From medical imaging to numerical simulations

International audienceIn the last 20 years there have been lots of progress in 3D medical imaging (such as Magnetic Resonance Imaging, MRI, and X-ray Computed Tomography, CT) and in particular in modalities to visualise vascular structures. The resulting images have been successfully used in various clinical applications, in particular for cerebrovascular pathologies (e.g., neurosurgery planning; stenoses, aneurysm or thrombosis quantification; arteriovenous malformation detection and follow-up, etc.). The complexity of the processing and analysis of these images (size, information vs noise, artifacts, etc) led to the development of imaging tools such as vessel filtering, segmentation and quantification. There is however, until now, no database of synthetic images and associated ground-truths (segmented data) available in cerebrovascular images contrary to morphological brain image analysis (e.g. brainweb).In the ANR Vivabrain project, we combine the skills of several communities: computer science, applied mathematics, biophysics, and medicine to remedy the aforementioned observation. In particular we focus on complex multi-disciplinary problems such as (i) the handling of inter-individual cerebrovascular variability, (ii) the generation of computational meshes, (iii) the simulation of blood flows in the complete cerebrovascular system 3D+time (3D+t) including calibration and validation and (iv) the accurate simulation of the physical processes involved in MRA acquisition sequences in order to finally obtain realistic virtual angiographic images

ANGIOTK : An Open Platform to reconstruct vessels from MRI images and simulate blood flows to ultimately provide Virtual Angiographies

National audienceFrom medical images to numerical simulations ANGIOTK The platform is still a prototype, but reached a level of maturity that requires very little human intervention. The overall objective is to make available, to the medical community, tools for computer aided modeling for conducting experiments in silico, otherwise difficult or impossible to carry on patients. A specific aim is to create an ecosystem around the platform composed of academic, research centers and enterprises and to provide services such as training, specific developments, consulting or deployment. The platform is operated by Cemosis and Kitware. An Open Platform to reconstruct vessels from MRI images and simulate blood flows to ultimately provide Virtual Angiographie

The apparent breastfeeding paradox in very preterm infants: relationship between breast feeding, early weight gain and neurodevelopment based on results from two cohorts, EPIPAGE and LIFT

Context: Supplementation of breast milk is difficult once infants suckle the breast and is often discontinued at end of hospitalisation and after discharge. Thus, breastfed preterm infants are exposed to an increased risk of nutritional deficit with a possible consequence on neurodevelopmental outcome. Objective: To assess the relationship between breast feeding at time of discharge, weight gain during hospitalisation and neurodevelopmental outcome. Design: Observational cohort study. Setting: Two large, independent population-based cohorts of very preterm infants: the Loire Infant Follow-up Team (LIFT) and the EPIPAGE cohorts. Patients: 2925 very preterm infants alive at discharge. Main outcome measure: Suboptimal neurodevelopmental outcome, defined as a score in the lower tercile, using Age and Stages Questionnaire at 2 years in LIFT and Kaufman Assessment Battery for Children Test at 5 years in EPIPAGE. Two propensity scores for breast feeding at discharge, one for each cohort, were used to reduce bias. Results: Breast feeding at time of discharge concerned only 278/1733 (16%) infants in LIFT and 409/2163 (19%) infants in EPIPAGE cohort. Breast feeding is significantly associated with an increased risk of losing one weight Z-score during hospitalisation (LIFT: n=1463, adjusted odd ratio (aOR)=2.51 (95% CI 1.87 to 3.36); EPIPAGE: n=1417, aOR=1.55 (95% CI 1.14 to 2.12)) and with a decreased risk for a suboptimal neurodevelopmental assessment (LIFT: n=1463, aOR=0.63 (95% CI 0.45 to 0.87); EPIPAGE: n=1441, aOR=0.65 (95% CI 0.47 to 0.89) and an increased chance of having a head circumference Z-score higher than 0.5 at 2 years in LIFT cohort (n=1276, aOR=1.43 (95% CI 1.02 to 2.02)) and at 5 years in EPIPAGE cohort (n=1412, aOR=1.47 (95% CI 1.10 to 1.95)). Conclusions: The observed better neurodevelopment in spite of suboptimal initial weight gain could be termed the 'apparent breastfeeding paradox' in very preterm infants. Regardless of the mechanisms involved, the current data provide encouragement for the use of breast feeding in preterm infants

PetaFlow: a global computing-networking-visualisation unitwith social impact

International audienceThe PetaFlow application aims to contribute to the use of high performance computational resources forthe benefit of society. To this goal the emergence of adequate information and communication technologies withrespect to high performance computing-networking-visualisation and their mutual awareness is required. Thedeveloped technology and algorithms are presented and applied to a real global peta-scale data intensive scientificproblem with social and medical importance, i.e. human upper airflow modelling

