Automatic and semi-automatic magnetic resonance angiography (MRA)s segmentation techniques can potentially save radiologists larges amounts of time required for manual segmentation and cans facilitate further data analysis. The proposed MRAs segmentation method uses a mathematical modeling technique whichs is well-suited to the complicated curve-like structure of bloods vessels. We define the segmentation task as ans energy minimization over all 3D curves and use a level set methods to search for a solution. Ours approach is an extension of previous level set segmentations techniques to higher co-dimension.

Thesis (M.Eng.)--Memorial University of Newfoundland, 2005. / Bibliography: leaves 110-113.

Thesis (Ph. D.)--Ohio State University, 2006. / Title from first page of PDF file. Includes bibliographical references (p. 143-150).

This thesis presents a novel three dimensional (3D) image-analysis method for characterizing the physical characteristics of coarse particles in the field, and introduces new methodology for the total analysis of glacial till samples. The novel image analysis method, called the GID method, is capable of determining the size, shape and surface texture of each individual clast analysed. Images of particles are taken in the field and analysis is done in the laboratory. Therefore the GID method makes it feasible to analyse statistically representative large sample in short period; for poorly sorted sediments, such as till, one-tonne is required if the analysis includes cobble size. The capability of the GID method was demonstrated by studying coarse clasts (20-200 mm) from till. There is excellent agreement in the results of the size distribution obtained from the GID method and sieve analysis. The GID method results for size and shape parameters show high and very high repeatability. The particle angularity in the GID method has not been measured to acceptable level; the repeatability test shows some variability. The new methodology for total analysis of till applied the GID method at four different locations in Sweden. The total analysis included 3D size and shape distribution of coarse particles coupled to electrical resistivity, lithological distribution and magnetic susceptibility of the clasts. The results show clear difference in the till samples from the different sites. / <p>QC 20120828</p>

In this thesis the focus is mainly on the development of segmentation techniques for human brain structures and of the visualisation of such structures. The images of the brain are both anatomical images (magnet resonance imaging (MRI) and autoradigraphy) and functional images that show blood flow (functional magnetic imaging (fMRI), positron emission tomography (PET), and single photon emission tomograpy (SPECT)). When working with anatomical images, the structures segmented are visible as different parts of the brain, e.g. the brain cortex, the hippocampus, or the amygdala. In functional images, the activity or the blood flow that be seen. Grey-level morphology methods are used in the segmentations to make tissue types in the images more homogenous and minimise difficulties with connections to outside tissue. A method for automatic histogram thresholding is also used. Furthermore, there are binary operations such as logic operation between masks and binary morphology operations. The visualisation of the segmented structures uses either surface rendering or volume rendering. For the visualisation of thin structures, surface rendering is the better choice since otherwise some voxels might be missed. It is possible to display activation from a functional image on the surface of a segmented cortex. A new method for autoradiographic images has been developed, which integrates registration, background compensation, and automatic thresholding to getfaster and more realible results than the standard techniques give.

Summer blooms of filamentous, diazotrophic cyanobacteria are typical of the Baltic Sea Proper, and are dominated by Aphanizomenon sp. and the toxic Nodularia spumigena. Although occurring every summer, the blooms vary greatly in timing and spatial distribution, making monitoring difficult and imprecise. This thesis studies how the spatial variability of Baltic cyanobacterial blooms influences estimates of abundance, vertical and horizontal distribution and N2-fixation. Implications for sampling and monitoring of cyanobacterial blooms are also discussed. The results of the thesis confirm the importance of diazotrophic cyanobacteria in providing N for summer production in the Baltic Proper. It also highlights the large spatial and temporal variation in these blooms and argues that improved spatial coverage and replication could make monitoring data more useful for demonstrating time trends, and for identifying the factors regulating the blooms. The vertical distribution of Aphanizomenon and Nodularia was found to be spatially variable, probably as a combination of species-specific adaptations and ambient weather conditions. Vertical migration in Aphanizomenon was more important towards the end of summer, and is probably regulated by a trade-off between P-availability and light and temperature.

In this thesis, methods to study gene and protein expression in cells and tissues were developed and utilized in combination with protein-specific antibodies, with the overall objective to attain greater understanding of protein function. To analyze protein expression in in vitro cultured cell lines, a cell microarray (CMA) was developed, facilitating antibody-based protein profiling of cell lines using immunohistochemistry (IHC). Staining patterns in cell lines were analyzed using image analysis, developed to automatically identify cells and immunohistochemical staining, providing qualitative and quantitative measurements of protein expression. Quantitative IHC data from CMAs stained with nearly 3000 antibodies was used to evaluate the adequacy of using cell lines as models for cancer tissue. We found that cell lines are homogenous with respect to protein expression profiles, and generally more alike each other, than corresponding cancer cells in vivo. However, we found variability between cell lines in regards to the level of retained tumor phenotypic traits, and identified cell lines with a preserved link to corresponding cancer, suggesting that some cell lines are appropriate model systems for specific tumor types. Specific gene expression patterns were analyzed in vitiligo vulgaris and malignant melanoma. Transcriptional profiling of vitiligo melanocytes revealed dysregulation of genes involved in melanin biosynthesis and melanosome function, thus highlighting some mechanisms possibly involved in the pathogenesis of vitiligo. Two new potential markers for infiltrating malignant melanoma, Syntaxin-7 and Discs large homolog 5, were identified using antibody-based protein profiling of melanoma in a tissue microarray format. Both proteins were expressed with high specificity in melanocytic lesions, and loss of Syntaxin-7 expression was associated with more high-grade malignant melanomas. In conclusion, the combination of antibody-based proteomics and microarray technology provided valuable information of expression patterns in cells and tissues, which can be used to better understand associations between protein signatures and disease.

