In this thesis, the results of microfossil, biofacies, and geochemical analyses (µXRF) of the Upper Cretaceous (Turonian) Ferron – Notom delta, Utah, USA are reported and discussed. The Notom delta is the oldest of three clastic deltas in the Ferron Sandstone Member, Mancos Shale Formation. Foraminifera and testate amoebae were recovered from ninety-eight mudstone samples among five well-exposed outcrops (Caineville North, Steamboat, Blue Hills, Neilson Wash, and Coalmine Wash). Detailed observations showed foraminifera, and testate amoebae tests have undergone post-burial compression (flattening), dissolution, and transport/reworking; therefore, identification of these assemblages to their species level is difficult. The micropaleontological analysis of the Ferron-Notom delta consists of three studies. Morphogroup analysis was applied on foraminifera and testate amoebae, where a relationship between the test morphology and habitat was established. Morphogroup analysis resulted in four main morphogroups and eleven morphotypes and were assigned to life mode, environment, and feeding strategies. Three foraminifera morphogroups and one testate amoebae morphogroup were established indicate a range of environments, from shallow shelf to shallow shelf to lagoon/estuary environments. Biofacies analysis using the morphotypes was applied on three outcrops (Caineville North, Steamboat, and Blue Hills). We use the morphotypes to define the four main biofacies using cluster analysis, and biodiversity indices. Four biofacies showed marine and fluvial (freshwater) influences. Salinity and OM indices were derived from the relationship of foraminifera morphotypes (BiS, TrS, TS) and testate amoebae morphotypes (Ta-F, Ta-D, Ta-S) that follows lithofacies trends. Because of the under-representation of calcareous foraminifera (due to taphonomic and/or diagenetic factors), the biodiversity indices are treated herein as relative measures. Despite this taphonomic bias, the agglutinated foraminifera and testate amoebae morphogroups show trends with salinity both among the outcrops and stratigraphically within the outcrops. The Blue Hills outcrop represents the most landward and lowest salinity environment (tidally-influenced backwater), Steamboat is more coast proximal with a higher salinity of the delta front and fluvial estuarine environments, and the Caineville North outcrop represents the most coast proximal (fluvial/estuarine to deltaic/prodeltaic) with salinities ranging from low to medium. It appears that the landward transport and coastward of tests was a significant source of taphonomic bias. Nonetheless, the assemblages provide useful depositional information that correlates with previously documented lithofacies data. A salinity index based on a ratio of trochospiral taxa versus testate amoebae was found to provide a useful measure of coastal proximity that matches lithofacies trends. The µXRF analysis was conducted on twenty-nine mudstone samples from the Caineville North outcrop to examine elemental proxies for paleo-salinity (Sr/Ba), organic matter (K/S), redox (V/Ni), and sediment sources (Zr/Rb, Ti/Fe, Ti/Ca). Twenty-nine surface mudstone samples collected from four lithofacies representing prodelta, delta front, fluvial valley fill and shelf environments. Fourteen elements (Ti, Fe, Ca, Sr, Ba, Ni, Rb, Zr, S, V, Cu, Mn, Si, and K) were used to calculate proxy ratios to detect variations in terrigenous sediments, carbonate production, salinity, grain size, and fluvial inputs in the Caineville North outcrop. Elemental data showed good correspondence between the elemental data and the lithofacies and microfossil indices. Sr/Ba and Ca/Fe showed relationships with carbonate content and proximity to the shoreline. The paleo-salinity proxy (Sr/Ba) did not respond to salinity, but was more responsive to lithological change of carbonate content. The microfossil salinity index seems to be a more accurate paleo-salinity indicator. The proxy for fluvial input of sediment (Zr/Rb and Ti/Fe) agree well with the lithofacies trends, and Zr/Rb and Ti/Fe showed highest values within the fluvial valley fill facies, with higher variability of Ti/Fe compared to the other lithofacies (prodelta, delta front, and shelf), corresponding to response to the proximity of the depositional sites to a fluvial sediment source. The redox proxy V/Ni matched the previously derived microfossil OM index ("bolivind-type" taxa) showing a strong relationship between eutrophication and redox trends. The study aims to establish important baseline geochemical compositions of sediment sources to establish patterns and trends with sediment succession in the deeper basin (offshore; i.e. Mancos Shale). Potentially, these nearshore to fluvial trends will provide important geochemical data to assess changes in paleoclimate, and sea-level in offshore sediment successions. / Dissertation / Doctor of Philosophy (PhD)

