Constrained parameterization with applications to graphics and image processing.

Surface parameterization is to establish a transformation that maps the points on a surface to a specified parametric domain. It has been widely applied to computer graphics and image processing fields. The challenging issue is that the usual positional constraints always result in triangle flipping in parameterizations (also called foldovers). Additionally, distortion is inevitable in parameterizations. Thus the rigid constraint is always taken into account. In general, the constraints are application-dependent. This thesis thus focuses on the various constraints depended on applications and investigates the foldover-free constrained parameterization approaches individually. Such constraints usually include, simple positional constraints, tradeoff of positional constraints and rigid constraint, and rigid constraint. From the perspective of applications, we aim at the foldover-free parameterization methods with positional constraints, the as-rigid-as-possible parameterization with positional constraints, and the well-shaped well-spaced pre-processing procedure for low-distortion parameterizations in this thesis. The first contribution of this thesis is the development of a RBF-based re-parameterization algorithm for the application of the foldover-free constrained texture mapping. The basic idea is to split the usual parameterization procedure into two steps, 2D parameterization with the constraints of convex boundaries and 2D re-parameterization with the interior positional constraints. Moreover, we further extend the 2D re-parameterization approach with the interior positional constraints to high dimensional datasets, such as, volume data and polyhedrons. The second contribution is the development of a vector field based deformation algorithm for 2D mesh deformation and image warping. Many presented deformation approaches are used to employ the basis functions (including our proposed RBF-based re-parameterization algorithm here). The main problem is that such algorithms have infinite support, that is, any local deformation always leads to small changes over the whole domain. Our presented vector field based algorithm can effectively carry on the local deformation while reducing distortion as much as possible. The third contribution is the development of a pre-processing for surface parameterization. Except the developable surfaces, the current parameterization approaches inevitably incur large distortion. To reduce distortion, we proposed a pre-processing procedure in this thesis, including mesh partition and mesh smoothing. As a result, the resulting meshes are partitioned into a set of small patches with rectangle-like boundaries. Moreover, they are well-shaped and well-spaced. This pre-processing procedure can evidently improve the quality of meshes for low-distortion parameterizations

Feature-based terrain editing from complex sketches

We present a new method for first person sketch-based editing of terrain models. As in usual artistic pictures, the input sketch depicts complex silhouettes with cusps and T-junctions, which typically correspond to non-planar curves in 3D. After analysing depth constraints in the sketch based on perceptual cues, our method best matches the sketched silhouettes with silhouettes or ridges of the input terrain. A deformation algorithm is then applied to the terrain, enabling it to exactly match the sketch from the given perspective view, while insuring that none of the user-defined silhouettes is hidden by another part of the terrain. We extend this sketch-based terrain editing framework to handle a collection of multi-view sketches. As our results show, this method enables users to easily personalize an existing terrain, while preserving its plausibility and style.This work was conducted during an internship of Flora Ponjou Tasse at Inria Rhône-Alpes in Grenoble. It was partly supported by the ERC advanced grant EXPRESSIVE.This is the accepted manuscript. The final version is available from Elsevier at http://www.sciencedirect.com/science/article/pii/S009784931400081

Patient-specific simulation environment for surgical planning and preoperative rehearsal

Surgical simulation is common practice in the fields of surgical education and training. Numerous surgical simulators are available from commercial and academic organisations for the generic modelling of surgical tasks. However, a simulation platform is still yet to be found that fulfils the key requirements expected for patient-specific surgical simulation of soft tissue, with an effective translation into clinical practice. Patient-specific modelling is possible, but to date has been time-consuming, and consequently costly, because data preparation can be technically demanding. This motivated the research developed herein, which addresses the main challenges of biomechanical modelling for patient-specific surgical simulation. A novel implementation of soft tissue deformation and estimation of the patient-specific intraoperative environment is achieved using a position-based dynamics approach. This modelling approach overcomes the limitations derived from traditional physically-based approaches, by providing a simulation for patient-specific models with visual and physical accuracy, stability and real-time interaction. As a geometrically- based method, a calibration of the simulation parameters is performed and the simulation framework is successfully validated through experimental studies. The capabilities of the simulation platform are demonstrated by the integration of different surgical planning applications that are found relevant in the context of kidney cancer surgery. The simulation of pneumoperitoneum facilitates trocar placement planning and intraoperative surgical navigation. The implementation of deformable ultrasound simulation can assist surgeons in improving their scanning technique and definition of an optimal procedural strategy. Furthermore, the simulation framework has the potential to support the development and assessment of hypotheses that cannot be tested in vivo. Specifically, the evaluation of feedback modalities, as a response to user-model interaction, demonstrates improved performance and justifies the need to integrate a feedback framework in the robot-assisted surgical setting.Open Acces

