Stabilization and Imaging of Cohesionless Soil Specimens

abstract: This dissertation describes development of a procedure for obtaining high quality, optical grade sand coupons from frozen sand specimens of Ottawa 20/30 sand for image processing and analysis to quantify soil structure along with a methodology for quantifying the microstructure from the images. A technique for thawing and stabilizing frozen core samples was developed using optical grade Buehler® Epo-Tek® epoxy resin, a modified triaxial cell, a vacuum/reservoir chamber, a desiccator, and a moisture gauge. The uniform epoxy resin impregnation required proper drying of the soil specimen, application of appropriate confining pressure and vacuum levels, and epoxy mixing, de-airing and curing. The resulting stabilized sand specimen was sectioned into 10 mm thick coupons that were planed, ground, and polished with progressively finer diamond abrasive grit levels using the modified Allied HTP Inc. polishing method so that the soil structure could be accurately quantified using images obtained with the use of an optical microscopy technique. Illumination via Bright Field Microscopy was used to capture the images for subsequent image processing and sand microstructure analysis. The quality of resulting images and the validity of the subsequent image morphology analysis hinged largely on employment of a polishing and grinding technique that resulted in a flat, scratch free, reflective coupon surface characterized by minimal microstructure relief and good contrast between the sand particles and the surrounding epoxy resin. Subsequent image processing involved conversion of the color images first to gray scale images and then to binary images with the use of contrast and image adjustments, removal of noise and image artifacts, image filtering, and image segmentation. Mathematical morphology algorithms were used on the resulting binary images to further enhance image quality. The binary images were then used to calculate soil structure parameters that included particle roundness and sphericity, particle orientation variability represented by rose diagrams, statistics on the local void ratio variability as a function of the sample size, and the local void ratio distribution histograms using Oda's method and Voronoi tessellation method, including the skewness, kurtosis, and entropy of a gamma cumulative probability distribution fit to the local void ratio distribution.Dissertation/ThesisM.S. Civil Engineering 201

Soil micromorphology and image analysis; a study of bronze age to recently improved soils at Lairg, Sutherland, Scotland

The applications of multispectral and morphometric image analysis to soil thin section descriptions is examined. It is shown that unsupervised classification and contrast stretching can be used to enhance and label features of interest. Morphometric measurements, allow the shape and abundance of features in thin sections to be compared and statistical relationships established. This method of analysis offers a precision beyond that which is possible using a qualitative approach. Using soil micromorphology as the main analytical technique a case study was carried out to evaluate the applicability of image analysis to an investigation of an archaeological site at Lairg in northern Scotland. The interactions of anthropogenic activity and pedogenesis since the Bronze Age is examined. The condition of the soils prior to the Bronze Age is not known because no buried soils predated this period. Evidence suggests that in freely draining situations complete podzols might have formed by this time. During the Bronze and Iron Age intensive cultivation of soils occurred with associated erosion. In areas of the site, where human activity is dated to the Post Medieval period, deepening of A horizons is apparent and the soils are maintained as Brown Podzols. In many areas where human activity stops stagnopodzols are the dominant soil type. The potential of image analysis to aid soil micromorphological descriptions is demonstrated. Contrast stretching aided a qualitative subdivision of thin section slides during the case study. Morphometric analysis confirmed a relationship between shape of voids and c/f ratios in an Iron Age buried A horizon, A PM buried A horizon and an undated deep topsoil. It is concluded that the full benefits of image analysis, when used as a routine tool to aid thin section descriptions, will only be realised when procedures become more interactive and processes can be speeded up

Pattern Recognition

A wealth of advanced pattern recognition algorithms are emerging from the interdiscipline between technologies of effective visual features and the human-brain cognition process. Effective visual features are made possible through the rapid developments in appropriate sensor equipments, novel filter designs, and viable information processing architectures. While the understanding of human-brain cognition process broadens the way in which the computer can perform pattern recognition tasks. The present book is intended to collect representative researches around the globe focusing on low-level vision, filter design, features and image descriptors, data mining and analysis, and biologically inspired algorithms. The 27 chapters coved in this book disclose recent advances and new ideas in promoting the techniques, technology and applications of pattern recognition

APPLICATIONS OF INNOVATIVE BUILDING MATERIAL AND COMPUTER VISION METHODS IN GEOTECHNICAL ENGINEERING

Ph.D

Improved methods for functional neuronal imaging with genetically encoded voltage indicators

