Reconstructing mass-conserved water surfaces using shape from shading and optical flow

This paper introduces a method for reconstructing water from real video footage. Using a single input video, the proposed method produces a more informative reconstruction from a wider range of possible scenes than the current state of the art. The key is the combination of vision algorithms and physics laws. Shape from shading is used to capture the change of the water's surface, from which a vertical velocity gradient field is calculated. Such a gradient field is used to constrain the tracking of horizontal velocities by minimizing an energy function as a weighted combination of mass-conservation and intensity-conservation. Hence the final reconstruction contains a dense velocity field that is incompressible in 3D. The proposed method is efficient and performs consistently well across water of different types

Innovative Techniques for Digitizing and Restoring Deteriorated Historical Documents

Recent large-scale document digitization initiatives have created new modes of access to modern library collections with the development of new hardware and software technologies. Most commonly, these digitization projects focus on accurately scanning bound texts, some reaching an efficiency of more than one million volumes per year. While vast digital collections are changing the way users access texts, current scanning paradigms can not handle many non-standard materials. Documentation forms such as manuscripts, scrolls, codices, deteriorated film, epigraphy, and rock art all hold a wealth of human knowledge in physical forms not accessible by standard book scanning technologies. This great omission motivates the development of new technology, presented by this thesis, that is not-only effective with deteriorated bound works, damaged manuscripts, and disintegrating photonegatives but also easily utilized by non-technical staff. First, a novel point light source calibration technique is presented that can be performed by library staff. Then, a photometric correction technique which uses known illumination and surface properties to remove shading distortions in deteriorated document images can be automatically applied. To complete the restoration process, a geometric correction is applied. Also unique to this work is the development of an image-based uncalibrated document scanner that utilizes the transmissivity of document substrates. This scanner extracts intrinsic document color information from one or both sides of a document. Simultaneously, the document shape is estimated to obtain distortion information. Lastly, this thesis provides a restoration framework for damaged photographic negatives that corrects photometric and geometric distortions. Current restoration techniques for the discussed form of negatives require physical manipulation to the photograph. The novel acquisition and restoration system presented here provides the first known solution to digitize and restore deteriorated photographic negatives without damaging the original negative in any way. This thesis work develops new methods of document scanning and restoration suitable for wide-scale deployment. By creating easy to access technologies, library staff can implement their own scanning initiatives and large-scale scanning projects can expand their current document-sets

Digital Restoration of Damaged Historical Parchment

In this thesis we describe the development of a pipeline for digitally restoring damaged historical parchment. The work was carried out in collaboration with London Metropolitan Archives (LMA), who are in possession of an extremely valuable 17th century document called The Great Parchment Book. This book served as the focus of our project and throughout this thesis we demonstrate our methods on its folios. Our aim was to expose the content of the book in a legible form so that it can be properly catalogued and studied. Our approach begins by acquiring an accurate digitisation of the pages. We have developed our own 3D reconstruction pipeline detailed in Chapter 5 in which each parchment is imaged using a hand-held digital-SLR camera, and the resulting image set is used to generate a high-resolution textured 3D reconstruction of each parchment. Investigation into methods for flatting the parchments demonstrated an analogy with surface parametrization. Flattening the entire parchment globally with various existing parametrization algorithms is problematic, as discussed in Chapters 4, 6, and 7, since this approach is blind to the distortion undergone by the parchment. We propose two complementary approaches to deal with this issue. Firstly, exploiting the fact that a reader will only ever inspect a small area of the folio at a given time, we proposed a method for performing local undistortion of the parchments inside an interactive viewer application. The application, described in Chapter 6, allows a user to browse a parchment folio as the application un-distorts in real-time the area of the parchment currently under inspection. It also allows the user to refer back to the original image set of the parchment to help with resolving ambiguities in the reconstruction and to deal with issues of provenance. Secondly, we proposed a method for estimating the actual deformation undergone by each parchment when it was damaged by using cues in the text. Since the text was originally written in straight lines and in a roughly uniform script size, we can detect the the variation in text orientation and size and use this information to estimate the deformation. in Chapter 7 we then show how this deformation can be inverted by posing the problem as a Poisson mesh deformation, and solving it in a way that guarantees local injectivity, to generate a globally flattened and undistorted image of each folio. We also show how these images can optionally be colour corrected to remove the shading cues baked into the reconstruction texture, and the discolourations in the parchment itself, to further improve legibility and give a more complete impression that the parchment has been restored. The methods we have developed have been very well received by London Metropolitan Archives, as well the the larger archival community. We have used the methods to digitise the entire Great Parchment Book, and have demonstrated our global flattening method on eight folios. As of the time of writing of this thesis, our methods are being used to virtually restore all of the remaining folios of the Great Parchment Book. Staff at LMA are also investigating potential future directions by experimenting with other interesting documents in their collections, and are exploring the possibility of setting up a service which would give access to our methods to other archival institutions with similarly damaged documents

