Tomographie et géométrie discrètes avec la transformée Mojette

We explore through this thesis the insights of discrete tomography over classical tomography in continuous space. We use the Mojette transform, a discrete and exact form of the Radon transform, as a link between classical tomography and discrete tomography. We focus especially on the study of the discrete space induced by the Mojette transform operator through four research axis.Axis 1 focuses on the Mojette space properties in regards to discrete affine transforms of digital images. We provide tools to achieve affine transforms directly from the projections of a digital object, without preliminary tomographic reconstruction. This property is well-known for the continuous Radon transform but non-trivial for its sampled versions.Axis 2 seeks for some links between continuous-sampled projections related to medical imaging acquisition modalities and discrete projections derived by the Mojette transform. We implement interpolation schemes to estimate discrete projections from the continuous ones — on either synthetic or real data — and their reconstruction.In axis 3, we provide an algebraic framework for the description and inversion of the Mojette transform. The input data, the projections as well as the operators are modeled as polynomials. Within this framework, the Mojette projection operator advantageously reduce to a Vandermonde matrix.This thesis has been realized at both IRCCyN Lab and Keosys company within the Quanticardi FUI project. Axis 4 focuses on the design and the implementation of a clinical software for the absolute quantification of myocardial perfusion with positron emission tomography.Dans cette thèse, nous explorons les voies offertes par la tomographie discrète par rapport à la tomographie classique en milieu continu. Nous utilisons la transformée Mojette, version discrète et exacte de la transformée de Radon, que nous présentons comme un lien entre la tomographie classique et la tomographie discrète. Nous nous attachons à l’étude de l’espace sous-jacent à l’opérateur de transformée Mojette. Ce travail se décline suivant quatre axes de recherche.L’axe 1 est consacré au comportement de l’espace Mojette pour les transformations affines discrètes de l’image. Nous montrons qu’il est possible de réaliser certaines transformations affines directement à partir des projections discrètes d’un objet, sans reconstruction préalable.L’axe 2 consiste à examiner les liens entre les projections continues issues de modalités d’acquisitions en imagerie médicale et celles obtenues par transformée Mojette. Nous présentons différentes méthodes d’estimation des projections discrètes à partir de projections continues — réelles ou simulées — et leur reconstruction.L’axe 3 a pour objet l’inversion algébrique de la transformée Mojette. Les données d’entrée, les projections et les opérateurs sont modélisés par des polynômes. Ce formalisme, relevant de la tomographie discrète, permet d’exprimer la matrice de transformation Mojette sous forme Vandermonde.Cette thèse a été réalisée conjointement à l’IRCCyN et à Keosys dans le cadre du projet FUI Quanticardi. L’axe 4 est dédié à la conception et au développement d’un logiciel de quantification absolue de la perfusion myocardique en tomographie par émission de positons

Contrôle pharmacologique de l'apoptose cardiovasculaire dans l'hypertension : implication de la voie de l'angiotensine et de la correction de la dysfonction endothéliale

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal

A data consistent variational segmentation approach suitable for real-time tomography

Computed Tomography (CT) is an imaging technique that allows to reconstruct volumetric information of the analyzed objects from their projections. The most popula

Alternative Lengthening of Telomeres Is Characterized by High Rates of Telomeric Exchange

Abstract Telomere maintenance activity is a hallmark of cancer. In some telomerase-negative tumors, telomeres become lengthened by alternative lengthening of telomeres (ALT), a recombination-mediated DNA replication process in which telomeres use other telomeric DNA as a copy template. Using chromosome orientation fluorescence in situ hybridization, we found that postreplicative exchange events involving a telomere and another TTAGGG-repeat tract occur at remarkably high frequencies in ALT cells (range 28–280/100 metaphases) and rarely or never in non-ALT cells, including cell lines with very long telomeres. Like the ALT phenotype itself, the telomeric exchanges were not suppressed when telomerase was activated in ALT cells. These exchanges are telomere specific because there was no correlation with sister chromatid exchange rates at interstitial locations, and they were not observed in non-ALT Bloom syndrome cells with very high sister chromatid exchange rates

A cone-beam X-ray computed tomography data collection designed for machine learning

Unlike previous works, this open data collection consists of X-ray cone-beam (CB) computed tomography (CT) datasets specifically designed for machine learning applications and high cone-angle artefact reduction. Forty-two walnuts were scanned with a laboratory X-ray set-up to provide not only data from a single object but from a class of objects with natural variability. For each walnut, CB projections on three different source orbits were acquired to provide CB data with different cone angles as well as being able to compute artefact-free, high-quality ground truth images from the combined data that can be used for supervised learning. We provide the complete image reconstruction pipeline: raw projection data, a description of the scanning geometry, pre-processing and reconstruction scripts using open software, and the reconstructed volumes. Due to this, the dataset can not only be used for high cone-angle artefact reduction but also for algorithm development and evaluation for other tasks, such as image reconstruction from limited or sparse-angle (low-dose) scanning, super resolution, or segmentation