Improving Radiotherapy Targeting for Cancer Treatment Through Space and Time

Radiotherapy is a common medical treatment in which lethal doses of ionizing radiation are preferentially delivered to cancerous tumors. In external beam radiotherapy, radiation is delivered by a remote source which sits several feet from the patient\u27s surface. Although great effort is taken in properly aligning the target to the path of the radiation beam, positional uncertainties and other errors can compromise targeting accuracy. Such errors can lead to a failure in treating the target, and inflict significant toxicity to healthy tissues which are inadvertently exposed high radiation doses. Tracking the movement of targeted anatomy between and during treatment fractions provides valuable localization information that allows for the reduction of these positional uncertainties. Inter- and intra-fraction anatomical localization data not only allows for more accurate treatment setup, but also potentially allows for 1) retrospective treatment evaluation, 2) margin reduction and modification of the dose distribution to accommodate daily anatomical changes (called `adaptive radiotherapy\u27), and 3) targeting interventions during treatment (for example, suspending radiation delivery while the target it outside the path of the beam). The research presented here investigates the use of inter- and intra-fraction localization technologies to improve radiotherapy to targets through enhanced spatial and temporal accuracy. These technologies provide significant advancements in cancer treatment compared to standard clinical technologies. Furthermore, work is presented for the use of localization data acquired from these technologies in adaptive treatment planning, an investigational technique in which the distribution of planned dose is modified during the course of treatment based on biological and/or geometrical changes of the patient\u27s anatomy. The focus of this research is directed at abdominal sites, which has historically been central to the problem of motion management in radiation therapy

A 3D+t Laplace operator for temporal mesh sequences

International audienceThe Laplace operator plays a fundamental role in geometry processing. Several discrete versions have been proposed for 3D meshes and point clouds, among others. We define here a discrete Laplace operator for temporally coherent mesh sequences, which allows to process mesh animations in a simple yet efficient way. This operator is a discretization of the Laplace-Beltrami operator using Discrete Exterior Calculus on CW complexes embedded in a four-dimensional space. A parameter is introduced to tune the influence of the motion with respect to the geometry. This enables straightforward generalization of existing Laplacian static mesh processing works to mesh sequences. An application to spacetime editing is provided as example