Modeling and Simulation in Engineering

This book provides an open platform to establish and share knowledge developed by scholars, scientists, and engineers from all over the world, about various applications of the modeling and simulation in the design process of products, in various engineering fields. The book consists of 12 chapters arranged in two sections (3D Modeling and Virtual Prototyping), reflecting the multidimensionality of applications related to modeling and simulation. Some of the most recent modeling and simulation techniques, as well as some of the most accurate and sophisticated software in treating complex systems, are applied. All the original contributions in this book are jointed by the basic principle of a successful modeling and simulation process: as complex as necessary, and as simple as possible. The idea is to manipulate the simplifying assumptions in a way that reduces the complexity of the model (in order to make a real-time simulation), but without altering the precision of the results

Physicochemical modulation of huntingtin aggregation on lipid membranes: Implications for Huntington\u27s disease

Huntington disease is a genetic, neurodegenerative disease caused by an expanded polyglutamine (polyQ) in the first exon of the huntingtin (htt) protein, facilitating its aggregation, leading to the formation of a diverse population of potentially toxic aggregate species, such as oligomers, fibrils, and annular aggregates. Htt interacts with a variety of membranous structures within the cell, and the first seventeen amino acids (Nt17) of htt directly flanking the polyQ domain is an amphipathic alpha-helix (AH) lipid-binding domain. AHs are also known to detect membrane curvature. Nt17 also promotes diverse aggregate species of htt and undergoes a number of posttranslational modifications that can modulate htt\u27s toxicity, subcellular localization, and trafficking of vesicles. To get in-depth mechanistic insights of huntingtin aggregation, both chemical and physical modulators of the aggregation process were explored. Specifically, the importance of htt acetylation and the role of membrane curvature on htt aggregation were investigated using atomic force microscopy (AFM), which has become a robust technique to obtain physical insights into the formation of toxic protein aggregates associated with amyloid diseases on lipid membranes. Acetylation of htt exon 1, and synthetic truncated htt exon1 mimicking peptide (Nt 17Q35P10KK) was achieved using a selective covalent label sulfo-N-hydroxysuccinimide (NHSA) in molar ratios of 1x, 2x, and 3x NHSA per peptide. Htt acetylation was found to decrease fibril formation in solution and promoted the formation of larger globular aggregates. Acetylation strongly altered htt\u27s ability to bind lipid membranes. However, one of the several limitations associated with using these current flat, supported bilayers as model surfaces is the absence of membrane curvature, which can heavily influence the interaction of proteins at lipid interfaces. Using an AFM force reconstruction technique, silicon substrate, and silica nanobeads, model lipid bilayer system was developed and validated in which the underlying solid support is comprised of flat and curved regions to induce regions of curvature in the bilayer. This model bilayer system was exposed to Nt17Q35P10KK peptide, and this peptide preferentially bound and accumulated to curved membranes, consistent with the ability of AHs to sense membrane curvature

Spatially resolved capture of hydrogen sulfide from the water column and sedimentary pore waters for abundance and stable isotopic analysis

Sulfur cycling is ubiquitous in sedimentary environments, where it plays a major role in mediating carbon remineralization and impacts both local and global redox budgets. Microbial sulfur cycling is dominated by metabolic activity that either produces (e.g., sulfate reduction, disproportionation) or consumes (sulfide oxidation) hydrogen sulfide (H2S). As such, improved constraints on the production, distribution, and consumption of H2S in the natural environment will increase our understanding of microbial sulfur cycling. These different microbial sulfur metabolisms are additionally associated with particular stable isotopic fractionations. Coupling measurements of the isotopic composition of the sulfide with its distribution can provide additional information about environmental conditions and microbial ecology. Here we investigate the kinetics of sulfide capture on photographic films as a way to document the spatial distribution of sulfide in complex natural environments as well as for in situ capture of H2S for subsequent stable isotopic analysis. Laboratory experiments and timed field deployments demonstrate the ability to infer ambient sulfide abundances from the yield of sulfide on the films. This captured sulfide preserves the isotopic composition of the ambient sulfide, offset to slightly lower δ34S values by ~ 1.2 ± 0.5‰ associated with the diffusion of sulfide into the film and subsequent reaction with silver to form Ag2S precipitates. The resulting data enable the exploration of cm-scale lateral heterogeneity that complement most geochemical profiles using traditional techniques in natural environments. Because these films can easily be deployed over a large spatial area, they are also ideal for real-time assessment of the spatial and temporal dynamics of a site during initial reconnaissance and for integration over long timescales to capture ephemeral processes