Image analysis in the morphological and morphometric study of teeth

The subject of this doctoral dissertation concerns the definition of a new methodology for the morphological and morphometric study of fossilized human teeth, and therefore strives to provide a contribution to the reconstruction of human evolutionary history that proposes to extend to the different species of hominid fossils. Standardized investigative methodologies are lacking both regarding the orientation of teeth subject to study and in the analysis that can be carried out on these teeth once they are oriented. The opportunity to standardize a primary analysis methodology is furnished by the study of certain early Neanderthal and preneanderthal molars recovered in two caves in southern Italy [Grotta Taddeo (Taddeo Cave) and Grotta del Poggio (Poggio Cave), near Marina di Camerata, Campania]. To these we can add other molars of Neanderthal and modern man of the upper Paleolithic era, specifically scanned in the paleoanthropology laboratory of the University of Arkansas (Fayetteville, Arkansas, USA), in order to increase the paleoanthropological sample data and thereby make the final results of the analyses more significant. The new analysis methodology is rendered as follows: 1. Standardization of an orientation system for primary molars (superior and inferior), starting from a scan of a sample of 30 molars belonging to modern man (15 M1 inferior and 15 M1 superior), the definition of landmarks, the comparison of various systems and the choice of a system of orientation for each of the two dental typologies. 2. The definition of an analysis procedure that considers only the first 4 millimeters of the dental crown starting from the collar: 5 sections parallel to the plane according to which the tooth has been oriented are carried out, spaced 1 millimeter between them. The intention is to determine a method that allows for the differentiation of fossilized species even in the presence of worn teeth. 3. Results and Conclusions. The new approach to the study of teeth provides a considerable quantity of information that can better be evaluated by increasing the fossil sample data. It has been demonstrated to be a valid tool in evolutionary classification that has allowed (us) to differentiate the Neanderthal sample from that of modern man. In a particular sense the molars of Grotta Taddeo, which up until this point it has not been possible to determine with exactness their species of origin, through the present research they are classified as Neanderthal.

Algorithms for on-line image registration from multiple views

Images of a scene, static or dynamic, are generally acquired at different epochs from different viewpoints. They potentially gather information about the whole scene and its relative motion with respect to the acquisition device. Data from different (in the spatial or temporal domain) visual sources can be fused together to provide a unique consistent representation of the whole scene, even recovering the third dimension, permitting a more complete understanding of the scene content. Moreover, the pose of the acquisition device can be achieved by estimating the relative motion parameters linking different views, thus providing localization information for automatic guidance purposes. Image registration is based on the use of pattern recognition techniques to match among corresponding parts of different views of the acquired scene. Depending on hypotheses or prior information about the sensor model, the motion model and/or the scene model, this information can be used to estimate global or local geometrical mapping functions between different images or different parts of them. These mapping functions contain relative motion parameters between the scene and the sensor(s) and can be used to integrate accordingly informations coming from the different sources to build a wider or even augmented representation of the scene. Accordingly, for their scene reconstruction and pose estimation capabilities, nowadays image registration techniques from multiple views are increasingly stirring up the interest of the scientific and industrial community. Depending on the applicative domain, accuracy, robustness, and computational payload of the algorithms represent important issues to be addressed and generally a trade-off among them has to be reached. Moreover, on-line performance is desirable in order to guarantee the direct interaction of the vision device with human actors or control systems. This thesis follows a general research approach to cope with these issues, almost independently from the scene content, under the constraint of rigid motions. This approach has been motivated by the portability to very different domains as a very desirable property to achieve. A general image registration approach suitable for on-line applications has been devised and assessed through two challenging case studies in different applicative domains. The first case study regards scene reconstruction through on-line mosaicing of optical microscopy cell images acquired with non automated equipment, while moving manually the microscope holder. By registering the images the field of view of the microscope can be widened, preserving the resolution while reconstructing the whole cell culture and permitting the microscopist to interactively explore the cell culture. In the second case study, the registration of terrestrial satellite images acquired by a camera integral with the satellite is utilized to estimate its three-dimensional orientation from visual data, for automatic guidance purposes. Critical aspects of these applications are emphasized and the choices adopted are motivated accordingly. Results are discussed in view of promising future developments.

Computational modelling of human stem cell-derived cardiomyocytes - Texture descriptors for biological image processing

This thesis investigates two distinct research topics. The main topic (Part I) is the computational modelling of cardiomyocytes derived from human stem cells, both embryonic (hESC-CM) and induced-pluripotent (hiPSC-CM). The aim of this research line lies in developing models of the electrophysiology of hESC-CM and hiPSC-CM in order to integrate the available experimental data and getting in-silico models to be used for studying/making new hypotheses/planning experiments on aspects not fully understood yet, such as the maturation process, the functionality of the Ca2+ hangling or why the hESC-CM/hiPSC-CM action potentials (APs) show some differences with respect to APs from adult cardiomyocytes. Chapter I.1 introduces the main concepts about hESC-CMs/hiPSC-CMs, the cardiac AP, and computational modelling. Chapter I.2 presents the hESC-CM AP model, able to simulate the maturation process through two developmental stages, Early and Late, based on experimental and literature data. Chapter I.3 describes the hiPSC-CM AP model, able to simulate the ventricular-like and atrial-like phenotypes. This model was used to assess which currents are responsible for the differences between the ventricular-like AP and the adult ventricular AP. The secondary topic (Part II) consists in the study of texture descriptors for biological image processing. Chapter II.1 provides an overview on important texture descriptors such as Local Binary Pattern or Local Phase Quantization. Moreover the non-binary coding and the multi-threshold approach are here introduced. Chapter II.2 shows that the non-binary coding and the multi-threshold approach improve the classification performance of cellular/sub-cellular part images, taken from six datasets. Chapter II.3 describes the case study of the classification of indirect immunofluorescence images of HEp2 cells, used for the antinuclear antibody clinical test. Finally the general conclusions are reported.