Graph matching using position coordinates and local features for image analysis

Encontrar las correspondencias entre dos imágenes es un problema crucial en el campo de la visión por ordenador i el reconocimiento de patrones. Es relevante para un amplio rango de propósitos des de aplicaciones de reconocimiento de objetos en las áreas de biometría, análisis de documentos i análisis de formas hasta aplicaciones relacionadas con la geometría desde múltiples puntos de vista tales cómo la recuperación de la pose, estructura desde el movimiento y localización y mapeo. La mayoría de las técnicas existentes enfocan este problema o bien usando características locales en la imagen o bien usando métodos de registro de conjuntos de puntos (o bien una mezcla de ambos). En las primeras, un conjunto disperso de características es primeramente extraído de las imágenes y luego caracterizado en la forma de vectores descriptores usando evidencias locales de la imagen. Las características son asociadas según la similitud entre sus descriptores. En las segundas, los conjuntos de características son considerados cómo conjuntos de puntos los cuales son asociados usando técnicas de optimización no lineal. Estos son procedimientos iterativos que estiman los parámetros de correspondencia y de alineamiento en pasos alternados. Los grafos son representaciones que contemplan relaciones binarias entre las características. Tener en cuenta relaciones binarias al problema de la correspondencia a menudo lleva al llamado problema del emparejamiento de grafos. Existe cierta cantidad de métodos en la literatura destinados a encontrar soluciones aproximadas a diferentes instancias del problema de emparejamiento de grafos, que en la mayoría de casos es del tipo "NP-hard". El cuerpo de trabajo principal de esta tesis está dedicado a formular ambos problemas de asociación de características de imagen y registro de conjunto de puntos como instancias del problema de emparejamiento de grafos. En todos los casos proponemos algoritmos aproximados para solucionar estos problemas y nos comparamos con un número de métodos existentes pertenecientes a diferentes áreas como eliminadores de "outliers", métodos de registro de conjuntos de puntos y otros métodos de emparejamiento de grafos. Los experimentos muestran que en la mayoría de casos los métodos propuestos superan al resto. En ocasiones los métodos propuestos o bien comparten el mejor rendimiento con algún método competidor o bien obtienen resultados ligeramente peores. En estos casos, los métodos propuestos normalmente presentan tiempos computacionales inferiores.Trobar les correspondències entre dues imatges és un problema crucial en el camp de la visió per ordinador i el reconeixement de patrons. És rellevant per un ampli ventall de propòsits des d’aplicacions de reconeixement d’objectes en les àrees de biometria, anàlisi de documents i anàlisi de formes fins aplicacions relacionades amb geometria des de múltiples punts de vista tals com recuperació de pose, estructura des del moviment i localització i mapeig. La majoria de les tècniques existents enfoquen aquest problema o bé usant característiques locals a la imatge o bé usant mètodes de registre de conjunts de punts (o bé una mescla d’ambdós). En les primeres, un conjunt dispers de característiques és primerament extret de les imatges i després caracteritzat en la forma de vectors descriptors usant evidències locals de la imatge. Les característiques son associades segons la similitud entre els seus descriptors. En les segones, els conjunts de característiques son considerats com conjunts de punts els quals son associats usant tècniques d’optimització no lineal. Aquests son procediments iteratius que estimen els paràmetres de correspondència i d’alineament en passos alternats. Els grafs son representacions que contemplen relacions binaries entre les característiques. Tenir en compte relacions binàries al problema de la correspondència sovint porta a l’anomenat problema de l’emparellament de grafs. Existeix certa quantitat de mètodes a la literatura destinats a trobar solucions aproximades a diferents instàncies del problema d’emparellament de grafs, el qual en la majoria de casos és del tipus “NP-hard”. Una part del nostre treball està dedicat a investigar els beneficis de les mesures de ``bins'' creuats per a la comparació de característiques locals de les imatges. La resta està dedicat a formular ambdós problemes d’associació de característiques d’imatge i registre de conjunt de punts com a instàncies del problema d’emparellament de grafs. En tots els casos proposem algoritmes aproximats per solucionar aquests problemes i ens comparem amb un nombre de mètodes existents pertanyents a diferents àrees com eliminadors d’“outliers”, mètodes de registre de conjunts de punts i altres mètodes d’emparellament de grafs. Els experiments mostren que en la majoria de casos els mètodes proposats superen a la resta. En ocasions els mètodes proposats o bé comparteixen el millor rendiment amb algun mètode competidor o bé obtenen resultats lleugerament pitjors. En aquests casos, els mètodes proposats normalment presenten temps computacionals inferiors

