Task-based Augmented Contour Trees with Fibonacci Heaps

This paper presents a new algorithm for the fast, shared memory, multi-core computation of augmented contour trees on triangulations. In contrast to most existing parallel algorithms our technique computes augmented trees, enabling the full extent of contour tree based applications including data segmentation. Our approach completely revisits the traditional, sequential contour tree algorithm to re-formulate all the steps of the computation as a set of independent local tasks. This includes a new computation procedure based on Fibonacci heaps for the join and split trees, two intermediate data structures used to compute the contour tree, whose constructions are efficiently carried out concurrently thanks to the dynamic scheduling of task parallelism. We also introduce a new parallel algorithm for the combination of these two trees into the output global contour tree. Overall, this results in superior time performance in practice, both in sequential and in parallel thanks to the OpenMP task runtime. We report performance numbers that compare our approach to reference sequential and multi-threaded implementations for the computation of augmented merge and contour trees. These experiments demonstrate the run-time efficiency of our approach and its scalability on common workstations. We demonstrate the utility of our approach in data segmentation applications

Coxarthrose : l’infiltration intra articulaire de corticoïdes constitue-t-elle une thérapeutique complémentaire des traitements médicaux et de l’arthroplastie ? À propos d’une série de 301 cas

INTRODUCTION : Les traitements médicaux de la coxarthrose sont efficaces mais parfois insuffisants, mal tolérés voire contre indiqués. Le traitement chirurgical n’est pas toujours possible. Les infiltrations de corticoïdes en intra articulaire peuvent être une alternative. L’objectif de l’étude est d’analyser la tolérance et la satisfaction immédiate et à distance des patients concernant cette thérapeutique.MATÉRIEL ET MÉTHODES : Il s’agit d’une étude rétrospective monocentrique portant sur 301 patients ayant une coxarthrose radiologique et clinique, infiltrés à l’Hôpital de la Croix Saint Simon sous radioscopie entre janvier 2010 et janvier 2012. Les patients ont été recrutés via le logiciel du service de radiologie de l’Hôpital. Un recueil de données rétrospectif sur la tolérance et la satisfaction des patients a été fait à partir des dossiers cliniques puis un questionnaire téléphonique a été réalisé auprès de chacun des patients inclus.RÉSULTATS : 150 patients ont été inclus. Un hématome, une ponction artérielle et deux cas d’allergie ont été rapportés. Leur évolution a été rapidement favorable, sans conséquence sur le pronostic vital. Sur les 105 entretiens téléphoniques, aucun cas d’arthrite septique n’a été relevé.59 patients (56,2%) ont eu une prothèse totale de hanche et 46 patients (43,8%), n’en ont pas eu. L’échelle de satisfaction retrouvait une moyenne modérée de 2,8 (1=très satisfait, 5=très insatisfait). CONCLUSION : L’infiltration de corticoïdes en intra articulaire dans la coxarthrose serait une bonne alternative au traitement médical chez le patient non candidat à la chirurgie. Les effets indésirables sont exceptionnels et bénins. La satisfaction moyenne rapportée s’explique par un effet transitoire qui doit être expliqué au patient

L’islam ibadite au Maghreb : histoire sociale et religieuse

Ce cours d’histoire sociale et religieuse présente les résultats de recherches menées depuis 2008 sur les communautés ibadites du Maghreb, principalement en Algérie

Task-based Augmented Reeb Graphs with Dynamic ST-Trees

International audienceThis paper presents, to the best of our knowledge, the first parallel algorithm for the computation of the augmented Reeb graph of piecewise linear scalar data. Such augmented Reeb graphs have a wide range of applications , including contour seeding and feature based segmentation. Our approach targets shared-memory multi-core workstations. For this, it completely revisits the optimal, but sequential, Reeb graph algorithm, which is capable of handing data in arbitrary dimension and with optimal time complexity. We take advantage of Fibonacci heaps to exploit the ST-Tree data structure through independent local propagations, while maintaining the optimal, linearithmic time complexity of the sequential reference algorithm. These independent propagations can be expressed using OpenMP tasks, hence benefiting in parallel from the dynamic load balancing of the task runtime while enabling us to increase the parallelism degree thanks to a dual sweep. We present performance results on triangulated surfaces and tetrahedral meshes. We provide comparisons to related work and show that our new algorithm results in superior time performance in practice, both in sequential and in parallel. An open-source C++ implementation is provided for reproducibility

An Open-Source Digital Archiving System for Medical and Scientific Research

In this paper, we present MIDAS, an open-source web-based digital archiving system that handles large collections of scientific data. We created a web-based digital archiving repository based on open standards. The MIDAS repository is specifically tuned for medical and scientific datasets and provides a flexible data management facility, a search engine, and an online image viewer. MIDAS allows researchers to store, manage and share scientific datasets, from the convenience of a web browser or through a generic programming interface, thereby facilitating the dissemination of valuable imaging datasets to research collaborators. The system is currently deployed at several research laboratories worldwide and has demonstrated its ability to streamline the full scientific processing workflow from data acquisition to analysis and reports

An Open-Source Digital Archiving System for Medical and Scientific Research

In this paper, we present MIDAS, an open-source web-based digital archiving system that handles large collections of scientific data. We created a web-based digital archiving repository based on open standards. The MIDAS repository is specifically tuned for medical and scientific datasets and provides a flexible data management facility, a search engine, and an online image viewer. MIDAS allows researchers to store, manage and share scientific datasets, from the convenience of a web browser or through a generic programming interface, thereby facilitating the dissemination of valuable imaging datasets to research collaborators. The system is currently deployed at several research laboratories worldwide and has demonstrated its ability to streamline the full scientific processing workflow from data acquisition to analysis and reports

Challenges of the Anthropocene epoch – supporting multi-focus research

International audienceWork on multiscale issues presents countless challenges that have been long attacked by GIScience researchers. Most results either concentrate on modeling or on data structures/database aspects. Solutions go either towards generalization (and/or virtualization of distinct scales) or towards linking entities of interest across scales. However, researchers seldom take into account the fact that multiscale scenarios are increasingly constructed cooperatively, and require distinct perspectives of the world. The combination of multiscale and multiple perspectives per scale constitutes what we call multifocus research. This paper presents our solution to these issues. It builds upon a specific database version model – the multiversion MVBD – which has already been successfully implemented in several geospatial scenarios, being extended here to support multi-focus research

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

Evaluation of atlas based mouse brain segmentation

Magentic Reasonance Imaging for mouse phenotype study is one of the important tools to understand human diseases. In this paper, we present a fully automatic pipeline for the process of morphometric mouse brain analysis. The method is based on atlas-based tissue and regional segmentation, which was originally developed for the human brain. To evaluate our method, we conduct a qualitative and quantitative validation study as well as compare of b-spline and fluid registration methods as components in the pipeline. The validation study includes visual inspection, shape and volumetric measurements and stability of the registration methods against various parameter settings in the processing pipeline. The result shows both fluid and b-spline registration methods work well in murine settings, but the fluid registration is more stable. Additionally, we evaluated our segmentation methods by comparing volume differences between Fmr1 FXS in FVB background vs C57BL/6J mouse strains