Recent advances in remote sensing image processing

Remote sensing image processing is nowadays a mature research area. The techniques developed in the field allow many real-life applications with great societal value. For instance, urban monitoring, fire detection or flood prediction can have a great impact on economical and environmental issues. To attain such objectives, the remote sensing community has turned into a multidisciplinary field of science that embraces physics, signal theory, computer science, electronics, and communications. From a machine learning and signal/image processing point of view, all the applications are tackled under specific formalisms, such as classification and clustering, regression and function approximation, image coding, restoration and enhancement, source unmixing, data fusion or feature selection and extraction. This paper serves as a survey of methods and applications, and reviews the last methodological advances in remote sensing image processing.

Model-based iterative reconstruction in pediatric chest CT: assessment of image quality in a prospective study of children with cystic fibrosis.

BACKGROUND: The potential effects of ionizing radiation are of particular concern in children. The model-based iterative reconstruction VEO(TM) is a technique commercialized to improve image quality and reduce noise compared with the filtered back-projection (FBP) method. OBJECTIVE: To evaluate the potential of VEO(TM) on diagnostic image quality and dose reduction in pediatric chest CT examinations. MATERIALS AND METHODS: Twenty children (mean 11.4 years) with cystic fibrosis underwent either a standard CT or a moderately reduced-dose CT plus a minimum-dose CT performed at 100 kVp. Reduced-dose CT examinations consisted of two consecutive acquisitions: one moderately reduced-dose CT with increased noise index (NI = 70) and one minimum-dose CT at CTDIvol 0.14 mGy. Standard CTs were reconstructed using the FBP method while low-dose CTs were reconstructed using FBP and VEO. Two senior radiologists evaluated diagnostic image quality independently by scoring anatomical structures using a four-point scale (1 = excellent, 2 = clear, 3 = diminished, 4 = non-diagnostic). Standard deviation (SD) and signal-to-noise ratio (SNR) were also computed. RESULTS: At moderately reduced doses, VEO images had significantly lower SD (P < 0.001) and higher SNR (P < 0.05) in comparison to filtered back-projection images. Further improvements were obtained at minimum-dose CT. The best diagnostic image quality was obtained with VEO at minimum-dose CT for the small structures (subpleural vessels and lung fissures) (P < 0.001). The potential for dose reduction was dependent on the diagnostic task because of the modification of the image texture produced by this reconstruction. CONCLUSIONS: At minimum-dose CT, VEO enables important dose reduction depending on the clinical indication and makes visible certain small structures that were not perceptible with filtered back-projection.

Isolated disturbance of written language-acquisition as an initial symptom of epileptic aphasia in a 7-year-old child - a 3-year follow-up-study

A 7-year-old right-handed girl developed partial complex seizures with a left-sided onset. A brief period of post-ictal aphasia of the conduction type was documented before seizure control and complete normalization of oral language were obtained. We also found that she had a history of previous unexplained difficulty with written language acquisition that had occurred prior to the clinically recognized epilepsy and a subsequent loss of this ability. This rapidly improved with control of the epilepsy. The evolution of written language were been followed for 3 years, and continued improvement has occurred with fluctuations related to her epilepsy. This observation adds support to the growing body of data indicating that specific cognitive disturbances can be due to epilepsy in young children. It shows the vulnerability of skills which are in a period of active development, and the possibility that oral/written language can be differentially involved by cerebral dysfunction in the young child.

Surface reconstruction from microscopic images in optical lithography.

This paper presents a method to reconstruct 3D surfaces of silicon wafers from 2D images of printed circuits taken with a scanning electron microscope. Our reconstruction method combines the physical model of the optical acquisition system with prior knowledge about the shapes of the patterns in the circuit; the result is a shape-from-shading technique with a shape prior. The reconstruction of the surface is formulated as an optimization problem with an objective functional that combines a data-fidelity term on the microscopic image with two prior terms on the surface. The data term models the acquisition system through the irradiance equation characteristic of the microscope; the first prior is a smoothness penalty on the reconstructed surface, and the second prior constrains the shape of the surface to agree with the expected shape of the pattern in the circuit. In order to account for the variability of the manufacturing process, this second prior includes a deformation field that allows a nonlinear elastic deformation between the expected pattern and the reconstructed surface. As a result, the minimization problem has two unknowns, and the reconstruction method provides two outputs: 1) a reconstructed surface and 2) a deformation field. The reconstructed surface is derived from the shading observed in the image and the prior knowledge about the pattern in the circuit, while the deformation field produces a mapping between the expected shape and the reconstructed surface that provides a measure of deviation between the circuit design models and the real manufacturing process.