Surface Deformation Potentials on Meshes for Computer Graphics and Visualization

Shape deformation models have been used in computer graphics primarily to describe the dynamics of physical deformations like cloth draping, collisions of elastic bodies, fracture, or animation of hair. Less frequent is their application to problems not directly related to a physical process. In this thesis we apply deformations to three problems in computer graphics that do not correspond to physical deformations. To this end, we generalize the physical model by modifying the energy potential. Originally, the energy potential amounts to the physical work needed to deform a body from its rest state into a given configuration and relates material strain to internal restoring forces that act to restore the original shape. For each of the three problems considered, this potential is adapted to reflect an application specific notion of shape. Under the influence of further constraints, our generalized deformation results in shapes that balance preservation of certain shape properties and application specific objectives similar to physical equilibrium states. The applications discussed in this thesis are surface parameterization, interactive shape editing and automatic design of panorama maps. For surface parameterization, we interpret parameterizations over a planar domain as deformations from a flat initial configuration onto a given surface. In this setting, we review existing parameterization methods by analyzing properties of their potential functions and derive potentials accounting for distortion of geometric properties. Interactive shape editing allows an untrained user to modify complex surfaces, be simply grabbing and moving parts of interest. A deformation model interactively extrapolates the transformation from those parts to the rest of the surface. This thesis proposes a differential shape representation for triangle meshes leading to a potential that can be optimized interactively with a simple, tailored algorithm. Although the potential is not physically accurate, it results in intuitive deformation behavior and can be parameterized to account for different material properties. Panorama maps are blends between landscape illustrations and geographic maps that are traditionally painted by an artist to convey geographic surveyknowledge on public places like ski resorts or national parks. While panorama maps are not drawn to scale, the shown landscape remains recognizable and the observer can easily recover details necessary for self location and orientation. At the same time, important features as trails or ski slopes appear not occluded and well visible. This thesis proposes the first automatic panorama generation method. Its basis is again a surface deformation, that establishes the necessary compromise between shape preservation and feature visibility.Potentiale zur Flächendeformation auf Dreiecksnetzen für Anwendungen in der Computergrafik und Visualisierung Deformationsmodelle werden in der Computergrafik bislang hauptsächlich eingesetzt, um die Dynamik physikalischer Deformationsprozesse zu modellieren. Gängige Beispiele sind Bekleidungssimulationen, Kollisionen elastischer Körper oder Animation von Haaren und Frisuren. Deutlich seltener ist ihre Anwendung auf Probleme, die nicht direkt physikalischen Prozessen entsprechen. In der vorliegenden Arbeit werden Deformationsmodelle auf drei Probleme der Computergrafik angewandt, die nicht unmittelbar einem physikalischen Deformationsprozess entsprechen. Zu diesem Zweck wird das physikalische Modell durch eine passende Änderung der potentiellen Energie verallgemeinert. Die potentielle Energie entspricht normalerweise der physikalischen Arbeit, die aufgewendet werden muss, um einen Körper aus dem Ruhezustand in eine bestimmte Konfiguration zu verformen. Darüber hinaus setzt sie die aktuelle Verformung in Beziehung zu internen Spannungskräften, die wirken um die ursprüngliche Form wiederherzustellen. In dieser Arbeit passen wir für jedes der drei betrachteten Problemfelder die potentielle Energie jeweils so an, dass sie eine anwendungsspezifische Definition von Form widerspiegelt. Unter dem Einfluss weiterer Randbedingungen führt die so verallgemeinerte Deformation zu einer Fläche, die eine Balance zwischen der Erhaltung gewisser Formeigenschaften und Zielvorgaben der Anwendung findet. Diese Balance entspricht dem Equilibrium einer physikalischen Deformation. Die drei in dieser Arbeit diskutierten Anwendungen sind Oberflächenparameterisierung, interaktives Bearbeiten von Flächen und das vollautomatische Erzeugen von Panoramakarten im Stile von Heinrich Berann. Zur Oberflächenparameterisierung interpretieren wir Parameterisierungen über einem flachen Parametergebiet als Deformationen, die ein ursprünglich ebenes Flächenstück in eine gegebene Oberfläche verformen. Innerhalb dieses Szenarios vergleichen wir dann existierende Methoden zur planaren Parameterisierung, indem wir die resultierenden potentiellen Energien analysieren, und leiten weitere Potentiale her, die die Störung geometrischer Eigenschaften wie Fläche und Winkel erfassen. Verfahren zur interaktiven Flächenbearbeitung ermöglichen schnelle und intuitive Änderungen an einer komplexen Oberfläche. Dazu wählt der Benutzer Teile der Fläche und bewegt diese durch den Raum. Ein Deformationsmodell extrapoliert interaktiv die Transformation der gewählten Teile auf die restliche Fläche. Diese Arbeit stellt eine neue differentielle Flächenrepräsentation für diskrete Flächen vor, die zu einem einfach und interaktiv zu optimierendem Potential führt. Obwohl das vorgeschlagene Potential nicht physikalisch korrekt ist, sind die resultierenden Deformationen intuitiv. Mittels eines Parameters lassen sich außerdem bestimmte Materialeigenschaften einstellen. Panoramakarten im Stile von Heinrich Berann sind eine Verschmelzung von Landschaftsillustration und geographischer Karte. Traditionell werden sie so von Hand gezeichnet, dass bestimmt Merkmale wie beispielsweise Skipisten oder Wanderwege in einem Gebiet unverdeckt und gut sichtbar bleiben, was große Kunstfertigkeit verlangt. Obwohl diese Art der Darstellung nicht maßstabsgetreu ist, sind Abweichungen auf den ersten Blick meistens nicht zu erkennen. Dadurch kann der Betrachter markante Details schnell wiederfinden und sich so innerhalb des Gebietes orientieren. Diese Arbeit stellt das erste, vollautomatische Verfahren zur Erzeugung von Panoramakarten vor. Grundlage ist wiederum eine verallgemeinerte Oberflächendeformation, die sowohl auf Formerhaltung als auch auf die Sichtbarkeit vorgegebener geographischer Merkmale abzielt

