearly double its 2010 population. The Upper Hickory Creek Watershed lies west of Denton and empties into Lake Lewisville. Lake Lewisville provides drinking water for Denton, Dallas, and other neighboring cities. Mitigation of non-point source pollutants as a result of urban and agricultural practices is essential to protecting Lake Lewisville water resources. A common best management practice used to mitigate pollutants is the protection of riparian ecotones that occupy river corridors; however, recent agricultural and urban practices are diminishing these ecosystems and their services. In this paper, the riparian buffer delineation equation (RBDE) is used to assess the current state of Upper Hickory Creek Watershed to aid in the monitoring of the riparian buffers along stream corridors. While the RBDE was used as pre-assessment tool for the riparian buffer effectiveness in the watershed, a new form of the equation was used to evaluate riparian buffer improvement potential (BP) in conjunction with Denton County parcel data to provide insights into buffer effectiveness and identify areas for improvement on a landowner scale.

Submitted by JÚLIO HEBER SILVA (julioheber@yahoo.com.br) on 2018-03-15T20:24:53Z No. of bitstreams: 2 Dissertação - Jéssica Gabriela de Almeida Cunha - 2018.pdf: 3483915 bytes, checksum: 12c37e736c4d6f53761fc0255e6bff6d (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2018-03-16T11:10:21Z (GMT) No. of bitstreams: 2 Dissertação - Jéssica Gabriela de Almeida Cunha - 2018.pdf: 3483915 bytes, checksum: 12c37e736c4d6f53761fc0255e6bff6d (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-03-16T11:10:21Z (GMT). No. of bitstreams: 2 Dissertação - Jéssica Gabriela de Almeida Cunha - 2018.pdf: 3483915 bytes, checksum: 12c37e736c4d6f53761fc0255e6bff6d (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2018-02-22 / Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG / This work brings the use of grid of points in the resolution of cutting and packing problems that consider rectangular shaped items. The grids can be considered for mathematical programming models and heuristics, and they are independent of the problem. The following grids that are defined by the literature are considered for this work: canonical dissections (also known as normal patterns), reduced raster points, useful numbers, corner points, regular normal patterns, extreme points, and meet-in-the-middle patterns. The objective is to assess the influence of each grid on the resolution of cutting and packing problems, before and after applying reduction procedures, as the one related to update the items size. Theoretical results are obtained from relations of set and size between the grids, showing that the grid of normal patterns and useful numbers are equivalent and, thus, proving formally that the grid of reduced raster points ensures an optimal solution (this result has been formally opened in the literature). In addition, we propose a new procedure to reduce the size of grids. In order to validate the proposed procedure and evaluate the grids, we perform experiments over instances from the literature, where it is possible to observe that the grids of reduced raster points and meet-in-the-middle patterns are the smallest. Experiments were also conducted in a two-dimensional packing problem that uses an integer linear programming model to pack the items in points of a grid. The results indicate that using the reduction procedures it is possible to obtain optimal solutions quicker. / Este trabalho traz o uso de malhas de pontos na resolução de problemas de corte e empacotamento para itens com formato retangular. As malhas podem ser consideradas em modelos de programação matemática e heurísticas, sendo independentes do problema tratado. As seguintes malhas definidas pela literatura, canonical dissections (também conhecida por normal patterns), reduced raster points, useful numbers, corner points, regular normal patterns, extreme points e meet-in-the-middle patterns, são consideradas neste trabalho. O objetivo é apresentar relações que existem entre as malhas e analisar a influência delas sobre o tempo gasto na resolução de problemas de corte e empacotamento, antes e após aplicar procedimentos de redução, como atualizar o tamanho dos itens. Resultados teóricos são obtidos envolvendo relações de conjunto e tamanho entre as malhas, mostrando que a malha de normal patterns e useful numbers são equivalentes e, assim, permitindo provar formalmente que a malha de reduced raster points garante uma solução ótima (resultado que estava em aberto na literatura). Além disso, propõe-se um novo procedimento visando reduzir o tamanho das malhas. Como forma de validar o procedimento proposto e avaliar a redução que ele proporciona nas malhas, executam-se experimentos sobre instâncias da literatura, sendo possível observar que as malhas de reduced raster points e meet-in-the-middle patterns são as menores. Experimentos também foram realizados sobre um problema de empacotamento bidimensional que utiliza um modelo de programação linear inteira para empacotar os itens em pontos da malha. Os resultados indicam que utilizando os procedimentos de redução é possível obter soluções ótimas mais rapidamente.

