Automatical segmentation : Application to 3D angiograms of the liver

As part of a hepatic surgery simulator, we have developed a new method for the extraction of the portal vein's vascular tree i n 3D liver angioscanners . In practice, this tree is used to localize the different anatomical segments that correspond to the unit o f surgical ablation of the liver . Our method thus facilitates the surgeon's task by automatically giving the 3D model of the portal vei n in a three-step segmentation . The first step reduces the image to the ROI defined by the liver contours and increases its qualit y by an anisotropic filtering . The second step performs the segmentation of vascular networks by a global thresholding followed b y a local analysis . The third step translates a priori knowledge in topological and geometrical constraints . This last step allows to remove mistakes due to the anisotropy of the images by disconnecting the different vascular trees in order to extract the porta l vein . Results on 12 patients, validated by a radiologist, showed that the algorithm automatically extracts the principal branche s of the portal vein, allowing to delimit the anatomical segments defined in the conventional liver anatomy .Dans le cadre de la réalisation d'un simulateur de chirurgie laparoscopique' du foie, nous avons développé une nouvelle méthode permettant d'extraire dans les angioscanners 3D du foie, le réseau vasculaire de la veine porte. Ce réseau est utilisé en pratique pour repérer les différents segments anatomiques, qui représentent l'unité d'intervention dans les exérèses2 du foie. Notre méthode facilite ainsi la tâche des chirurgiens, en leur fournissant automatiquement le modèle 3D de la veine porte par une segmentation décomposée en trois étapes. La première étape réduit l'image à la région d'intérêt correspondant au contour du foie et améliore sa qualité en réalisant un filtrage anisotrope. La seconde segmente les réseaux vasculaires et appliquant un seuillage global, suivi d'une analyse locale. La troisième étape traduit les connaissances a priori que nous avons des réseaux vasculaires, en contraintes topologiques et géométriques. Cette dernière étape permet de corriger les problèmes résultant de l'anisotropie des images, en déconnectant les différentes arborescences du foie pour en extraire la veine porte. Les résultats obtenus sur douze patients, et vérifiés par un radiologue, montrent que l'algorithme extrait automatiquement les principales branches de la veine porte, permettant de délimiter les segments anatomiques définis dans l'anatomie conventionnelle du foie

Mechanical based rigid registration of 3D objects: application to multimodal medical images

The registration of 3-D objects is an important problem in computer vision and especially in medical imaging. It arises when data acquired by different sensors and/or at different times have to be fused. Under the basic assumption that the objects to be registered are rigid, the problem is to recover the six parameters of a rigid transformation. If landmarks or common characteristics are not available, the problem has to be solved by an iterative method . However such methods are inevitably attracted to local minima. This paper presents a novel iterative method designed for the rigid registration of 3-D objects . Its originality lies in its physical basis : instead of minimizing an energy function with respect to the parameters of the rigid transformation (the classical approach) the minimization is achieved by studying the motion of a rigid object in a potential field. In particular we consider the kinetic energy of the solid during the registration process, which allows it to "jump over" some local maxima of the potential energy and so avoid some local minima of that energy. We present extensive experimental results on real 3-D medical images. In that particular application, we perform the matching process with the whole segmented volumes .La mise en correspondance d'objets 3D est un problème important dans le domaine du traitement d'image. Il apparaît lorsque des données acquises par différents capteurs, à des moments ou/et des instants différents doivent être fusionnées. Si l'on suppose que les objets à mettre en correspondance sont rigides, nous avons a retrouver les paramètres d'une transformation rigide. Lorsque l'utilisatin d'amers ou de caractéristiques communes n'est pas possible pour résoudre cette tache, une méthode itérative peut êre utilisée avec profit. Cet article présente une méthode itérative générale pour la mise en correspondance d'objets 3D. Son originalité réside dans ses fondements mecaniques: plutôt que de minimiser une énergie potentielle par rapport aux paramètres de la transformation rigide, qui est l'approche classique, nous étudions le mouvement d'un objet rigide, c'est-à-dire un solide, dans un champ de potentiel. Cette approche particulière prend en compte l'énergie cinétique du solide, ce qui permet de «sauter» certains maxima locaux de l'énergie potentielle et donc d'en éviter certains minima locaux. Nous montrons que notre approche, si l'on considère l'énergie cinétique toujours nulle, est équivalente à une méthode de descente de gradient, l'introduction de la vitesse permet donc d'en accélérer la convergence. En outre, nous montrons que notre méthode se laisse moins facilement «piéger» par les minima locaux de l'énergie que les méthodes classiques de minimisation. L'article est illustré par l'application de la méthode au recalage d'images médicales réelles, ou nous utilisons la totalité du volume segment