CT perfusion image processing: analysis of liver tumors

Perfusion CT imaging of the liver has potential to improve evaluation of tumour angiogenesis. Quantitative parameters can be obtained applying mathematical models to Time Attenuation Curve (TAC). However, there are still some difficulties for an accurate quantification of perfusion parameters due, for example, to algorithms employed, to mathematical model, to patient’s weight and cardiac output and to the acquisition system. In this thesis, new parameters and alternative methodologies about liver perfusion CT are presented in order to investigate the cause of variability of this technique. Firstly analysis were made to assess the variability related to the mathematical model used to compute arterial Blood Flow (BFa) values. Results were obtained implementing algorithms based on “ maximum slope method” and “Dual input one compartment model” . Statistical analysis on simulated data demonstrated that the two methods are not interchangeable. Anyway slope method is always applicable in clinical context. Then variability related to TAC processing in the application of slope method is analyzed. Results compared with manual selection allow to identify the best automatic algorithm to compute BFa. The consistency of a Standardized Perfusion Index (SPV) was evaluated and a simplified calibration procedure was proposed. At the end the quantitative value of perfusion map was analyzed. ROI approach and map approach provide related values of BFa and this means that pixel by pixel algorithm give reliable quantitative results. Also in pixel by pixel approach slope method give better results. In conclusion the development of new automatic algorithms for a consistent computation of BFa and the analysis and definition of simplified technique to compute SPV parameter, represent an improvement in the field of liver perfusion CT analysis.

Towards the 3D attenuation imaging of active volcanoes: methods and tests on real and simulated data

The purpose of my PhD thesis has been to face the issue of retrieving a three dimensional attenuation model in volcanic areas. To this purpose, I first elaborated a robust strategy for the analysis of seismic data. This was done by performing several synthetic tests to assess the applicability of spectral ratio method to our purposes. The results of the tests allowed us to conclude that: 1) spectral ratio method gives reliable differential attenuation (dt*) measurements in smooth velocity models; 2) short signal time window has to be chosen to perform spectral analysis; 3) the frequency range over which to compute spectral ratios greatly affects dt* measurements. Furthermore, a refined approach for the application of spectral ratio method has been developed and tested. Through this procedure, the effects caused by heterogeneities of propagation medium on the seismic signals may be removed. The tested data analysis technique was applied to the real active seismic SERAPIS database. It provided a dataset of dt* measurements which was used to obtain a three dimensional attenuation model of the shallowest part of Campi Flegrei caldera. Then, a linearized, iterative, damped attenuation tomography technique has been tested and applied to the selected dataset. The tomography, with a resolution of 0.5 km in the horizontal directions and 0.25 km in the vertical direction, allowed to image important features in the off-shore part of Campi Flegrei caldera. High QP bodies are immersed in a high attenuation body (Qp=30). The latter is well correlated with low Vp and high Vp/Vs values and it is interpreted as a saturated marine and volcanic sediments layer. High Qp anomalies, instead, are interpreted as the effects either of cooled lava bodies or of a CO2 reservoir. A pseudo-circular high Qp anomaly was detected and interpreted as the buried rim of NYT caldera.

Métamorphoses de l'Image des Tartares dans la littérature européenne du XXème siècle

Ce travail doctoral analyse le changement de l’image des Tartares dans la littérature européenne en langue allemande, anglaise, française et italienne du XXe siècle par l’étude de trois figures : la horde mongole, Gengis-khan et Khoubilaï-khan. Il soutient la thèse que, grâce à quelques facteurs historico-culturels comme la remise en question du concept de barbarie, l’essor des totalitarismes, l’ouverture de la Mongolie vers l’Occident, la redécouverte de l’Histoire secrète des Mongols et la fortune de Le divisament dou monde, au cours du XXe siècle, l’image littéraire des gengiskhanides de négative devient positive. Cette étude se compose d’une introduction, de trois chapitres et d’une conclusion. Dans l’introduction, on analyse la formation de l’image des Tartares et son évolution jusqu’à la fin du XIXe siècle, on retrace les facteurs historico-culturels qui la remettent au goût du jour et en provoquent le changement au XXe siècle et on présente le travail. Dans le premier chapitre, on se penche sur la prosopographie des Tartares dans les textes littéraires du XXe siècle, en la confrontant avec leur représentation dans l’art contemporain. Dans le deuxième chapitre, on étudie la façon des Tartares de se rapporter aux autres au sein de la société dans les textes littéraires du XXe siècle. Dans le troisième chapitre, on examine les lieux des gengiskhanides dans les textes littéraires du XXe siècle. Enfin, dans la conclusion, les données acquises au moyen de l’analyse conduite sont confrontées et interprétées. Le changement de l’image des Tartares va de pair avec une Europe qui, après avoir fait l’expérience de deux guerres mondiales, avoir assisté aux revendications de la décolonisation et avoir introjecté la thèse freudienne du « malaise dans la civilisation », remet en discussion sa façon de concevoir la barbarie et l’Altérité.