Restoration of Hyperspectral Astronomical Data with Spectrally Varying Blur

This book is a collection of 19 articles which reflect the courses given at the Collège de France/Summer school “Reconstruction d'images − Applications astrophysiques“ held in Nice and Fréjus, France, from June 18 to 22, 2012. The articles presented in this volume address emerging concepts and methods that are useful in the complex process of improving our knowledge of the celestial objects, including Earth

Approche problème inverse pour l’alignement de séries en tomographie électronique

International audienceIn the refining industry, morphological measurements of particles have become an essential part in the characterization catalyst supports. Through these parameters, one can infer the specific physicochemical properties of the studied materials. One of the main acquisition techniques is electron tomography (or nanotomography). 3D volumes are reconstructed from sets of projections from different angles made by a Transmission Electron Microscope (TEM). This technique provides a real three-dimensional information at the nanometric scale. A major issue in this method is the misalignment of the projections that contributes to the reconstruction. The current alignment techniques usually employ fiducial markers such as gold particles for a correct alignment of the images. When the use of markers is not possible, the correlation between adjacent projections is used to align them. However, this method sometimes fails. In this paper, we propose a new method based on the inverse problem approach where a certain criterion is minimized using a variant of the Nelder and Mead simplex algorithm. The proposed approach is composed of two steps. The first step consists of an initial alignment process, which relies on the minimization of a cost function based on robust statistics measuring the similarity of a projection to its previous projections in the series. It reduces strong shifts resulting from the acquisition between successive projections. In the second step, the pre-registered projections are used to initialize an iterative alignment-refinement process which alternates between (i) volume reconstructions and (ii) registrations of measured projections onto simulated projections computed from the volume reconstructed in (i). At the end of this process, we have a correct reconstruction of the volume, the projections being correctly aligned. Our method is tested on simulated data and shown to estimate accurately the translation, rotation and scale of arbitrary transforms. We have successfully tested our method with real projections of different catalyst supports.Dans le domaine du raffinage, les mesures morphologiques de particules sont devenues indispensables pour caractériser les supports de catalyseurs. A travers ces paramètres, on peut remonter aux spécificités physico-chimiques des matériaux étudiés. Une des techniques d’acquisition utilisées est la tomographie électronique (ou nanotomographie). Des volumes 3D sont reconstruits à partir de séries de projections sous différents angles obtenues par Microscopie Électronique en Transmission (MET). Cette technique permet d’obtenir une réelle information tridimensionnelle à l’échelle du nanomètre. Un problème majeur dans ce contexte est le mauvais alignement des projections qui contribuent à la reconstruction. Les techniques d’alignement actuelles emploient habituellement des marqueurs de réference tels que des nanoparticules d’or pour un alignement correct des images. Lorsque l’utilisation de marqueurs n’est pas possible, l’alignement de projections adjacentes est obtenu par corrélation entre ces projections. Cependant, cette méthode échoue parfois. Dans cet article, nous proposons une nouvelle méthode basée sur une approche de type problème inverse où un certain critère est minimisé en utilisant une variante de l’algorithme de Nelder et Mead, qui exploite le concept de simplexe. Elle est composéé de deux étapes. La première étape consiste en un processus d’alignement initial s’appuyant sur la minimisation d’une fonction de coût basée sur des statistiques robustes, mesurant la similarité entre une projection et les projections précédentes de la série. Elle vise à réduire les forts déplacements, résultant de l’acquisition entre les projections successives. Dans la seconde étape, les projections pré-recalées sont employées pour initialiser un processus itératif et alterné d’alignement et reconstruction, minimisant alternativement une fonction de coût basée sur la reconstruction du volume et une fonction basée sur l’alignement d’une projection avec sa version simulée obtenue à partir du volume reconstruit. A la fin de ce processus, nous obtenons une reconstruction correcte du volume, les projections étant correctement alignées. Notre méthode a été testée sur des données simulées et prouve qu’elle récupère d’une manière précise les changements dans les paramètres de translation, rotation et mise à l’échelle. Nous avons testé avec succès notre méthode pour les projections réelles de différents supports de catalyseur

A low optical depth region in the inner disk of the HerbigAe star HR5999

Circumstellar disks surrounding young stars are known to be the birthplaces of planets, and the innermost astronomical unit is of particular interest. We present new long-baseline spectro-interferometric observations of the HerbigAe star, HR5999, obtained in the H and K bands with the AMBER instrument at the VLTI, and aim to produce near-infrared images at the sub-AU spatial scale. We spatially resolve the circumstellar material and reconstruct images using the MiRA algorithm. In addition, we interpret the interferometric observations using models that assume that the near-infrared excess is dominated by the emission of a circumstellar disk. We compare the images reconstructed from the VLTI measurements to images obtained using simulated model data. The K-band image reveals three main elements: a ring-like feature located at ~0.65 AU, a low surface brightness region inside, and a central spot. At the maximum angular resolution of our observations (1.3 mas), the ring is resolved while the central spot is only marginally resolved, preventing us from revealing the exact morphology of the circumstellar environment. We suggest that the ring traces silicate condensation, i.e., an opacity change, in a circumstellar disk around HR 5999. We build a model that includes a ring at the silicate sublimation radius and an inner disk of low surface brightness responsible for a large amount of the near-infrared continuum emission. The model successfully fits the SED, visibilities, and closure phases, and provides evidence of a low surface brightness region inside the silicate sublimation radius. This study provides additional evidence that in HerbigAe stars, there is material in a low surface brightness region, probably a low optical depth region, located inside the silicate sublimation radius and of unknown nature.Comment: 11 pages, 10 figure