Research and development of triploid brown trout Salmo trutta (Linnaeus, 1758) for use in aquaculture and fisheries management

Freshwater sport fisheries contribute substantially to the economies of England and Wales. However, many trout fisheries rely partly or entirely on stocking farmed trout to maintain catches within freshwater fisheries. Farmed trout often differ genetically from their wild counterparts and wild trout could be at risk of reduced fitness due to interbreeding or competition with farmed fish. Therefore, to protect remaining wild brown trout (Salmo trutta L) populations and as a conservation measure, stocking policy has changed. Legislation introduced by the Environment Agency (EA, 2009) will now only give consent to stocking of rivers and some stillwaters with sterile, all-female triploid brown trout. There are reliable triploidy induction protocols for some other commercially important salmonid species however; there is limited knowledge on triploid induction in brown trout. Previously, triploid brown trout have been produced by heat shocks although reduced survivals were obtained suggesting that an optimised heat shock had not been identified, or that heat shock gives less consistent success than hydrostatic pressure shock (HP), which is now recognised as a more reliable technique to produce triploid fish. Thus the overall aim of this thesis was to conduct novel research to support the aquaculture and freshwater fisheries sector within the United Kingdom by optimising the production and furthering the knowledge of triploid brown trout. Firstly, this PhD project investigated an optimised triploidy induction protocol using hydrostatic pressure (Chapter 2). In order to produce an optimised hydrostatic pressure induction protocol three experiments were conducted to (1) determine the optimal timing of HP shock application post-fertilisation, (2) define optimal pressure intensity and duration of the HP shock and (3) study the effect of temperature (6-12 °C) on triploid yields. Results indicated high survival to yolk sac absorption stage (69.2 - 93.6 %) and high triploid yields (82.5 - 100 %) from the range of treatments applied. Furthermore, no significant differences in triploid rates were shown when shock timings and durations were adjusted according to the temperature used. In all treatments deformity prevalence remained low during incubation (<1.8 %) up to yolk sac absorption (~550 degree days post hatch). Overall, this study indicated that the optimised pressure shock for the induction of triploidy in brown trout delivering high survival and 100 % triploid rate (a prerequisite to brown trout restocking) is a shock with a magnitude of 689 Bar applied at 300 Centigrade Temperature Minutes (CTM) for 50 CTM duration. Regarding the assessment of triploid status, the second experimental chapter tested the accuracy and efficacy of three ploidy verification techniques (Chapter 3). Techniques studied were erythrocyte nuclei measurements (Image analysis), flow cytometry (Becton Dickinson Facscalibur flow cytometer) and DNA profiling (22 polymorphic microsatellite loci) to assess the effectiveness of triploidy induction in brown trout. Results indicated the validity of using erythrocyte indices major nuclear axis measurements, flow cytometric DNA distributions expressed as relative fluorescence (FL2-Area), and polymorphic microsatellite loci (Ssa410UOS, SSa197, Str2 and SsaD48) for assessing ploidy status in brown trout. Accuracy of each technique was assessed and indicated that all techniques correctly identified ploidy level indicating 100 % triploid rate for that commercial batch of brown trout. These techniques may be utilised within aquaculture and freshwater fisheries to ensure compliance with the legislation introduced by the EA. As a result of the legislation introduced by the Environment Agency triploid brown trout will freely interact with diploid trout therefore there is a need to assess feeding response and behavioural differences between diploid and triploid trout prior to release. Therefore, in the third experimental chapter (Chapter 4) diploid and triploid brown trout were acclimated for six weeks on two feeding regimes (floating/sinking pellet). Thereafter, aggression and surface feeding response was compared