Dense Motion Estimation for Smoke

Motion estimation for highly dynamic phenomena such as smoke is an open challenge for Computer Vision. Traditional dense motion estimation algorithms have difficulties with non-rigid and large motions, both of which are frequently observed in smoke motion. We propose an algorithm for dense motion estimation of smoke. Our algorithm is robust, fast, and has better performance over different types of smoke compared to other dense motion estimation algorithms, including state of the art and neural network approaches. The key to our contribution is to use skeletal flow, without explicit point matching, to provide a sparse flow. This sparse flow is upgraded to a dense flow. In this paper we describe our algorithm in greater detail, and provide experimental evidence to support our claims.Comment: ACCV201

Microsphere Traction Force Microscopy

This work is a culmination of our efforts in understanding cellular mechanics at the scale of single cells and small tissues. We developed methods to quantify cell-generated traction forces using cell-sized, synthetic, functionalized hydrogel microspheres. Cell-sized solid microspheres can provide information regarding cell-generated normal and shear forces while allowing natural cell-cell interactions and facilitating a convex cell-hydrogel interface. Therefore, they are a better mimic than the current methods for understanding the natural cell-cell interactions in a physiologically relevant geometry. In the analysis of the microsphere deformations, we use a boundary spectral method based on spherical harmonics decomposition of the traction field on the spherical gel surface. Using the techniques developed here, we measure the boundary traction profiles that mammalian cells exert on the synthetic microspherical hydrogel bodies. In this report, we briefly review the state of the art in cellular force quantification methods and discuss the contributions of our work to the field and its strengths as well as its limitations

Physics Avoidance & Cooperative Semantics: Inferentialism and Mark Wilson’s Engagement with Naturalism Qua Applied Mathematics

Mark Wilson argues that the standard categorizations of "Theory T thinking"— logic-centered conceptions of scientific organization (canonized via logical empiricists in the mid-twentieth century)—dampens the understanding and appreciation of those strategic subtleties working within science. By "Theory T thinking," we mean to describe the simplistic methodology in which mathematical science allegedly supplies ‘processes’ that parallel nature's own in a tidily isomorphic fashion, wherein "Theory T’s" feigned rigor and methodological dogmas advance inadequate discrimination that fails to distinguish between explanatory structures that are architecturally distinct. One of Wilson's main goals is to reverse such premature exclusions and, thus, early on Wilson returns to John Locke's original physical concerns regarding material science and the congeries of descriptive concern insofar as capturing varied phenomena (i.e., cohesion, elasticity, fracture, and the transmission of coherent work) encountered amongst ordinary solids like wood and steel are concerned. Of course, Wilson methodologically updates such a purview by appealing to multiscalar techniques of modern computing, drawing from Robert Batterman's work on the greediness of scales and Jim Woodward's insights on causation

Local Structure in Hard Particle Self-Assembly and Assembly Failure

The relationship between local order and global structure is not often a straightforward one in systems on the nano- and microscale in which interactions are usually weak and thermal fluctuations drive self-assembly. Moreover, structure in systems for which particle symmetry is broken is difficult to describe theoretically on any level higher than a pairwise one, due to the prohibitively high-dimensional nature of the relevant configuration space. However, a thorough understanding of local structure in all phases of soft matter systems is necessary to gain a complete picture of the physics of these systems and to leverage them for technological and materials science applications. In this dissertation, I investigate local structure in systems of anisotropic particles mediated exclusively by entropy maximization. Specifically, I explore the role of local structure in crystallization and its failure by tackling two related lines of inquiry. First, I study the interplay between particle shape and spherical confinement in systems of hard polyhedral particles, to examine locally dense clusters of anisotropic particles and their possible connection to preferred local structures during unconfined self-assembly. I use Monte Carlo simulation methods to find putative densest clusters of the Platonic solids in spherical confinement, for up to N = 60 constituent particles. I find that a spherical boundary suppresses the packing influence of particle shape and produces a robust class of common cluster structures. I also find a range of especially dense clusters at so-called "magic numbers" of constituent particles, and discover that a magic-number cluster of tetrahedra is a prominent motif in the self-assembled structure of tetrahedra, the dodecagonal quasicrystal. Second, I explore the influence of local structure in systems of hard polyhedral particles that fail to crystallize. I use a shape landscape, or a two-dimensional space of particles that are continuously interrelated by a set of shape perturbations, to investigate why slight changes to particle shape sometimes result in the vitrification rather than crystallization of dense monatomic systems of these particles. I show that assembly failure in these systems arises from a multiplicity of competing local structures, each of which is prevalent in ordered phases crystallized by particles that are only slightly different in shape. Thus, systems that fail to assemble do so because they cannot crystallize into any one ordered phase. Third, I demonstrate that fragility in these systems, a technologically relevant measure of glass-forming ability, can be tuned by slight changes to particle shape. I relate this finding to simulations of molecular systems in which fragility is linked to intermolecular bond angle. Finally, I detail the methods and applications of software I developed to detect multi-particle local structure in real space. This software is open-source and in current use, and has already been utilized for local structure detection in several papers by myself and others. I conclude this dissertation by providing an outlook on the implications and future directions of my work.PHDApplied PhysicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/147721/1/erteich_1.pd