Death and the Societies of Late Antiquity

Ce volume bilingue, comprenant un ensemble de 28 contributions disponibles en français et en anglais (dans leur version longue ou abrégée), propose d’établir un état des lieux des réflexions, recherches et études conduites sur le fait funéraire à l’époque tardo-antique au sein des provinces de l’Empire romain et sur leurs régions limitrophes, afin d’ouvrir de nouvelles perspectives sur ses évolutions possibles. Au cours des trois dernières décennies, les transformations considérables des méthodologies déployées sur le terrain et en laboratoire ont permis un renouveau des questionnements sur les populations et les pratiques funéraires de l’Antiquité tardive, période marquée par de multiples changements politiques, sociaux, démographiques et culturels. L’apparition de ce qui a été initialement désigné comme une « Anthropologie de terrain », qui fut le début de la démarche archéothanatologique, puis le récent développement d’approches collaboratives entre des domaines scientifiques divers (archéothanatologie, biochimie et géochimie, génétique, histoire, épigraphie par exemple) ont été décisives pour le renouvellement des problématiques d’étude : révision d’anciens concepts comme apparition d’axes d’analyse inédits. Les recherches rassemblées dans cet ouvrage sont articulées autour de quatre grands thèmes : l’évolution des pratiques funéraires dans le temps, l’identité sociale dans la mort, les ensembles funéraires en transformation (organisation et topographie) et les territoires de l’empire (du cœur aux marges). Ces études proposent un réexamen et une révision des données, tant anthropologiques qu’archéologiques ou historiques sur l’Antiquité tardive, et révèlent, à cet égard, une mosaïque de paysages politiques, sociaux et culturels singulièrement riches et complexes. Elles accroissent nos connaissances sur le traitement des défunts, l’emplacement des aires funéraires ou encore la structure des sépultures, en révélant une diversité de pratiques, et permettent au final de relancer la réflexion sur la manière dont les sociétés tardo-antiques envisagent la mort et sur les éléments permettant d’identifier et de définir la diversité des groupes qui les composent. Elles démontrent ce faisant que nous pouvons véritablement appréhender les structures culturelles et sociales des communautés anciennes et leurs potentielles transformations, à partir de l’étude des pratiques funéraires.This bilingual volume proposes to draw up an assessment of the recent research conducted on funerary behavior during Late Antiquity in the provinces of the Roman Empire and on their borders, in order to open new perspectives on its possible developments. The considerable transformations of the methodologies have raised the need for a renewal of the questions on the funerary practices during Late Antiquity, a period marked by multiple political, social, demographic and cultural changes. The emergence field anthropology, which was the beginning of archaeothanatology, and then the recent development of collaborative approaches between various scientific fields (archaeothanatology, biochemistry and geochemistry, genetics, history, epigraphy, for example), have been decisive. The research collected in this book is structured around four main themes: Evolution of funerary practices over time; Social identity through death; Changing burial grounds (organisation and topography); Territories of the Empire (from the heart to the margins). These studies propose a review and a revision of the data, both anthropological and archaeological or historical on Late Antiquity, and reveal a mosaic of political, social, and cultural landscapes singularly rich and complex. In doing so, they demonstrate that we can truly understand the cultural and social structures of ancient communities and their potential transformations, based on the study of funerary practices

Lighting for high-performance volume rendering

Le rendu volumique direct est une technique permettant la visualisation de données volumiques scalaires. L'objectif de cette technique est de permettre l'analyse des structures présentes dans ces données en leur associant des propriétés optiques (couleur, opacité) avec l'aide d'une fonction de transfert. L'ajout d'éclairage au rendu volumique direct permet d'apporter des indices visuels supplémentaires pour l'analyse des données. En effet, l'éclairage joue un rôle fondamental dans la manière dont nous percevons notre environnement, car il permet d'évaluer le positionnement et la forme des objets qui nous entourent. Nous présentons dans cette thèse différentes techniques permettant d'améliorer l'intégration et l'utilisation d'éclairage dans le rendu volumique direct. Nous proposons ainsi une méthode d'interpolation non-linéaire qui permet d'améliorer la précision numérique des méthodes d'éclairage basées sur une normale dans le contexte du rendu volumique direct pré-intégré. Dans un second temps, nous nous intéressons à une technique d'éclairage spécifique : l'ambient occlusion (ou occultation ambiante en français). Nous introduisons pour celle-ci un découpage en structures qui permet d'améliorer la perception des structures internes en améliorant le contraste dans l'image finale. Afin de réduire les temps de pré-calcul inhérents à cette méthode, nous la parallélisons sur une architecture multi-GPU, en intégrant la gestion de l'équilibrage de charge et s'appuyant sur deux approches différentes de répartition : statique et dynamique.Direct volume rendering allows the visualization of scalar volume data. This technique aims at helping the analysis of the different features in datasets by giving them optical properties (color, opacity) using a transfer function. Adding lighting to direct volume rendering allows to bring additional and important visual cues for data analysis. Indeed, lighting plays a fundamental role in the way we perceive our environment, because it helps evaluating the relative positions and shapes of objects surrounding us. In this thesis, we introduce different techniques improving the integration and the use of lighting methods in direct volume rendering. We first propose a nonlinear interpolation method for the gradient. It allows to numerically improve the integration of gradient based lighting methods in the context of direct volume rendering. We then put the focus on a specific lighting method : ambient occlusion. By introducing a feature separation in the pre-computation step, we improve the perception of internal features by improving picture contrast. In order to reduce the pre-computation times induced by this method, we parallelize it on a multi-GPU architecture while integrating load balancing mechanisms and relying on two data repartition strategies : static and dynamic