Modern medical imaging techniques provide an increasing amount of high-dimensional and high-resolution image data that need to be visualized, analyzed, and interpreted for diagnostic and treatment planning purposes. As a consequence, efficient ways of exploring these images are needed. In order to work with specific patient cases, it is necessary to be able to work directly with the medical image volumes and to generate the relevant 3D structures directly as they are needed for visualization and analysis. This requires efficient tools for segmentation, i.e., separation of objects from each other and from the background. Segmentation is hard to automate due to, e.g., high shape variability of organs and limited contrast between tissues. Manual segmentation, on the other hand, is tedious and error-prone. An approach combining the merits from automatic and manual methods is semi-automatic segmentation, where the user interactively provides input to the methods. For complex medical image volumes, the interactive part can be highly 3D oriented and is therefore dependent on the user interface. This thesis presents methods for interactive segmentation and visualization where true 3D interaction with haptic feedback and stereo graphics is used. Well-known segmentation methods such as fast marching, fuzzy connectedness, live-wire, and deformable models, have been tailored and extended for implementation in a 3D environment where volume visualization and haptics are used to guide the user. The visualization is accelerated with graphics hardware and therefore allows for volume rendering in stereo at interactive rates. The haptic feedback is rendered with constraint-based direct volume haptics in order to convey information about the data that is hard to visualize and thereby facilitate the interaction. The methods have been applied to real medical images, e.g., 3D liver CT data and 4D breast MR data with good results. To provide a tool for future work in this area, a software toolkit containing the implementations of the developed methods has been made publicly available.

To reproduce color images in print, the continuous tone image is first transformed into a binary halftone image, producing various colors by discrete dots with varying area coverage. In halftone prints on paper, physical and optical dot gains generally occur, making the print look darker than expected, and making the modeling of halftone color reproduction a challenge. Most available models are based on macroscopic color measurements, averaging the reflectance over an area that is large in relation to the halftone dots. The aim of this study is to go beyond the macroscopic approach, and study halftone color reproduction on a micro-scale level, using high resolution images of halftone prints. An experimental imaging system, combining the accuracy of color measurement instruments with a high spatial resolution, opens up new possibilities to study and analyze halftone color prints. The experimental image acquisition offers a great flexibility in the image acquisition setup. Besides trichromatic RGB filters, the system is also equipped with a set of 7 narrowband filters, for multi-channel images. A thorough calibration and characterization of all the components in the imaging system is described. The spectral sensitivity of the CCD camera, which can not be derived by direct measurements, is estimated using least squares regression. To reconstruct spectral reflectance and colorimetric values from the device response, two conceptually different approaches are used. In the model-based characterization, the physical model describing the image acquisition process is inverted, to reconstruct spectral reflectance from the recorded device response. In the empirical characterization, the characteristics of the individual components are ignored, and the functions are derived by relating the device response for a set of test colors to the corresponding colorimetric and spectral measurements, using linear and polynomial least squares regression techniques. Micro-scale images, referring to images whose resolution is high in relation to the resolution of the halftone, allow for measurements of the individual halftone dots, as well as the paper between them. To capture the characteristics of large populations of halftone dots, reflectance histograms are computed as well as 3D histograms in CIEXYZ color space. The micro-scale measurements reveal that the reflectance for the halftone dots, as well as the paper between the dots, is not constant, but varies with the dot area coverage. By incorporating the varying micro-reflectance in an expanded Murray-Davies model, the nonlinearity caused by optical dot gain can be accounted for without applying the nonphysical exponentiation of the reflectance values, as in the commonly used Yule-Nielsen model. Due to their different intrinsic nature, physical and optical dot gains need to be treated separately when modeling the outcome of halftone prints. However, in measurements of reflection colors, physical and optical dot gains always co-exist, making the separation a difficult task. Different methods to separate the physical and optical dot gain are evaluated, using spectral reflectance measurements, transmission scans and micro-scale images. Further, the relation between the physical dot gain and the halftone dot size is investigated, demonstrated with FM halftones of various print resolutions. The physical dot gain exhibits a clear correlation with the dot size and the dot gain increase is proportional to the increase in print resolution. The experimental observations are followed by discussions and a theoretical explanation.

This paper presents a method for resampling a sequence of high dynamic range light probe images into a representation of Incident Light Field (ILF) illumination which enables realtime rendering. The light probe sequences are captured at varying positions in a real world environment using a high dynamic range video camera pointed at a mirror sphere. The sequences are then resampled to a set of radiance maps in a regular three dimensional grid before projection onto spherical harmonics. The capture locations and amount of samples in the original data make it inconvenient for direct use in rendering and resampling is necessary to produce an efficient data structure. Each light probe represents a large set of incident radiance samples from different directions around the capture location. Under the assumption that the spatial volume in which the capture was performed has no internal occlusion, the radiance samples are projected through the volume along their corresponding direction in order to build a new set of radiance maps at selected locations, in this case a three dimensional grid. The resampled data is projected onto a spherical harmonic basis to allow for realtime lighting of synthetic objects inside the incident light field.