between pairs of all diploid, diploid and triploid and all triploid brown trout in a semi natural stream (flume). In each pairwise matching, fish of similar size were placed in allopatry and rank determined by the total number of aggressive interactions initiated. Dominant individuals initiated more aggression than subordinates, spent more time defending a territory and positioned themselves closer to the food source (Gammarus pulex) whereas subordinates occupied the peripheries. When ploidy was considered, diploid trout were more aggressive than triploid, and dominated their siblings when placed in pairwise matchings. However, surface feeding did not differ statistically between ploidy irrespective of feeding regime. Triploids adopted a sneak feeding strategy while diploids expended more time defending a territory. In addition, an assessment of whether triploids exhibited a similar social dominance to diploids when placed in allopatry was conducted. Although aggression was lower in triploid pairs than in the diploid/triploid pairs, a dominance hierarchy was observed between individuals of the same ploidy. Dominant triploid fish were more aggressive and consumed more feed items than subordinate individuals. Subordinate fish displayed a darker colour index than dominant fish suggesting increased stress levels. However, dominant triploid fish seemed more tolerant of subordinate individuals and did not display the same degree of invasive aggression as observed in the diploid/diploid or diploid/triploid matchings. These novel findings suggest that sterile triploid brown trout feed similarly but are less aggressive than diploid trout and therefore may provide freshwater fishery managers an alternative to stocking diploid brown trout. In addition to research at the applied level in triploid brown trout, this thesis also examined the fundamental physiological effects of ploidy in response to temperature regime. Triploid salmonids have been shown to differ in their tolerance to environmental temperature. Therefore the fourth experimental chapter (Chapter 5) investigated whether temperature tolerance affected feed intake and exercise recovery. Diploid and triploid brown trout were exposed to an incremental temperature challenge (10 and 19 °C) and subsequent survival and feed intake rates were monitored. Triploids took longer to acclimate to the increase in temperature however feed intake were significantly greater in triploids at high temperature. In a follow on study, we investigated post-exercise recovery processes under each temperature regime (10 and 19 °C). Exhaustion was induced by 10 minutes of forced swimming, with subsequent haematological responses measured to determine the magnitude of recovery from exercise. Plasma parameters (alkaline phosphatase, aspartate aminotransferase, calcium, cholesterol, triglycerides, phosphorous, total protein, lactate, glucose, pH, magnesium, osmolality, potassium, sodium, chloride, lactate dehydrogenase) were measured for each ploidy. Basal samples were taken prior to exercise and then at: 1; 4, and 24 hours post-exercise. Contrary to previous studies, there was no triploid mortality during or after the exercise at either temperature. Although diploid and triploid brown trout responded metabolically to the exercise, the magnitude of the response was affected by ploidy and temperature. In particular, triploids had higher levels of plasma lactate, osmolality, and lower pH than diploids at 1 hour post exhaustive exercise. By 4 hours post-exercise plasma parameters analysed had returned to near basal levels. It was evident that the magnitude of the physiological disturbance post-exercise was greater in triploids than diploids at 19 °C. This may have implications where catch and release is practiced on freshwater fisheries. Overall, this work aimed to develop and/or refine current industry induction and assessment protocols while better understand the behaviour and physiology of diploid and triploid brown trout. The knowledge gained from this work provides aquaculture and freshwater fisheries with an optimised protocol, which delivers 100 % triploid rates and profitability without compromising farmed trout welfare, thus ultimately leading towards a more sustainable brown trout industry within the United Kingdom