Milli-arcsecond astrophysics with VSI, the VLTI spectro-imager in the ELT era

Nowadays, compact sources like surfaces of nearby stars, circumstellar environments of stars from early stages to the most evolved ones and surroundings of active galactic nuclei can be investigated at milli-arcsecond scales only with the VLT in its interferometric mode. We propose a spectro-imager, named VSI (VLTI spectro-imager), which is capable to probe these sources both over spatial and spectral scales in the near-infrared domain. This instrument will provide information complementary to what is obtained at the same time with ALMA at different wavelengths and the extreme large telescopes.Comment: 8 pages. To be published in the proceedings of the ESO workshop "Science with the VLT in the ELT Era", held in Garching (Germany) on 8-12 October 2007, A. Moorwood edito

Chaotic Genetic Patchiness in the Highly Valued Atlantic Stalked Barnacle Pollicipes pollicipes from the Iberian Peninsula: Implications for Fisheries Management. Frontiers in Marine Science

The stalked barnacle Pollicipes pollicipes inhabits rocky shores from the Atlantic coasts of Brittany (France) to Senegal. Because of the culinary traditions of southern Europe, stalked barnacles represent an important target species for local fisheries on the Iberian Peninsula. To manage this fishery sustainably, it is therefore important to assess the dynamics of local populations over the Iberian coast, and how they are interconnected at a wider scale using finely tuned genetic markers. In this work, a new enriched library of GT microsatellites for P. pollicipes was prepared and sequenced using Ion TorrentTM Next Gen-Sequencing Technology. 1,423 adults and juveniles were sampled in 15 localities of three geographic regions: southern Portugal, Galicia and Asturias (both in northern Spain). Twenty polymorphic loci arranged in five multiplex PCRs were then tested and validated as new molecular tools to address the spatial and temporal genetic patterns of P. pollicipes. Our results revealed high genetic diversity among adults. However, juveniles were genetically more structured than their adult counterparts, which alternatively displayed much more connectivity among the three studied regions. The lack of spatial genetic heterogeneity in adults may be due to the overlapping of several generations of settlers coming from different geographic origins, which mainly depends on the orientation of residual currents along the coast during reproduction. The genetic differentiation of juveniles may indeed be congruent with Iberian Peninsula hydrodynamics, which can produce chaotic genetic patchiness (CGP) at small temporal scales due to sweepstake reproductive success, collective dispersal and/or self-recruitment. Remarkably, most of the genetic heterogeneity of juveniles found in this work was located in Galicia, which could represent an admixture between distinct metapopulations or an old refuge for the most northern populations. To conclude, high genetic variation in P. pollicipes can lead to the false impression of population panmixia at the Iberian scale by masking more restricted and current-driven larval exchanges between regions. This possibility should be taken into consideration for further specific management and conservation plans for the species over the Iberian Peninsula

New insights on the population genetic structure of the great scallop (Pecten maximus) in the English Channel coupling microsatellite data and demogenetic simulations.

International audienceThe great scallop (Pecten maximus) is a commercially important bivalve in Europe, particularly in the English Channel, where fisheries are managed at regional and local scales through the regulation of fishing effort. In the long term, knowledge about larval dispersal and gene flow between populations is essential to ensure proper stock management. Yet, previous population genetic studies have reported contradictory results. In this study, scallop samples collected across the main fishing grounds along the French and English coasts of the English Channel (20 samples with temporal replicates for three sites,n= 1059 individuals), and the population genetic structure was analysed using 13 microsatellite loci. Coupling empirical genetic data with demogenetic modelling based on a biophysical model simulating larval exchanges among scallop beds revealed a subtle genetic differentiation between south-west English populations and the rest of the English Channel, which was consistent with larval dispersal simulations. The present study provides a step forward in the understanding of great scallop population biology in the English Channel, underlining the fact that even in a context of potentially high gene flow and recent divergence times since the end of the last glacial maximum, weak but significant spatial genetic structure can be identified at a regional scale