Can MRI replace CT in evaluating semicircular canal dehiscence?

BACKGROUND AND PURPOSE: Patients with symptoms of semicircular canal dehiscence often undergo both CT and MR imaging. We assessed whether FIESTA can replace temporal bone CT in evaluating patients for SC dehiscence. MATERIALS AND METHODS: We retrospectively reviewed 112 consecutive patients (224 ears) with vestibulocochlear symptoms who underwent concurrent MR imaging and CT of the temporal bones between 2007 and 2009. MR imaging protocol included a FIESTA sequence covering the temporal bone (axial 0.8-mm section thickness, 0.4-mm spacing, coronal/oblique reformations; 41 patients at 1.5T, 71 patients at 3T). CT was performed on a 64-row multidetector row scanner (0.625-mm axial acquisition, with coronal/oblique reformations). Both ears of each patient were evaluated for dehiscence of the superior and posterior semicircular canals in consensual fashion by 2 neuroradiologists. Analysis of the FIESTA sequence and reformations was performed first for the MR imaging evaluation. CT evaluation was performed at least 2 weeks after the MR imaging review, resulting in a blinded comparison of CT with MR imaging. CT was used as the reference standard to evaluate the MR imaging results. RESULTS: For SSC dehiscence, MR imaging sensitivity was 100%, specificity was 96.5%, positive predictive value was 61.1%, and negative predictive value was 100% in comparison with CT. For PSC dehiscence, MR imaging sensitivity was 100%, specificity was 99.1%, positive predictive value was 33.3%, and negative predictive value was 100% in comparison with CT. CONCLUSIONS: MR imaging, with a sensitivity and negative predictive value of 100%, conclusively excludes SSC or PSC dehiscence. Negative findings on MR imaging preclude the need for CT to detect SC dehiscence. Only patients with positive findings on MR imaging should undergo CT evaluation.

Étude des sédiments quaternaires, de la molasse et sa tectonique, dans le Grand Lac (Léman) à partir de données sismiques 2D et 3D

