Framework for Automatic Identification of Paper Watermarks with Chain Codes

Title from PDF of title page viewed May 21, 2018Dissertation advisor: Reza DerakhshaniVitaIncludes bibliographical references (pages 220-235)Thesis (Ph.D.)--School of Computing and Engineering. University of Missouri--Kansas City, 2017In this dissertation, I present a new framework for automated description, archiving, and identification of paper watermarks found in historical documents and manuscripts. The early manufacturers of paper have introduced the embedding of identifying marks and patterns as a sign of a distinct origin and perhaps as a signature of quality. Thousands of watermarks have been studied, classified, and archived. Most of the classification categories are based on image similarity and are searchable based on a set of defined contextual descriptors. The novel method presented here is for automatic classification, identification (matching) and retrieval of watermark images based on chain code descriptors (CC). The approach for generation of unique CC includes a novel image preprocessing method to provide a solution for rotation and scale invariant representation of watermarks. The unique codes are truly reversible, providing high ratio lossless compression, fast searching, and image matching. The development of a novel distance measure for CC comparison is also presented. Examples for the complete process are given using the recently acquired watermarks digitized with hyper-spectral imaging of Summa Theologica, the work of Antonino Pierozzi (1389 – 1459). The performance of the algorithm on large datasets is demonstrated using watermarks datasets from well-known library catalogue collections.Introduction -- Paper and paper watermarks -- Automatic identification of paper watermarks -- Rotation, Scale and translation invariant chain code -- Comparison of RST_Invariant chain code -- Automatic identification of watermarks with chain codes -- Watermark composite feature vector -- Summary -- Appendix A. Watermarks from the Bernstein Collection used in this study -- Appendix B. The original and transformed images of watermarks -- Appendix C. The transformed and scaled images of watermarks -- Appendix D. Example of chain cod

Development of a holoscopic imaging system and applied high-resolution fluorescence microscopy

Biomedical imaging helps extending our comprehension of ourselves and our environment. Advances in camera, laser and computation technologies have enabled an ever-increasing number of imaging technologies. Imaging with visible and infrared light has the advantage that it is less harmful than other radiation and its wavelength is in the order of magnitude of cells and subcellular components. Fluorescence microscopy provides good chemical contrast and multi-colour imaging can help elucidate cellular architecture. Incoherent superresolution methods permit us to bypass Abbe's diffraction limit of lateral resolution and visualize previously unnoticed details. Coherent imaging methods such as optical coherence tomography or holoscopy do not require any previous labelling and have the advantage that they record both the amplitude and phase of the light emitted from a scattering sample by interferometric superposition with a reference wave. Both incoherent an coherent imaging methods are used in this thesis. The results of two interdisciplinary research collaborations using different fluorescence microscopy methods, including superresolution methods, are presented. Podosomes in macrophages were studied with stimulated emission depletion microscopy, structured illumination microscopy and localisation microscopy and a distinctly polygonal shape in their vinculin rings was found. Image processing routines allowed for a quantitative analysis of the acquired images [1]. In the second study, chlorophyll, the most prominent natural pigments, and digested chlorophyll metabolites were detected in gut section of the herbivorous Spodoptera littoralis larva. Widefield and high-resolution autofluorescence microscopy revealed that the brush border membranes of their gut are covered with the chlorophyllide binding protein tightly bound to the gut membrane. A function in defense against gut microbes is discussed [2]. Optical coherence tomography (OCT) offers a slightly lower spatial resolution than light microscopy but generally better penetration depths. In order to use a higher numerical aperture for detection in OCT, the dilemma of the resulting reduced depth of field has to be overcome. Different extended focus possibilities are explored in this thesis. Bessel illumination is an established method to achieve an extended depth of field without compromising the lateral resolution. When broadband or multicolour imaging is required, wavelength-dependent changes in the radial profile of the Bessel illumination can however complicate further image processing and analysis. A solution for engineering a multicolour Bessel beam was implemented with a phase-only spatial light modulator in the image plane and an iterative Fourier Transformation algorithm [3]. For higher acquisition speed, full-field recording is favourable to scanning the scattering sample with a Bessel beam. OCT can be combined with reconstruction methods from digital holography to achieve an extended focus numerically. A suitable experimental imaging setup and a custom-written reconstruction algorithm are presented. [1] M. Walde, J. Monypenny, R. Heintzmann, G. E. Jones, and S. Cox, “Vinculin binding angle in podosomes revealed by high resolution microscopy”, PLoS ONE, vol. 9, no. 2, 2014. [2] A. Badgaa, R. Büchler, N. Wielsch, M. Walde, R. Heintzmann, Y. Pauchet, A. Svatos, K. Ploss, and W. Boland, “The Green Gut: Chlorophyll Degradation in the Gut of Spodoptera littoralis”, Journal of Chemical Ecology, vol. 41, no. 11, pp. 965-974, 2015. [3] M. Walde, A. Jost, K. Wicker, and R. Heintzmann, “Engineering an achromatic Bessel beam using a phase-only spatial light modulator and an iterative Fourier transformation algorithm”, Optics Communications, vol. 383, pp. 64-68, 2017

Transient Study of the Wetting Films in Porous Media Using 3D X-Ray Computed Micro-Tomography: Effect of Imbibition Rate and Pore Geometry