Amélioration de l'image et la segmentation (applications en imagerie médicale)

Avancement dans l'acquisition d'image et le progrès dans les méthodes de traitement d'image ont apporté les mathématiciens et les informaticiens dans les domaines qui sont d'une importance énorme pour les médecins et les biologistes. Le diagnostic précoce de maladies (comme la cécité, le cancer et les problèmes digestifs) ont été des domaines d'intérêt en médecine. Développement des équipements comme microscope bi-photonique à balayage laser et microscope de fluorescence par réflexion totale interne fournit déjà une bonne idée des caractéristiques très intéressantes sur l'objet observé. Cependant, certaines images ne sont pas appropriés pour extraire suffisamment d'informations sur de cette image. Les méthodes de traitement d'image ont été fournit un bon soutien à extraire des informations utiles sur les objets d'intérêt dans ces images biologiques. Rapide méthodes de calcul permettent l'analyse complète, dans un temps très court, d'une série d'images, offrant une assez bonne idée sur les caractéristiques souhaitées. La thèse porte sur l'application de ces méthodes dans trois séries d'images destinées à trois différents types de diagnostic ou d'inférence. Tout d'abord, Images de RP-muté rétine ont été traités pour la détection des cônes, où il n'y avait pas de bâtonnets présents. Le logiciel a été capable de détecter et de compter le nombre de cônes dans chaque image. Deuxièmement, un processus de gastrulation chez la drosophile a été étudié pour observer toute la mitose et les résultats étaient cohérents avec les recherches récentes. Enfin, une autre série d'images ont été traités où la source était une vidéo à partir d'un microscopie photonique à balayage laser. Dans cette vidéo, des objets d'intérêt sont des cellules biologiques. L'idée était de suivre les cellules si elles subissent une mitose. La position de la cellule, la dispersion spatiale et parfois le contour de la membrane cellulaire sont globalement les facteurs limitant la précision dans cette vidéo. Des méthodes appropriées d'amélioration de l'image et de segmentation ont été choisies pour développer une méthode de calcul pour observer cette mitose. L'intervention humaine peut être requise pour éliminer toute inférence fausse.Advancement in Image Acquisition Equipment and progress in Image Processing Methods have brought the mathematicians and computer scientists into areas which are of huge importance for physicians and biologists. Early diagnosis of diseases like blindness, cancer and digestive problems have been areas of interest in medicine. Development of Laser Photon Microscopy and other advanced equipment already provides a good idea of very interesting characteristics of the object being viewed. Still certain images are not suitable to extract sufficient information out of that image. Image Processing methods have been providing good support to provide useful information about the objects of interest in these biological images. Fast computational methods allow complete analysis, in a very short time, of a series of images, providing a reasonably good idea about the desired characteristics. The thesis covers application of these methods in 3 series of images intended for 3 different types of diagnosis or inference. Firstly, Images of RP-mutated retina were treated for detection of rods, where there were no cones present. The software was able to detect and count the number of cones in each frame. Secondly, a gastrulation process in drosophila was studied to observe any mitosis and results were consistent with recent research. Finally, another series of images were treated where biological cells were observed to undergo mitosis. The source was a video from a photon laser microscope. In this video, objects of interest were biological cells. The idea was to track the cells if they undergo mitosis. Cell position, spacing and sometimes contour of the cell membrane are broadly the factors limiting the accuracy in this video. Appropriate method of image enhancement and segmentation were chosen to develop a computational method to observe this mitosis. Cases where human intervention may be required have been proposed to eliminate any false inference.SAVOIE-SCD - Bib.électronique (730659901) / SudocGRENOBLE1/INP-Bib.électronique (384210012) / SudocGRENOBLE2/3-Bib.électronique (384219901) / SudocSudocFranceF

Geometric Numerical Integration

The subject of this workshop was numerical methods that preserve geometric properties of the flow of an ordinary or partial differential equation. This was complemented by the question as to how structure preservation affects the long-time behaviour of numerical methods

From plain visualisation to vibration sensing: using a camera to control the flexibilities in the ITER remote handling equipment