Voltage imaging has the potential to revolutionise neuronal physiology, enabling high temporal and spatial resolution monitoring of sub- and supra-threshold activity in genetically defined cell classes. Before this goal is reached a number of challenges must be overcome: novel optical, genetic, and experimental techniques must be combined to deal with voltage imaging’s unique difficulties. In this thesis three techniques are applied to genetically encoded voltage indicator (GEVI) imaging. First, I describe a multifocal two-photon microscope and present a novel source localisation control and reconstruction algorithm to increase scattering resistance in functional imaging. I apply this microscope to image population and single-cell voltage signals from voltage sensitive fluorescent proteins in the first demonstration of multifocal GEVI imaging. Second, I show that a recently described genetic technique that sparsely labels cortical pyramidal cells enables single-cell resolution imaging in a one-photon widefield imaging configuration. This genetic technique allows simple, high signal-to-noise optical access to the primary excitatory cells in the cerebral cortex. Third, I present the first application of lightfield microscopy to single cell resolution neuronal voltage imaging. This technique enables single-shot capture of dendritic arbours and resolves 3D localised somatic and dendritic voltage signals. These approaches are finally evaluated for their contribution to the improvement of voltage imaging for physiology.Open Acces

Single-Molecule Localization, Dynamics and Interactions of DNA Replication and Repair Proteins Revealed by Live-Cell Super-Resolution Microscopy.

The error-free progression of DNA replication is essential for all organisms. Approximately 80 known human diseases are caused by malfunction in DNA replication, and deficiencies in DNA repair mechanisms can also lead to severe consequences such as increased antibiotic resistance in bacteria and cancers in humans. A better understanding of DNA replication and repair requires knowledge of the key players along relevant pathways at the molecular level and in the cellular context. This characterization calls for a technique with superior sensitivity, accuracy and biocompatibility. In this thesis, we integrate single-molecule super-resolution microscopy and single-particle tracking with genetic and genomic approaches to study two proteins that play a pivotal role in maintaining genomic integrity: MutS and PolC. From prokaryotes to human cells, homologs of the highly conserved mismatch repair (MMR) protein MutS recognize mispaired nucleotides and recruit the proteins responsible for downstream repair. Although the structure and function of MutS have been extensively characterized in biochemical isolation, it remains unclear how MutS efficiently identifies, among millions of correctly paired bases, a single mismatch in the complex and crowded cellular environment. To obtain mechanistic insights into MMR initiation from an in vivo perspective, we applied super-resolution imaging in live Bacillus subtilis cells to follow the motion of single MutS proteins in real time, and we monitored how MutS behavior is affected by sequentially blocking critical steps along the MMR pathway. Our results demonstrate an intimate and dynamic coupling between MutS and the replisome which stages MutS to sites of DNA replication, allowing MutS to scan newly synthesized DNA in anticipation of errors largely free of obstacles. We then turn our focus to DNA replication itself. Specifically, we focused on PolC, one of the two essential DNA polymerases in B. subtilis. Based on photobleaching-assisted microscopy and three-dimensional super-resolution microscopy, we quantified the stoichiometry, intracellular locations and dynamics of PolC. Finally, we extended the application of super-resolution microscopy to the field of renewable energy by tracking single molecules and visualizing guest-host interactions in microporous coordination polymers (MCPs).PHDChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113498/1/liaoy_1.pd

The cartography of cell motion

Cell motility plays an important role throughout biology, the polymerisation of actin being fundamental in producing protrusive force. However, it is increasingly apparent that intracellular pressure, arising from myosin-II contraction, is a co-driver of motility. In its extreme form, pressure manifests itself as hemispherical protrusions, referred to as blebs, where membrane is torn from the underlying cortex. Although many components and signalling pathways have been identified, we lack a complete model of motility, particularly of the regulation and mechanics of blebbing. Advances in microscopy are continually improving the quality of time series image data, but the absence of highthroughput tools for extracting quantitative numbers remains an analysis bottle-neck. We develop the next generation of the successful QuimP software designed for automated analysis of motile cells, producing quantitative spatio-temporal maps of protein distributions and changes in cell morphology. Key to QuimP's new functionality, we present the Electrostatic Contour Migration Method (ECMM) that provides high resolution tracking of local deformation with better uniformity and efficiency than rival methods. Photobleaching experiments are used to give insight into the accuracy and limitations of in silico membrane tracking algorithms. We employ ECMM to build an automated protrusion tracking method (ECMM-APT) sensitive not only to pseudopodia, but also the complex characteristics of high speed blebs. QuimP is applied to characterising the protrusive behaviour of Dictyostelium, induced to bleb by imaging under agar. We show blebs are characterised by distinct speed-displacement distributions, can reach speeds of 4.9μm/sec, and preferentially form at the anks during chemotaxis. Significantly, blebs emerge from at to concave membrane regions suggesting curvature is a major determinant of bleb location, size, and speed. We hypothesise that actin driven pseudopodia at the leading edge induce changes in curvature and therefore membrane tension, positive curvature inhibiting blebbing at the very front, and negative curvature enhancing blebbing at the sides. This possibly provides the necessary space for rear advancement. Furthermore, bleb kymographs reveal a retrograde shift of the cortex at the point of bleb expansion, suggesting inward contractive forces acting on the cortex even at concave regions. Strains defficient in phospholipid signalling show impaired chemotaxis and blebbing. Finally, we present further applications of QuimP, for example, we conclusively show that dishevelled is not polarised during Xenopus gastrulation, contrary to hypotheses in the literature