RESUME L'Institut de Géophysique de l'Université de Lausanne a développé au cours de ces dernières années un système d'acquisition de sismique réflexion multitrace à haute résolution 2D et 3D. L'objectif de cette thèse était de poursuivre ce développement tout améliorant les connaissances de la géologie sous le lac Léman, en étudiant en particulier la configuration des grands accidents sous-lacustres dans la Molasse (Tertiaire) qui forme l'essentiel du substratum des formations quaternaires. En configuration 2D, notre système permet d'acquérir des profils sismiques avec une distance inter-CDP de 1,25 m. La couverture varie entre 6 et 18 selon le nombre de traces et la distance inter-tir. Le canon à air (15/15 eu. in.), offre une résolution verticale de 1,25 ni et une pénétration maximale de 300 m sous le fond de l'eau. Nous avons acquis au total plus de 400 km de sections 2D dans le Grand Lac et le Haut Lac entre octobre 2000 et juillet 2004. Une campagne de sismique 3D a fourni des données au large d'Evian sur une surface de 442,5 m sur 1450 m, soit 0,64 km2. La navigation ainsi que le positionnement des hydrophones et de la source ont été réalisés avec des GPS différentiels. Nous avons utilisé un traitement sismique conventionnel, sans appliquer d'AGC et en utilisant une migration post-stack. L'interprétation du substratum antéquaternaire est basée sur l'identification des sismofaciès, sur leurs relations avec les unités géologiques adjacentes au lac, ainsi que sur quelques données de forages. Nous obtenons ainsi une carte des unités géologiques dans le Grand Lac. Nous précisons la position du chevauchement subalpin entre la ville de Lausanne, sur la rive nord, et le bassin de Sciez, sur la rive sud. Dans la Molasse de Plateau, nous avons identifié les décrochements de Pontarlier et de St. Cergue ainsi que plusieurs failles non reconnues jusqu'ici. Nous avons cartographié les accidents qui affectent la Molasse subalpine ainsi que le plan de chevauchement du flysch sur la Molasse près de la rive sud du lac. Une nouvelle carte tectonique de la région lémanique a ainsi pu être dressée. L'analyse du substratum ne montre pas de failles suggérant une origine tectonique de la cuvette lémanique. Par contre, nous suggérons que la forme du creusement glaciaire, donc de la forme du lac Léman, a été influencée par la présence de failles dans le substratum antéquaternaire. L'analyse des sédiments quaternaires nous a permis de tracer des cartes des différentes interfaces ou unités qui les composent. La carte du toit du substratum antéquaternaire montre la présence de chenaux d'origine glaciaire dont la profondeur maximale atteint la cote -200 ni. Leur pente est dirigée vers le nord-est, à l'inverse du sens d'écoulement actuel des eaux. Nous expliquons cette observation par l'existence de circulations sous-glaciaires d'eau artésienne. Les sédiments glaciaires dont l'épaisseur maximale atteint 150 ni au centre du lac ont enregistré les différentes récurrences glaciaires. Dans la zone d'Evian, nous mettons en évidence la présence de lentilles de sédiments glaciolacustres perchées sur le flanc de la cuvette lémanique. Nous avons corrélé ces unités avec des données de forage et concluons qu'il s'agit du complexe inférieur de la pile sédimentaire d'Evian. Celui-ci, âgé de plus de 30 000 ans, serait un dépôt de Kame associé à un lac périglaciaire. La sismique réflexion 3D permet de préciser l'orientation de l'alimentation en matériel détritique de l'unité. La finesse des images obtenues nous permet également d'établir quels types d'érosion ont affecté certaines unités. Les sédiments lacustres, dont l'épaisseur maximale imagée atteint plus de 225 m et sans doute 400 ni sous le delta du Rhône, indiquent plusieurs mécanismes de dépôts. A la base, une mégaturbidite, épaisse d'une trentaine de mètres en moyenne, s'étend entre l'embouchure de la Dranse et le delta du Rhône. Au-dessus, la décantation des particules en suspension d'origine biologique et détritique fournit l'essentiel des sédiments. Dans la partie orientale du lac, les apports détritiques du Rhône forment un delta qui prograde vers l'ouest en s'imbriquant avec les sédiments déposés par décantation. La structure superficielle du delta a brutalement évolué, probablement à la suite de l'évènement catastrophique du Tauredunum (563 A.D.). Sa trace probable se marque par la présence d'une surface érosive que nous avons cartographiée. Le delta a ensuite changé de géométrie, avec notamment un déplacement des chenaux sous-lacustres. Sur l'ensemble de nos sections sismiques, nous n'observons aucune faille dans les sédiments quaternaires qui attesterait d'une tectonique postglaciaire du substratum. ABSTRACT During the last few years the institute of Geophysics of the University of Lausanne cleveloped a 2D and 3D high-resolution multichannel seismic reflection acquisition system. The objective of the present work was to carry on this development white improving our knowledge of the geology under Lake Geneva, in particular by studying the configuration of the large accidents affecting the Tertiary Molasse that makes up the basement of most Quaternary deposits. In its 2D configuration, our system makes it possible to acquire seismic profiles with a CDP interval of 1.25 m. The fold varies from 6 to 18 depending on the number of traces and the shooting interval. Our air gun (15/15 cu. in.) provides a vertical resolution of 1.25 m and a maximum penetration depth of approximately 300 m under water bottom. We acquired more than 400 km of 2D sections in the Grand Lac and the Haut Lac between October 2000 and July 2004. A 3D seismic survey off the city of Evian provided data on a surface of 442.5 m x 1450 m (0.64 km2). Ship's navigation as well as hydrophone- and source positioning were carried out with differential GPS. The seismic data were processed following a conventional sequence without .applying AGC and using post-stack migration. The interpretation of the pre-Quaternary substratum is based on sismofacies, on their relationships with terrestrial geological units and on some borehole data. We thus obtained a map of the geological units in the Grand Lac. We defined the location of the subalpine thrust from Lausanne, on the north shore, to the Sciez Basin, on the south shore. Within the Molasse de Plateau, we identified the already know Pontarlier and St Cergue transforms Fault as well as faults. We mapped faults that affect subalpine Molasse as well as the thrust fault plane between alpine flysch and Molasse near the lake's south shore. A new tectonic map of the Lake Geneva region could thus be drawn up. The substratum does not show faults indicating a tectonic origin for the Lake Geneva Basin. However, we suggest that the orientation of glacial erosion, and thus the shape of Lake Geneva, vas influenced by the presence of faults in the pre-Quaternary basement. The analysis of Quaternary sediments enabled us to draw up maps of various discontinuities or internal units. The top pre-Quaternary basement map shows channels of glacial origin, the deepest of them reaching an altitude of 200 m a.s.l. The channel's slopes are directed to the North-East, in opposite direction of the present water flow. We explain this observation by the presence of artesian subglacial water circulation. Glacial sediments, the maximum thickness of which reaches 150 m in the central part of the lake, record several glacial recurrences. In the Evian area, we found lenses of glacio-lacustrine sediments set high up on the flank of the Lake Geneva Bassin. We correlated these units with on-land borehole data and concluded that they represent the lower complex of the Evian sedimentary pile. The lower complex is aider than 30 000 years, and it could be a Kame deposit associated with a periglacial lake. Our 3D seismic reflexion survey enables us to specify the supply direction of detrital material in this unit. With detailed seismic images we established how some units were affected by different erosion types. The lacustrine sediments we imaged in Lake Geneva are thicker than 225 m and 400 m or more Linder the Rhone Delta. They indicate several depositional mechanisms. Their base is a major turbidite, thirty meters thick on average, that spreads between the Dranse mouth and the Rhone delta. Above this unit, settling of suspended biological and detrital particles provides most of the sediments. In the eastern part of the lake, detrital contribution from the Rhone builds a delta that progrades to the west and imbricates with the settling sediments. The shallow structure of the Rhone delta abruptly evolved, probably after the catastrophic Tauredunum event (563 A.D.). It probably coincides with an erosive surface that we mapped. As a result, the delta geometry changed, in particular associated with a displacement of water bottom channels. In all our seismic sections, we do not observe fault in the Quaternary sediments that would attest postglacial tectonic activity in the basement.