Various techniques in microscopy are based on point-wise acquisition, which provides advantages in acquiring sectioned images, for example in confocal or two-photon microscopy. The advantages come along with the need to perform three-dimensional scanning, which is often realized by mechanical movement achieved by stage-scanning or piezo-based scanning in the axial direction. Lateral scanning often employs galvo-mirrors, leading to a reflective setup and hence to a folded beam path. In this paper, we introduce a fully refractive microscope capable of three-dimensional scanning, which employs the combination of an adaptive lens, an adaptive prism, and a tailored telecentric f-theta objective. Our results show that this microscope is capable to perform flexible three-dimensional scanning, with low scan-induced aberrations, at a uniform resolution over a large tuning range of X = Y = 6300 µm and Z = 480 µm with only transmissive components. We demonstrate the capabilities at the example of volumetric measurements on the transgenic fluorescence of the thyroid of a zebrafish embryo and mixed pollen grains. This is the first step towards flexible aberration-free volumetric smart microscopy of three-dimensional samples like embryos and organoids, which could be exploited for the demands in both lateral and axial dimensions in biomedical samples without compromising image quality

[Abstract]: The disposal of animal waste has become a problem in many parts of the world due to the rapid growth in the number and the size of intensive animal industries. Safe waste disposal sites are rarely available and the relocation and/or treatment of animal waste is seldom economically viable. The reuse of animal waste for energy recovery and re-feeding is also not popular. Animal waste is a valuable source of plant nutrients and a very good soil conditioner, and has been commonly applied as fertiliser to agricultural fields. However, due to the increasing oversupply of animal waste in recent years, it has often been applied in excess to the agricultural fields. Excessive application of animal waste, without due consideration of its implications, is a serious concern. The run-off and leaching losses of nutrients from the fields fertilised with animal waste have contributed significantly to the eutrophication and toxic blue-green algae blooms in surface water systems and nitrification of ground water systems. It has also led to nutrient imbalances in the soils and odour pollution to the surrounding communities. The animal waste, which is a valuable source of plant nutrients, has thus become both an economic and environmental burden, and there is a need to develop a strategy for its sensible use as a fertiliser in agricultural fields. Sensible use of animal waste involves the consideration of all the agricultural, environmental, social, and economical limitations. A rational method of achieving this is to restrict the use of animal waste to sites suitable for such uses, identify areas where it can be relocated and applied economically, limit the application rates to a safe level, and observe appropriate manure management practices. This study addressed each of these components by developing a comprehensive manure application plan (MAP) for the site-specific use of animal waste as fertiliser in agricultural fields. Various geographic information systems (GIS) based techniques, including a weighted linear combination model and map algebra based cartographic modelling, were employed to achieve the goal. The appropriateness of the existing techniques and procedures were evaluated and modified to meet the current input requirements. New methods of analysis were devised as necessary. The Westbrook sub-catchment of the Condamine River catchment in south-east Queensland was selected as the study area. The sub-catchment covers 24,903 hectares and contains 39 intensive animal industries. The catchment is also a part of the Murray-Darling Basin, which has been suffering from toxic blue green algae blooms recurrently since 1991. This study identified that only about one-fifth of the sub-catchment area is suitable for animal waste application. Depending on the method of site suitability analysis and the number of input factors used the suitable area ranged between 16 and 22 percent. This comparatively small area is mainly due to the presence of a large proportion of non-agricultural areas in the sub-catchment. The suitable areas were also found to have various degrees of suitability for waste application. However, the degree of site suitability was affected by the number of input factors used in the analysis, the weighting of the factors, and the method of factor attribute standardisation. Conventional methods of weighting input factors were found to be cumbersome and not particularly suitable. Hence, this study developed a new ‘objective oriented comparison’ method of factor weighting. Standardisation of input factors using a continuous, rather than discrete, classification (ie fuzzy set) method was found to be more consistent in degree of suitability determination. The discrete classification of factor attributes into classes of different numbers and sizes, and the weighting of classes to a sum of one, were identified as a limitation in using this standardisation method. A new ‘weight adjustment’ method was devised and demonstrated to reduce factor-weighting biases. The suitable sites, degree of site suitability, and other relevant spatial and non-spatial information were processed within a GIS framework to develop a comprehensive manure application plan. The inherently high presence of available phosphorus in the soils of the study area was recognised and the P2O5 content in the manure was used as the basis for determining manure application rates. A complimentary nitrogen supply map was also generated. Manure management practices applicable to the areas with a lower degree of suitability were also suggested.