Thermonuclear fusion is expected to play a key role in the energy market during the second half of this century, reaching 20% of the electricity generation by 2100. For many years, fusion scientists and engineers have been developing the various technologies required to build nuclear power stations allowing a sustained fusion reaction. To the maximum possible extent, maintenance operations in fusion reactors are performed manually by qualified workers in full accordance with the "as low as reasonably achievable" (ALARA) principle. However, the option of hands-on maintenance becomes impractical, difficult or simply impossible in many circumstances, such as high biological dose rates. In this case, maintenance tasks will be performed with remote handling (RH) techniques. The International Thermonuclear Experimental Reactor ITER, to be commissioned in southern France around 2025, will be the first fusion experiment producing more power from fusion than energy necessary to heat the plasma. Its main objective is “to demonstrate the scientific and technological feasibility of fusion power for peaceful purposes”. However ITER represents an unequalled challenge in terms of RH system design, since it will be much more demanding and complex than any other remote maintenance system previously designed. The introduction of man-in-the-loop capabilities in the robotic systems designed for ITER maintenance would provide useful assistance during inspection, i.e. by providing the operator the ability and flexibility to locate and examine unplanned targets, or during handling operations, i.e. by making peg-in-hole tasks easier. Unfortunately, most transmission technologies able to withstand the very specific and extreme environmental conditions existing inside a fusion reactor are based on gears, screws, cables and chains, which make the whole system very flexible and subject to vibrations. This effect is further increased as structural parts of the maintenance equipment are generally lightweight and slender structures due to the size and the arduous accessibility to the reactor. Several methodologies aiming at avoiding or limiting the effects of vibrations on RH system performance have been investigated over the past decade. These methods often rely on the use of vibration sensors such as accelerometers. However, reviewing market shows that there is no commercial off-the-shelf (COTS) accelerometer that meets the very specific requirements for vibration sensing in the ITER in-vessel RH equipment (resilience to high total integrated dose, high sensitivity). The customisation and qualification of existing products or investigation of new concepts might be considered. However, these options would inevitably involve high development costs. While an extensive amount of work has been published on the modelling and control of flexible manipulators in the 1980s and 1990s, the possibility to use vision devices to stabilise an oscillating robotic arm has only been considered very recently and this promising solution has not been discussed at length. In parallel, recent developments on machine vision systems in nuclear environment have been very encouraging. Although they do not deal directly with vibration sensing, they open up new prospects in the use of radiation tolerant cameras. This thesis aims to demonstrate that vibration control of remote maintenance equipment operating in harsh environments such as ITER can be achieved without considering any extra sensor besides the embarked rad-hardened cameras that will inevitably be used to provide real-time visual feedback to the operators. In other words it is proposed to consider the radiation-tolerant vision devices as full sensors providing quantitative data that can be processed by the control scheme and not only as plain video feedback providing qualitative information. The work conducted within the present thesis has confirmed that methods based on the tracking of visual features from an unknown environment are effective candidates for the real-time control of vibrations. Oscillations induced at the end effector are estimated by exploiting a simple physical model of the manipulator. Using a camera mounted in an eye-in-hand configuration, this model is adjusted using direct measurement of the tip oscillations with respect to the static environment. The primary contribution of this thesis consists of implementing a markerless tracker to determine the velocity of a tip-mounted camera in an untrimmed environment in order to stabilise an oscillating long-reach robotic arm. In particular, this method implies modifying an existing online interaction matrix estimator to make it self-adjustable and deriving a multimode dynamic model of a flexible rotating beam. An innovative vision-based method using sinusoidal regression to sense low-frequency oscillations is also proposed and tested. Finally, the problem of online estimation of the image capture delay for visual servoing applications with high dynamics is addressed and an original approach based on the concept of cross-correlation is presented and experimentally validated

Dynamics of chromatin structure and nuclear multiprotein complexes investigated by quantitative fluorescence live cell microscopy and computational modeling

Biology has rapidly been transformed into a mainly data-driven, quantitative science. Demands on biological imaging are moving towards quantitative annotations of genes in vivo. In this work I have studied in detail the spatio-temporal distribution and the molecular interaction of protein ensembles as well as of multiprotein aggregates. I have provided the methodology to estimate biophysical parameters such as diffusion coefficients, anomalous diffusion and the free fraction in the binding equilibrium of protein ensembles using fluorescence photobleaching analysis and numcerical modeling and parameter estimation. On the side of protein complexes I have extended existing single particle tracking approaches to allow to automatically detect the exact timing of mobility changes of single particles in live cells. Here, I was able to provide quantitative parameters also on the diffusion coefficient, anomalous diffusion, velocity and chromatin interaction. The nuclear protein ensemble I studied was murine linker histone H1° fused to GFP. I was able to show that diffusion and binding of H1°-GFP to chromatin can be addressed using photobleaching analysis and numcerical modeling. I have thus obtained diffusion coefficients for wild-type H1° and seven point mutants with differential binding affinity ranging from D = 0.01 mm²/s (strongest binder) to D = 0.1 mm²/s (weakest binder). Likewise, I was able to estimate the free fraction to range from = 400 ppm to = 3000 ppm. Exemplary of large multiprotein complexes I chose PML nuclear bodies (PML NBs), named after their constituent promyelotic leukemia protein. I studied in detail their dynamic mobility during early mitosis, ranging from prophase to prometaphase. A dramatic global increase in PML NB mobility was found during this period with the diffusion coefficient increasing from D = 0.001 mm²/s at interphase to D = 0.005 mm²/s at prophase. Similarly, velocities increased from v = 0.7 mm/min to v = 1.4mm/min and concomittant with a loss in subdiffusive motion. I was able to establish loss of tethering to chromatin as the most likely reason behind this increase as opposed to material flow or chromatin condensation. Lastly, I was also able to relate the timing of the mobility increase to other important cellular events. The increase of PML NB mobility predominantly occured after nuclear entry of cyclin B1, which irreversibly commits the cell to mitosis, and before nuclear envelope breakdown (NEBD)