Physical Modelling of the Flow Field in an Undular Tidal Bore

A tidal bore may form in a converging channel with a funnel shape when the tidal range exceeds 6-9 m. The advancing surge has a major impact on the estuarine ecosystem. Physical modelling of an undular bore has been conducted based upon a quasi-steady flow analogy. The experimental data highlight rapid flow redistributions between successive wave troughs and crests as well as large bottom shear stress variations. The results suggest a sediment transport process combining scour beneath wave troughs associated with upward matter dispersion between a trough and the following wave crest. The process is repeated at each trough and significant sediment transport takes place with deposition in upstream intertidal zones. The conceptual model is supported by field observations showing murky waters after the bore passage and long-lasting chaotic waves

First Results for the Beam Commissioning of the CERN Multi-Turn Extraction

The Multi-Turn Extraction (MTE), a new type of extraction based on beam trapping inside stable islands in horizontal phase space, has been commissioned during the 2008 run of the CERN Proton Synchrotron. Both singleand multi-bunch beams with a total intensity up to 1.4 1013 protons have been extracted with efficiencies up to 98%. Furthermore, injection tests in the CERN Super Proton Synchrotron were performed, with the beam then accelerated and extracted to produce neutrinos for the CERN Neutrino-to-Gran Sasso experiments. The results of the extensive measurement campaign are presented and discussed in detail

Lab to Field Assessment of the Ecotoxicological Impact of Chlorpyrifos, Isoproturon, or Tebuconazole on the Diversity and Composition of the Soil Bacterial Community

Pesticides are intentionally applied to agricultural fields for crop protection. They can harm non-target organisms such as soil microorganisms involved in important ecosystem functions with impacts at the global scale. Within the frame of the pesticide registration process, the ecotoxicological impact of pesticides on soil microorganisms is still based on carbon and nitrogen mineralization tests, despite the availability of more extensive approaches analyzing the abundance, activity or diversity of soil microorganisms. In this study, we used a high-density DNA microarray (PhyloChip) and 16S rDNA amplicon next-generation sequencing (NGS) to analyze the impact of the organophosphate insecticide chlorpyrifos (CHL), the phenyl-urea herbicide isoproturon (IPU), or the triazole fungicide tebuconazole (TCZ) on the diversity and composition of the soil bacterial community. To our knowledge, it is the first time that the combination of these approaches are applied to assess the impact of these three pesticides in a lab-to-field experimental design. The PhyloChip analysis revealed that although no significant changes in the composition of the bacterial community were observed in soil microcosms exposed to the pesticides, significant differences in detected operational taxonomic units (OTUs) were observed in the field experiment between pesticide treatments and control for all three tested pesticides after 70 days of exposure. NGS revealed that the bacterial diversity and composition varied over time. This trend was more marked in the microcosm than in the field study. Only slight but significant transient effects of CHL or TCZ were observed in the microcosm and the field study, respectively. IPU was not found to significantly modify the soil bacterial diversity or composition. Our results are in accordance with conclusions of the Environmental Food Safety Authority (EFSA), which concluded that these three pesticides may have a low risk toward soil microorganisms

Assessment of the automated multiplex-PCR Unyvero i60 ITI cartridge system to diagnose prosthetic joint infection: a multicentre study

OBJECTIVES: Prosthetic joint infections (PJI) are responsible for significant morbidity and mortality and their number continues to rise. Their management remains complex, especially the microbiological diagnosis. Besides \u27homemade\u27 tests developed by several teams, new molecular biology methods are now available with different analytical performance and usability. METHODS: We studied the performances of one of these tests: ITI multiplex PCR (mPCR) by the Curetis company and compared it to either \u27optimized\u27 culture or 16S rRNA PCR. We performed a retrospective multicentre study to assess the contributions of mPCR in the diagnosis of PJI. We randomly selected 484 intraoperative specimens among 1252 of various types (biopsy, bone, tissue around the prosthesis, synovial fluid) from 251 patients in seven different hospitals. Each sample was treated according to the recommendations of the manufacturer. RESULTS: In all, 154 out of 164 (93.9%) samples negative in culture were negative with the mPCR. Among the 276 positive samples in culture, 251 (90.9%) were monomicrobial, of which 119 (47.4%) were positive with the mPCR, and 25 (9.1%) were polymicrobial, of which 12 (48%) were positive with the mPCR. The concordance rate of mPCR with culture was 58.1% (53.6%-62.7%) and the concordance rate with 16S rRNA PCR was 70.1% (65.5%-74.6%). CONCLUSION: This new standardized molecular test showed a lack of detection when the bacterial inoculum was low (number of positive media per sample and number of colonies per media) but can be useful when patients have received antibiotic therapy previously

La tomographie en mouvement

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