Craniometrics is a very reliable and effective tool for studying the difference in animal morphology. Previously, traditional craniometrics were conducted with the aid of calipers in two dimensional format (2D). Such discounting of actual three-dimensional 3D form may result in loss of some relevant and critical information leading to compromised and unreliable results for studies such as population variation analysis of morphology. The employment of 3D photogrammetry allows a close to complete representation of the physical dimensions of a specimen. The use of photogrammetry in mammalogy concentrated on measuring of body size/mass, but little has been done on animal skull delineation through photogrammetry. This dissertation describes advances in morphometrics and 3D photogrammetry application in craniometrics, investigates the craniometric variation between closely related species (Arctocephalus gazella and A. tropicalis), and A. tropicalis interpopulation craniometrics between two geographically distinct populations, at Marion Island and Gough Island, using Photomodeler Scanner® (PMSc®) three-dimensional (3D) modelling software to produce accurate, high resolution 3D skull models. A total of 117 3D models were created from adult male fur seal crania, and 16 traditional measurements recorded, using specimens archived at the Port Elizabeth Museum, Bayworld, South Africa. Sixteen linear measurements, (8 caliper recordings and 8 3D recordings) were used for PMSc® methodology testing, 16 (A. gazella n= 8 and A. tropicalis n= 8) used for species cranial comparison and 85 (Marion Island n= 54 and Gough Island n= 31) used for interpopulation variation. The craniometric variations were analysed using the Statistica® v11 software package, StatSoft, Inc. The comparison between linear traditional caliper cranial measurements and 3D measurements produced significantly similar results, attesting to the accuracy of the PMSc® 3D model production. Photomodeler Scanner® therefore produces accurate and high resolution 3D models of skulls which allow 3D measurements. I predicted that PMSc® would detect the existing significant differences between the skulls of adult male A. gazella and A. tropicalis and modelled and compared their 3D models, and I further predicted that PMSc® would detect any existing differences between the skulls of A. tropicalis from Gough and Marion islands by comparison of their 3D models. The Gough Island and Marion Island A. tropicalis populations could not be discriminated based on linear 3D cranial I conclude that PMSc® is a reliable and effective tool for accurate and high resolution 3D modelling. The present study confirms previous findings and contributes additional evidence that suggests that adult A. tropicalis males from Gough Island and Marion Island cannot be discriminated based on linear measurements of craniometrics, and deviates from the Bergmanian rule as applied to large mammals. The present study, however, makes several noteworthy contributions to the use of PMSc® and 3D modelling in morphometrics. Taken together, these findings suggest a role for PMSc® 3D modelling in promoting accurate digitization of museum specimens and creation of online museum libraries. This research will serve as a baseline for future studies and usefulness of PMSc® in 3D morpho-volumetric measurements. / Dissertation (MSc (Zoology))--University of Pretoria, 2014. / Zoology and Entomology / MSc (Zoology) / Unrestricted