Basic life support teaching in the second year predraduate medical curriculum: quality of acquisition after 6 months

Purpose of the study: Basic life support (BLS) and automated externaldefibrillation (AED) represent important skills to be acquired duringpregraduate medical training. Since 3 years, our medical school hasintroduced a BLS-AED course (with certification) for all second yearmedical students. Few reports about quality and persistence over timeof BLS-AED learning are available to date in the medical literature.Comprehensive evaluation of students' acquired skills was performedat the end of the 2008 academic year, 6 month after certification.Materials and methods: The students (N = 142) were evaluated duringa 9 minutes «objective structured clinical examination» (OSCE) station.Out of a standardized scenario, they had to recognize a cardiac arrestsituation and start a resuscitation process. Their performance wererecorded on a PC using an Ambuman(TM) mannequin and the AmbuCPR software kit(TM) during a minimum of 8 cycles (30 compressions:2 ventilations each). BLS parameters were systematically checked. Nostudent-rater interactions were allowed during the whole evaluation.Results: Response of the victim was checked by 99% of the students(N = 140), 96% (N = 136) called for an ambulance and/or an AED. Openthe airway and check breathing were done by 96% (N = 137), 92% (N =132) gave 2 rescue breaths. Pulse was checked by 95% (N=135), 100%(N = 142) begun chest compression, 96% (N = 136) within 1 minute.Chest compression rate was 101 ± 18 per minute (mean ± SD), depthcompression 43 ± 8 mm, 97% (N = 138) respected a compressionventilationratio of 30:2.Conclusions: Quality of BLS skills acquisition is maintained during a6-month period after a BLS-AED certification. Main targets of 2005 AHAguidelines were well respected. This analysis represents one of thelargest evaluations of specific BLS teaching efficiency reported. Furtherfollow-up is needed to control the persistence of these skills during alonger time period and noteworthy at the end of the pregraduatemedical curriculum.

Language Resources Factory: case study on the acquisition of Translation Memories

This paper demonstrates a novel distributed architecture to facilitate the acquisition of Language Resources. We build a factory that automates the stages involved in the acquisition, production, updating and maintenance of these resources. The factory is designed as a platform where functionalities are deployed as web services, which can be combined in complex acquisition chains using workflows. We show a case study, which acquires a Translation Memory for a given pair of languages and a domain using web services for crawling, sentence alignment and conversion to TMX.

Human-to-bovine jump of Staphylococcus aureus CC8 is associated with the loss of a β-hemolysin converting prophage and the acquisition of a new staphylococcal cassette chromosome.