Imbibition in porous media is governed by the complex interplay between viscous and capillary forces, pore structure and fluid properties. Understanding and predicting imbibition is important in many natural and engineered applications; it affects the efficiency of oil production operations, the moisture and contaminant transport in soil science, and the formation of defects in certain types of composite materials. Majority of the studies published on the transient imbibition behavior in a porous medium were conducted in the simplified 2D transparent micromodels or the 2D projection visualization (X-ray or visible light) of the 3D porous medium. However, the pore level transient imbibition studies have not been reported on real three dimensional porous medium. The main challenge arises from the slowness of the present 3D imaging techniques in comparison with the speed of the pore filling events. To overcome these difficulties, we have developed a novel experimental technique using UV-induced polymerization, which allows the fluid phase distributions to be frozen in place during transient imbibition. Pore-scale structure of the front can then be examined in the 3D microscopic details using the X-ray Computed micro-Tomography (XCT). We have also developed a suite of advanced image segmentation programs to segment the grayscale XCT data. Image-based physically representative pore network generation techniques were unitized to quantify the geometry and topology of pore, wetting and nonwetting phase structure. Using UV initiated polymerization technique and image-based quantitative analysis tools; we have studied the effects of capillary number, pore structure and surface roughness on the structure of the transient imbibition front

Quantification of the plant endoplasmic reticulum

One of the challenges of quantitative approaches to biological sciences is the lack of understanding of the interplay between form and function. Each cell is full of complex-shaped objects, which moreover change their form over time. To address this issue, we exploit recent advances in confocal microscopy, by using data collected from a series of optical sections taken at short regular intervals along the optical axis to reconstruct the Endoplasmic Reticulum (ER) in 3D, obtain its skeleton, then associate to each of its edges key geometric and dynamic characteristics obtained from the original filled in ER specimen. These properties include the total length, surface area, and volume of the ER specimen, as well as the length surface area, and volume of each of its branches. In a view to benefit from the well established graph theory algorithms, we abstract the obtained skeleton by a mathematical entity that is a graph. We achieve this by replacing the inner points in each edge in the skeleton by the line segment connecting its end points. We then attach to this graph the ER geometric properties as weights, allowing therefore a more precise quantitative characterisation, by thinning the filled in ER to its essential features. The graph plays a major role in this study and is the final and most abstract quantification of the ER. One of its advantages is that it serves as a geometric invariant, both in static and dynamic samples. Moreover, graph theoretic features, such as the number of vertices and their degrees, and the number of edges and their lengths are robust against different kinds of small perturbations. We propose a methodology to associate parameters such as surface areas and volumes to its individual edges and monitor their variations with time. One of the main contributions of this thesis is the use of the skeleton of the ER to analyse the trajectories of moving junctions using confocal digital videos. We report that the ER could be modeled by a network of connected cylinders (0.87μm±0.36 in diameter) with a majority of 3-way junctions. The average length, surface area and volume of an ER branch are found to be 2.78±2.04μm, 7.53±5.59μm2 and 1.81±1.86μm3 respectively. Using the analysis of variance technique we found that there are no significant differences in four different locations across the cell at 0.05 significance level. The apparent movement of the junctions in the plant ER consists of different types, namely: (a) the extension and shrinkage of tubules, and (b) the closing and opening of loops. The average velocity of a junction is found to be 0.25μm/sec±0.23 and lies in the range 0 to 1.7μm/sec which matches the reported actin filament range

Quantification of the plant endoplasmic reticulum

One of the challenges of quantitative approaches to biological sciences is the lack of understanding of the interplay between form and function. Each cell is full of complex-shaped objects, which moreover change their form over time. To address this issue, we exploit recent advances in confocal microscopy, by using data collected from a series of optical sections taken at short regular intervals along the optical axis to reconstruct the Endoplasmic Reticulum (ER) in 3D, obtain its skeleton, then associate to each of its edges key geometric and dynamic characteristics obtained from the original filled in ER specimen. These properties include the total length, surface area, and volume of the ER specimen, as well as the length surface area, and volume of each of its branches. In a view to benefit from the well established graph theory algorithms, we abstract the obtained skeleton by a mathematical entity that is a graph. We achieve this by replacing the inner points in each edge in the skeleton by the line segment connecting its end points. We then attach to this graph the ER geometric properties as weights, allowing therefore a more precise quantitative characterisation, by thinning the filled in ER to its essential features. The graph plays a major role in this study and is the final and most abstract quantification of the ER. One of its advantages is that it serves as a geometric invariant, both in static and dynamic samples. Moreover, graph theoretic features, such as the number of vertices and their degrees, and the number of edges and their lengths are robust against different kinds of small perturbations. We propose a methodology to associate parameters such as surface areas and volumes to its individual edges and monitor their variations with time. One of the main contributions of this thesis is the use of the skeleton of the ER to analyse the trajectories of moving junctions using confocal digital videos. We report that the ER could be modeled by a network of connected cylinders (0.87μm±0.36 in diameter) with a majority of 3-way junctions. The average length, surface area and volume of an ER branch are found to be 2.78±2.04μm, 7.53±5.59μm2 and 1.81±1.86μm3 respectively. Using the analysis of variance technique we found that there are no significant differences in four different locations across the cell at 0.05 significance level. The apparent movement of the junctions in the plant ER consists of different types, namely: (a) the extension and shrinkage of tubules, and (b) the closing and opening of loops. The average velocity of a junction is found to be 0.25μm/sec±0.23 and lies in the range 0 to 1.7μm/sec which matches the reported actin filament range.EThOS - Electronic Theses Online ServiceEngineering and Physical Sciences Research Council (Great Britain) (EPSRC)University of Warwick. Molecular Organisation and Assembly in Cells (MOAC)Rodger, AlisonGBUnited Kingdo