Introduktion:Modellanalys har traditionellt gjorts på fysiska gipsmodeller. Idag finns ny teknik som möjliggör framställning av digitala modeller utan behov av konventionella avtryck. Syftet med den här studien är att undersöka tillförlitligheten hos digitala modeller framställda med en intraoral scanner, patientupplevelsen och olika tidsaspekter förenade med tekniken.Metod:På ett urval av 20 vuxna personer gjordes både konventionell avtryckstagning och en intraoral scanning (TRIOS, 3Shape) av bettet för framställning av gipsmodeller och digitala modeller. Den kliniska tidsåtgången mättes och personerna besvarade ett frågeformulär gällande sin upplevelse av metoderna. Fyra observatörer diagnostiserade bettrelationer och utförde ortodontiska mätningar på gipsmodeller med ett skjutmått och digitala modeller med OrthoAnalyzer Orthodontics (3Shape, Danmark). Tidsåtgången mättes för digital- respektive konventionell modellanalys. Statistiska analyser gjordes utifrån Paired samples t test, korstabeller och frekvensanalys.Resultat:Diagnostik av horisontella-, vertikala- och transversella bettrelationer på digitala modeller har hög tillförlitlighet. Få statistiskt signifikanta skillnader fanns för linjära mätningar på digitala modeller jämfört med gipsmodeller. För majoriteten av observatörerna tog digital modellanalys längre tid än konventionell modellanalys. Likaså var den kliniska tidsåtgången för intraoral scanning signifikant längre än för konventionell avtryckstagning och metoden prioriterades lägre av försökspersonerna.Konklusion:Digitala modeller framställda med en intraoral scanner är en tillförlitlig metod för ortodontisk diagnostik och terapiplanering. Tekniken har en rad fördelar och förbättras ständigt men dess acceptans för den enskilde klinikern blir i slutändan en kostnadsfråga. / Introduction:Model analysis has traditionally been carried out on physical plaster models. New technology allows the production of digital models without the need for conventional impressions. The purpose of this study was to evaluate the validity of digital models made with an intraoral scanner, patient experience and different time aspects associated with this technology.Methods:A sample of 20 adults was selected. Plaster models and digital models were obtained from conventional impressions and an intraoral scanning (TRIOS, 3Shape) respectively. The clinical time required for impression taking and intraoral scanning was recorded and the subjects were asked to answer a questionnaire regarding their experience of both methods. Four independent examiners diagnosed malocclusions and performed measurements with a digital caliper on plaster models and by using OrthoAnalyzer Orthodontics (3Shape, Denmark) for digital models. Time required for digital- and conventional model analysis respectively, was recorded. Statistical analysis was performed by using Paired samples t test, crosstabs and frequency analysis.Results:Diagnostics of horizontal-, vertical- and transversal malocclusions with digital models showed high validity. Few statistically significant differences were found for measurements made on digital models compared to direct measurements on plaster models. For a majority of the examiners, digital model analysis was more time consuming than conventional model analysis. Also, clinical time required for intraoral scanning was significantly greater than for conventional impression taking. The subjects preferred conventional impression taking.Conclusions:Digital models made with an intraoral scanner are a reliable method for orthodontic diagnostics and treatment planning. The technique has a number of advantages and is constantly improving but its acceptance depends ultimately on the cost-effectiveness ratio to the individual practitioner.

Photon counting computed tomography scanners constitute a major improvement of the field of computed tomography, opening various prospective and enabling the decomposition of computed tomography images into different materials. The material decomposition algorithm, mapping photon counts to material pathlengths, relies on a forward model with Poisson statistics. This model though suffers from noise and residual bias due to its sensitivity to calibration errors and specificities in single-pixel responses that are not captured by the material decomposition model.           This study proposes a pixel-specific and projection-based correction of the residual bias in the material decomposition estimates using artificial neural networks trained for each pixel of the detector. The neural network models were trained under supervised learning using material decomposition calibration data, scans of PE and PVC slabs of various thicknesses acquired for the calibration of the model. This method aims at the mapping of the singularities of the pixels’ responses and correct them in the projection domain. The trained models were evaluated on a set of evaluation slabs and on scans of a water phantom, in order to assess performances of homogeneity and bias correction.           The implemented solution exhibited promising results for the correction of residual bias in single pixels without impairment of the noise levels. An array of trained neural networks demonstrates its ability to correct calibration and evaluation slab data while conserving pixel-to-pixel difference. The application of the correction to the water phantom however offered nuanced results which call for further investigation of the identified issues and induced improvements of the model.

Yes / Recent studies have reported that quantifying symphyseal and auricular surfaces curvature changes on 3D models acquired by laser scanners have a potential for age estimation. However, no tests have been carried out to evaluate the repeatability of the results between different laser scanners. 3D models of the two pelvic joints were generated using three laser scanners (Custom, Faro, Minolta). The surface curvature, the surface area and the distance between co-registered meshes were investigated. Close results were found for surface areas (differences between 0.3% and 2.4%) and for distance deviations (average < 20 μm, SD < 200 μm). The curvature values were found to be systematically biased between different laser scanners, but still showing similar trends with increasing phases / scores. Applying a smoothing factor to the 3D models, it was possible to separate anatomy from the measurement error of each instrument, so that similar curvature values could be obtained (p < 0.05) independent of the specific laser scanner. / The full text was made available at the end of the publisher's embargo: 31st March 2016