Direct constraint on the distance of y2 Velorum from AMBER/VLTI observations

In this work, we present the first AMBER observations, of the Wolf-Rayet and O (WR+O) star binary system y2 Velorum. The AMBER instrument was used with the telescopes UT2, UT3, and UT4 on baselines ranging from 46m to 85m. It delivered spectrally dispersed visibilities, as well as differential and closure phases, with a resolution R = 1500 in the spectral band 1.95-2.17 micron. We interpret these data in the context of a binary system with unresolved components, neglecting in a first approximation the wind-wind collision zone flux contribution. We show that the AMBER observables result primarily from the contribution of the individual components of the WR+O binary system. We discuss several interpretations of the residuals, and speculate on the detection of an additional continuum component, originating from the free-free emission associated with the wind-wind collision zone (WWCZ), and contributing at most to the observed K-band flux at the 5% level. The expected absolute separation and position angle at the time of observations were 5.1±0.9mas and 66±15° respectively. However, we infer a separation of 3.62+0.11-0.30 mas and a position angle of 73+9-11°. Our analysis thus implies that the binary system lies at a distance of 368+38-13 pc, in agreement with recent spectrophotometric estimates, but significantly larger than the Hipparcos value of 258+41-31 pc

Heterogeneity in outcomes of treated HIV-positive patients in Europe and North America: relation with patient and cohort characteristics

Background HIV cohort collaborations, which pool data from diverse patient cohorts, have provided key insights into outcomes of antiretroviral therapy (ART). However, the extent of, and reasons for, between-cohort heterogeneity in rates of AIDS and mortality are unclear. Methods We obtained data on adult HIV-positive patients who started ART from 1998 without a previous AIDS diagnosis from 17 cohorts in North America and Europe. Patients were followed up from 1 month to 2 years after starting ART. We examined between-cohort heterogeneity in crude and adjusted (age, sex, HIV transmission risk, year, CD4 count and HIV-1 RNA at start of ART) rates of AIDS and mortality using random-effects meta-analysis and meta-regression. Results During 61 520 person-years, 754/38 706 (1.9%) patients died and 1890 (4.9%) progressed to AIDS. Between-cohort variance in mortality rates was reduced from 0.84 to 0.24 (0.73 to 0.28 for AIDS rates) after adjustment for patient characteristics. Adjusted mortality rates were inversely associated with cohorts' estimated completeness of death ascertainment [excellent: 96-100%, good: 90-95%, average: 75-89%; mortality rate ratio 0.66 (95% confidence interval 0.46-0.94) per category]. Mortality rate ratios comparing Europe with North America were 0.42 (0.31-0.57) before and 0.47 (0.30-0.73) after adjusting for completeness of ascertainment. Conclusions Heterogeneity between settings in outcomes of HIV treatment has implications for collaborative analyses, policy and clinical care. Estimated mortality rates may require adjustment for completeness of ascertainment. Higher mortality rate in North American, compared with European, cohorts was not fully explained by completeness of ascertainment and may be because of the inclusion of more socially marginalized patients with higher mortality ris

Pharmacokinetic/pharmacodynamic modelling approaches in paediatric infectious diseases and immunology.

Pharmacokinetic/pharmacodynamic (PKPD) modelling is used to describe and quantify dose-concentration-effect relationships. Within paediatric studies in infectious diseases and immunology these methods are often applied to developing guidance on appropriate dosing. In this paper, an introduction to the field of PKPD modelling is given, followed by a review of the PKPD studies that have been undertaken in paediatric infectious diseases and immunology. The main focus is on identifying the methodological approaches used to define the PKPD relationship in these studies. The major findings were that most studies of infectious diseases have developed a PK model and then used simulations to define a dose recommendation based on a pre-defined PD target, which may have been defined in adults or in vitro. For immunological studies much of the modelling has focused on either PK or PD, and since multiple drugs are usually used, delineating the relative contributions of each is challenging. The use of dynamical modelling of in vitro antibacterial studies, and paediatric HIV mechanistic PD models linked with the PK of all drugs, are emerging methods that should enhance PKPD-based recommendations in the future

Imaging the heart of astrophysical objects with optical long-baseline interferometry

The number of publications of aperture-synthesis images based on optical long-baseline interferometry measurements has recently increased due to easier access to visible and infrared interferometers. The interferometry technique has now reached a technical maturity level that opens new avenues for numerous astrophysical topics requiring milli-arcsecond model-independent imaging. In writing this paper our motivation was twofold: 1) review and publicize emblematic excerpts of the impressive corpus accumulated in the field of optical interferometry image reconstruction; 2) discuss future prospects for this technique by selecting four representative astrophysical science cases in order to review the potential benefits of using optical long baseline interferometers. For this second goal we have simulated interferometric data from those selected astrophysical environments and used state-of-the-art codes to provide the reconstructed images that are reachable with current or soon-to-be facilities. The image reconstruction process was "blind" in the sense that reconstructors had no knowledge of the input brightness distributions. We discuss the impact of optical interferometry in those four astrophysical fields. We show that image reconstruction software successfully provides accurate morphological information on a variety of astrophysical topics and review the current strengths and weaknesses of such reconstructions. We investigate how to improve image reconstruction and the quality of the image possibly by upgrading the current facilities. We finally argue that optical interferometers and their corresponding instrumentation, existing or to come, with 6 to 10 telescopes, should be well suited to provide images of complex sceneries.Comment: Acccepted to Astronomy and Astrophysics Revie