Influence of head positioning during cone-beam CT imaging on the accuracy of virtual 3D models

Objective: Cone beam computed tomography (CBCT) images are being increasingly used to acquire three- dimensional (3D) models of the skull for additive manufacturing purposes. However, the accuracy of such models remains a challenge, especially in the orbital area. The aim of this study is to assess the impact of four different CBCT imaging positions on the accuracy of the resulting 3D models in the orbital area. Methods: An anthropomorphic head phantom was manufactured by submerging a dry human skull in silicon to mimic the soft tissue attenuation and scattering properties of the human head. The phantom was scanned on a ProMax 3D MAX CBCT scanner using 90 and 120 kV for four different field of view positions: standard; elevated; backwards tilted; and forward tilted. All CBCT images were subsequently converted into 3D models and geometrically compared with a "gold- standard" optical scan of the dry skull. Results: Mean absolute deviations of the 3D models ranged between 0.15 +/- 0.11 mm and 0.56 +/- 0.28 mm. The elevated imaging position in combination with 120 kV tube voltage resulted in an improved representation of the orbital walls in the resulting 3D model without compromising the accuracy. Conclusions: Head positioning during CBCT imaging can influence the accuracy of the resulting 3D model. The accuracy of such models may be improved by positioning the region of interest (e.g. the orbital area) in the focal plane (Figure 2a) of the CBCT X- ray beam.Peer reviewe

A cone-beam X-ray computed tomography data collection designed for machine learning

Unlike previous works, this open data collection consists of X-ray cone-beam (CB) computed tomography (CT) datasets specifically designed for machine learning applications and high cone-angle artefact reduction. Forty-two walnuts were scanned with a laboratory X-ray set-up to provide not only data from a single object but from a class of objects with natural variability. For each walnut, CB projections on three different source orbits were acquired to provide CB data with different cone angles as well as being able to compute artefact-free, high-quality ground truth images from the combined data that can be used for supervised learning. We provide the complete image reconstruction pipeline: raw projection data, a description of the scanning geometry, pre-processing and reconstruction scripts using open software, and the reconstructed volumes. Due to this, the dataset can not only be used for high cone-angle artefact reduction but also for algorithm development and evaluation for other tasks, such as image reconstruction from limited or sparse-angle (low-dose) scanning, super resolution, or segmentation

Population history from the Neolithic to present on the Mediterranean island of Sardinia: an ancient DNA perspective

Recent ancient DNA studies of western Eurasia have revealed a dynamic history of admixture, with evidence for major migrations during the Neolithic and Bronze Age. The population of the Mediterranean island of Sardinia has been notable in these studies –} Neolithic individuals from mainland Europe cluster more closely with Sardinian individuals than with all other present-day Europeans. The current model to explain this result is that Sardinia received an initial influx of Neolithic ancestry and then remained relatively isolated from expansions in the later Neolithic and Bronze Age that took place in continental Europe. To test this model, we generated genome-wide capture data (approximately 1.2 million variants) for 43 ancient Sardinian individuals spanning the Neolithic through the Bronze Age, including individuals from Sardinia{’}s Nuragic culture, which is known for the construction of numerous large stone towers throughout the island. We analyze these new samples in the context of previously generated genome-wide ancient DNA data from 972 ancient individuals across western Eurasia and whole-genome sequence data from approximately 1,500 modern individuals from Sardinia. The ancient Sardinian individuals show a strong affinity to western Mediterranean Neolithic populations and we infer a high degree of genetic continuity on the island from the Neolithic (around fifth millennium BCE) through the Nuragic period (second millennium BCE). In particular, during the Bronze Age in Sardinia, we do not find significant levels of the {“}Steppe{” ancestry that was spreading in many other parts of Europe at that time. We also characterize subsequent genetic influx between the Nuragic period and the present. We detect novel, modest signals of admixture between 1,000 BCE and present-day, from ancestry sources in the eastern and northern Mediterranean. Within Sardinia, we confirm that populations from the more geographically isolated mountainous provinces have experienced elevated levels of genetic drift and that northern and southwestern regions of the island received more gene flow from outside Sardinia. Overall, our genetic analysis sheds new light on the origin of Neolithic settlement on Sardinia, reinforces models of genetic continuity on the island, and provides enhanced power to detect post-Bronze-Age gene flow. Together, these findings offer a refined demographic model for future medical genetic studies in Sardinia

The Role of Subjective Temporality in Future-Oriented Mental Time Travel

In this chapter we examine the tendency to view future-oriented mental time travel as a unitary faculty that, despite task-driven surface variation, ultimately reduces to a common phenomenological state. We review evidence that FMTT is neither unitary nor beholden to episodic memory: Rather, it is varied both in its memorial underpinnings and experiential realization. We conclude that the phenomenological diversity characterizing FMTT is dependent not on the type of memory activated during task performance, but on the kind of subjective temporality associated with the memory in play

Well-Being in the Christian Tradition

This paper discusses well-being in the Christian tradition