L’indice de surface foliaire (Leaf Area Index, LAI), défini comme la moitié de la surface foliaire par unité de surface de sol, est un paramètre clé du cycle écologique de la Terre, et sa précision d'acquisition a toujours la nécessité et la possibilité d'amélioration. La technologie du scanner laser actif offre une possibilité d'obtention cohérente du LAI à plusieurs échelles, car le scanner laser terrestre et le scanner laser aéroporté fonctionnent sur le même mécanisme physique. Cependant, les informations tridimensionnelles du scanner laser ne sont pas complètement explorées dans les méthodes actuelles et les théories traditionnelles ont besoin d'adaptation. Dans cette thèse, le modèle de distribution de longueur de trajet est introduit pour corriger l'effet d’agrégation, et il est appliqué aux données du scanner laser terrestre et du scanner laser aéroporté. La méthode d'obtention de la distribution de longueur de trajet de différentes plates-formes est étudiée et le modèle de récupération cohérent est établi. Cette méthode permet d’améliorer la mesure du LAI des arbres individuels dans les zones urbaines et la cartographie LAI dans les forêts naturelles, et ses résultats sont cohérents à différentes échelles. Le modèle devrait faciliter la détermination cohérente de l'indice de surface foliaire des forêts à l'aide de données au sol et aéroportées. / Leaf Area Index (LAI), defined as one half of the total leaf area per unit ground surface area, is a key parameter of vegetation structure for modeling Earth's ecological cycle and its acquisition accuracy always has the need and opportunity for improvement. Active laser scanning provides an opportunity for consistent LAI retrieval at multiple scales because terrestrial laser scanning (TLS) and airborne laser scanning (ALS) have the similar physical mechanism. However, the three-dimensional information of laser scanning is not fully explored in current methods and the traditional theories require adaptation. In this thesis, the path length distribution model is proposed to model the clumping effect, and it is applied to the TLS and ALS data. The method of obtaining the path length distribution of different platforms is studied, and the consistent retrieval model is established. This method is found to improve the individual tree measurement in urban areas and LAI mapping in natural forest, and its results at consistent at different scales. The model is expected to facilitate the consistent retrieval of the forest leaf area index using ground and airborne data.

Tato práce popisuje konstrukci skenovacího systému pro tvorbu trojrozměrných modelů. Kombinace laserového scanneru a robotického manipulátoru tvoří velice flexibilní zařízení schopné snímat jak velké, tak malé a detailní objekty. Zařízení nachází uplatnění v mnoha aplikacích, zejména v lékařství, kde přináší řadu nesporných výhod proti stávajícím systémům. Práce popisuje mechanickou konstrukci zařízení, funkční principy a jeho kalibrační proceduru. Součástí práce je i software pro vizualizaci naměřených dat a jejich zpracování do podoby modelů se stínovaným povrchem. Výsledkem práce je funkční zařízení a rozsáhlý obslužný software.

Ce mémoire décrit le développement opto-mécanique et électro-mécanique de la 2ième version du scanner TomOptUS pour tomographie optique diffuse (TOD).Ce scanner est destiné à l'imagerie moléculaire 3D de l'intérieur d'un petit animal. Les buts de la TOD sont : 1) d'obtenir la distribution spatiale des coefficients d'absorption ([mu][indice inférieur a]) et de diffusion ([mu][indice inférieur s]) dans les tissus biologiques (imagerie intrinsèque) et 2) de localiser des agents fluorescents injectés et à suivre leur distribution spatiale (imagerie par fluorescence). La TOD sur petit animal est d'un grand intérêt en pharmacologie et en oncologie pour l'étiquetage de médicaments afin de suivre leur progression, pour suivre l'évolution d'une pathologie sous traitement sur un même individu, ou pour repérer des cellules cancéreuses par marquage des protéines membranaires qu'elles expriment. La diffusion de la lumière dans les tissus biologiques est le plus grand obstacle en TOD. Les mesures en régime continu ne permettent pas de distinguer les photons détectés selon le degré de diffusion qu'ils subissent. La diffusion mène à une perte d'information quant à la trajectoire suivie par les photons. La détection résolue en temps permet de garder une partie de cette information. Le scanner TomOptUS utilise un système ultra-rapide de comptage de photons corrélé en temps et des tubes photomultiplicateurs pour mesurer la distribution temporelle de pulses lumineux transmis et/ou rétrodiffusés dans le sujet à imager suite à l'illumination à l'aide d'impulsions laser ultra-brèves. La 2 ième version du scanner est un système multicanal à géométrie annulaire sur 360 [degrés] autour du sujet. Il est muni de 7 canaux de détection optique permettant l'acquisition simultanée de données tomographiques dans deux bandes de longueurs d'onde (intrinsèque et fluorescence). L'acquisition des données est automatisée par ordinateur.Ce scanner a l'avantage d'effectuer des mesures sans contact avec le sujet. Ceci facilite l'acquisition des données et permettra éventuellement de le combiner à d'autres modalités d'imagerie médicale sans contact (tomographie d'émission par positrons, tomodentométrie [i.e. tomodensitométrie] ou imagerie par résonance magnétique) pour réaliser des séances d'imagerie multimodales. Le scanner est aussi équipé d'un système de vision numérique stéréo à 2 caméras permettant de mesurer la surface externe du sujet en 3D. Les mesures tomographiques et de surface se font simultanément en utilisant le faisceau laser incident sur le sujet. On présente des résultats de localisation d'un nombre a priori inconnu d'inclusions fluorescentes ponctuelles dans une mire (ou fantôme) absorbante et diffusante. L'algorithme de localisation repose sur la mesure des temps d'arrivée des premiers photons à différentes positions angulaires autour du sujet. Ceci requiert une résolution temporelle très élevée dans la détection des photons, une très grande synchronisation des différents canaux de détection et une grande stabilité dans la détection des signaux optiques. L'architecture du scanner ainsi qu'une méthode de calibration élaborée dans le cadre des présents travaux permettent d'atteindre de telles performances. On présente également des résultats préliminaires de l'effet d'un milieu hétérogène sur le temps de vol des photons.