Lighting for high-performance volume rendering

Le rendu volumique direct est une technique permettant la visualisation de données volumiques scalaires. L'objectif de cette technique est de permettre l'analyse des structures présentes dans ces données en leur associant des propriétés optiques (couleur,Direct volume rendering allows the visualization of scalar volume data. This technique aims at helping the analysis of the different features in datasets by giving them optical properties (color, opacity) using a transfer function. Adding lighting to dir

PHANTOM project: development and validation of the pipeline from MRA acquisition to MRA simulations

The aim of this project is to validate the Vivabrain pipeline with a physical phantom from real MRI acquisition to MRI simulations through image segmentation and computational fluid dynamics (CFD) simulations. For that purpose, we set up three comparison benchmarks. The first benchmark compares dimensions of the reconstructed geometry from real MRI acquisition to the physical phantom dimensions. The second aims to validate the CFD simulations by comparing the outputs of two simulations, one carried out using Feel++ and the other using FreeFem++. The CFD outputs are also compared to MRI flow measurement data. The goal of the last comparison benchmark is to compare the MRI simulations outputs to the numerical fluid simulations

PHANTOM project: development and validation of the pipeline from MRA acquisition to MRA simulations

The aim of this project is to validate the Vivabrain pipeline with a physical phantom from real MRI acquisition to MRI simulations through image segmentation and computational fluid dynamics (CFD) simulations. For that purpose, we set up three comparison benchmarks. The first benchmark compares dimensions of the reconstructed geometry from real MRI acquisition to the physical phantom dimensions. The second aims to validate the CFD simulations by comparing the outputs of two simulations, one carried out using Feel++ and the other using FreeFem++. The CFD outputs are also compared to MRI flow measurement data. The goal of the last comparison benchmark is to compare the MRI simulations outputs to the numerical fluid simulations

Éclairage pour visualisation volumique haute-performance

Le rendu volumique direct est une technique permettant la visualisation de données volumiques scalaires. L objectif de cette technique est de permettre l analyse des structures présentes dans ces données en leur associant des propriétés optiques (couleur, opacité) avec l aide d une fonction de transfert. L ajout d éclairage au rendu volumique direct permet d apporter des indices visuels supplémentaires pour l analyse des données. En effet, l éclairage joue un rôle fondamental dans la manière dont nous percevons notre environnement, car il permet d évaluer le positionnement et la forme des objets qui nous entourent. Nous présentons dans cette thèse différentes techniques permettant d améliorer l intégration et l utilisation d éclairage dans le rendu volumique direct. Nous proposons ainsi une méthode d interpolation non-linéaire qui permet d améliorer la précision numérique des méthodes d éclairage basées sur une normale dans le contexte du rendu volumique direct pré-intégré. Dans un second temps, nous nous intéressons à une technique d éclairage spécifique : l ambient occlusion (ou occultation ambiante en français). Nous introduisons pour celle-ci un découpage en structures qui permet d améliorer la perception des structures internes en améliorant le contraste dans l image finale. Afin de réduire les temps de pré-calcul inhérents à cette méthode, nous la parallélisons sur une architecture multi-GPU, en intégrant la gestion de l équilibrage de charge et s appuyant sur deux approches différentes de répartition : statique et dynamique.Direct volume rendering allows the visualization of scalar volume data. This technique aims at helping the analysis of the different features in datasets by giving them optical properties (color, opacity) using a transfer function. Adding lighting to direct volume rendering allows to bring additional and important visual cues for data analysis. Indeed, lighting plays a fundamental role in the way we perceive our environment, because it helps evaluating the relative positions and shapes of objects surrounding us. In this thesis, we introduce different techniques improving the integration and the use of lighting methods in direct volume rendering. We first propose a nonlinear interpolation method for the gradient. It allows to numerically improve the integration of gradient based lighting methods in the context of direct volume rendering. We then put the focus on a specific lighting method : ambient occlusion. By introducing a feature separation in the pre-computation step, we improve the perception of internal features by improving picture contrast. In order to reduce the pre-computation times induced by this method, we parallelize it on a multi-GPU architecture while integrating load balancing mechanisms and relying on two data repartition strategies : static and dynamic.STRASBOURG-Sc. et Techniques (674822102) / SudocSudocFranceF