Στην παρούσα διπλωματική αναπτύσσεται συσκευή ανάγνωσης των δεδομένων του διαύλου CAN (CAN - controller area network - bus) με σκοπό τη λήψη δεδομένων για την τεχνική διάγνωση βλαβών και τη λήψη δεδομένων τηλεμετρίας σε πραγματικό χρόνο. Η διεπαφή μπορεί να χρησιμοποιηθεί για την εξαγωγή δεδομένων που βοηθούν στην έγκαιρη διάγνωση βλαβών πριν αυτές εξελιχθούν σε κοστοβόρες, στη μελέτη της λειτουργίας του αυτοκινήτου σε πραγματικό χρόνο για την επιβεβαίωση της καλής λειτουργίας του ή για τη συγκέντρωση στοιχείων για τη βελτίωση των επιδόσεών του κλπ. Στα πλαίσια της διπλωματικής, υλοποιείται συσκευή ανάγνωσης η οποία χρησιμοποιεί τα πρωτόκολλα επικοινωνίας που υποστηρίζονται από τη διεπαφή OBD-II ώστε να συλλέγει δεδομένα από τους διαύλους αυτοκινήτων και να τα αποστέλλει σε συνοδευτικό λογισμικό το οποίο αναλαμβάνει την παρουσίασή τους και την περαιτέρω επεξεργασία τους για την εξαγωγή χρήσιμων πληροφοριών και συμπερασμάτων. / In this thesis a scan tool is developed for vehicles' CAN buses (CAN - controller area network - bus) in order to obtain data for fault diagnosis and receiving telemetry data in real time. The interface can be used to export data to help in diagnosing faults before they become costly, to study the function of the car in real time, to confirm proper operation or to gather data for improving performance etc. In this thesis an OBD scanner is developed that uses the communication protocols supported by OBD-II interface in order to collect data from car buses and sends it to a bundled software for presentation and further processing for extracting useful information and draw further conclusions.

Cette thèse s'intègre dans le processus qui conduit de l'acquisition numérique 3D à<br />la réalisation de maquettes virtuelles destinées à l'architecture et à l'archéologie.<br />Elle débute par l'étude des techniques d'acquisition 3D utilisées, la lasergrammétrie<br />et la photogrammétrie architecturale, et se poursuit par une analyse comparative<br />détaillée de ces dispositifs, basée sur de multiples expérimentations réalisées sur le<br />terrain lors de la collaboration entre le Map-Crai et le Map-Page.<br />Ensuite une réflexion sur la morphologie architecturale est abordée autour de ses<br />variantes typologiques et architectoniques, suivie par les questions théoriques<br />soulevées par la modélisation 3D et plus spécifiquement la modélisation<br />architecturale.<br />Diverses expérimentations sont ensuite présentées, elles constituent le support<br />d'une réflexion sur le développement d'outils numériques destinés à faciliter la<br />modélisation géométrique architecturale. La principale contribution de cette thèse<br />correspond à l'association de cette réflexion empirique à une approche analytique<br />fondée sur nos connaissances théoriques en architecture, qui aboutit à l'identification<br />de primitives géométriques contraintes, les moulures. Les outils numériques ainsi<br />développés dans un logiciel de CAO définissent ces primitives géométriques<br />ajustables dont le champ d'application initial, spécifique à l'architecture classique,<br />sera étendu à l'architecture khmère.<br />Enfin une proposition plus évoluée correspondant à la téléologie de cette thèse,<br />obtenir de façon efficace un résultat conforme au cahier des charges de la<br />modélisation architecturale et archéologique, est intégrée dans un logiciel de<br />synthèse d'image.