Staphylococcus aureus can colonize and infect both humans and animals, but isolates from both hosts tend to belong to different lineages. Our recent finding of bovine-adapted S. aureus showing close genetic relationship to the human S. aureus clonal complex 8 (CC8) allowed us to examine the genetic basis of host adaptation in this particular CC. Using total chromosome microarrays, we compared the genetic makeup of 14 CC8 isolates obtained from cows suffering subclinical mastitis, with nine CC8 isolates from colonized or infected human patients, and nine S. aureus isolates belonging to typical bovine CCs. CC8 isolates were found to segregate in a unique group, different from the typical bovine CCs. Within this CC8 group, human and bovine isolates further segregated into three subgroups, among which two contained a mix of human and bovine isolates, and one contained only bovine isolates. This distribution into specific clusters and subclusters reflected major differences in the S. aureus content of mobile genetic elements (MGEs). Indeed, while the mixed human-bovine clusters carried commonly human-associated β-hemolysin converting prophages, the bovine-only isolates were devoid of such prophages but harbored an additional new non-mec staphylococcal cassette chromosome (SCC) unique to bovine CC8 isolates. This composite cassette carried a gene coding for a new LPXTG-surface protein sharing homologies with a protein found in the environmental bacterium Geobacillus thermoglucosidans. Thus, in contrast to human CC8 isolates, the bovine-only CC8 group was associated with the combined loss of β-hemolysin converting prophages and gain of a new SCC probably acquired in the animal environment. Remaining questions are whether the new LPXTG-protein plays a role in bovine colonization or infection, and whether the new SCC could further acquire antibiotic-resistance genes and carry them back to human.

Kernel-based Mapping of Meteorological Fields in Complex Orography

Due to the advances in sensor networks and remote sensing technologies, the acquisition and storage rates of meteorological and climatological data increases every day and ask for novel and efficient processing algorithms. A fundamental problem of data analysis and modeling is the spatial prediction of meteorological variables in complex orography, which serves among others to extended climatological analyses, for the assimilation of data into numerical weather prediction models, for preparing inputs to hydrological models and for real time monitoring and short-term forecasting of weather.In this thesis, a new framework for spatial estimation is proposed by taking advantage of a class of algorithms emerging from the statistical learning theory. Nonparametric kernel-based methods for nonlinear data classification, regression and target detection, known as support vector machines (SVM), are adapted for mapping of meteorological variables in complex orography.With the advent of high resolution digital elevation models, the field of spatial prediction met new horizons. In fact, by exploiting image processing tools along with physical heuristics, an incredible number of terrain features which account for the topographic conditions at multiple spatial scales can be extracted. Such features are highly relevant for the mapping of meteorological variables because they control a considerable part of the spatial variability of meteorological fields in the complex Alpine orography. For instance, patterns of orographic rainfall, wind speed and cold air pools are known to be correlated with particular terrain forms, e.g. convex/concave surfaces and upwind sides of mountain slopes.Kernel-based methods are employed to learn the nonlinear statistical dependence which links the multidimensional space of geographical and topographic explanatory variables to the variable of interest, that is the wind speed as measured at the weather stations or the occurrence of orographic rainfall patterns as extracted from sequences of radar images. Compared to low dimensional models integrating only the geographical coordinates, the proposed framework opens a way to regionalize meteorological variables which are multidimensional in nature and rarely show spatial auto-correlation in the original space making the use of classical geostatistics tangled.The challenges which are explored during the thesis are manifolds. First, the complexity of models is optimized to impose appropriate smoothness properties and reduce the impact of noisy measurements. Secondly, a multiple kernel extension of SVM is considered to select the multiscale features which explain most of the spatial variability of wind speed. Then, SVM target detection methods are implemented to describe the orographic conditions which cause persistent and stationary rainfall patterns. Finally, the optimal splitting of the data is studied to estimate realistic performances and confidence intervals characterizing the uncertainty of predictions.The resulting maps of average wind speeds find applications within renewable resources assessment and opens a route to decrease the temporal scale of analysis to meet hydrological requirements. Furthermore, the maps depicting the susceptibility to orographic rainfall enhancement can be used to improve current radar-based quantitative precipitation estimation and forecasting systems and to generate stochastic ensembles of precipitation fields conditioned upon the orography.

Sample size for measurement of root traits on common bean by image analysis

Evaluation of root traits may be facilitated if they are assessed on samples of the root system. The objective of this work was to determine the sample size of the root system in order to estimate root traits of common bean (Phaseolus vulgaris L.) cultivars by digital image analysis. One plant was grown per pot and harvested at pod setting, with 64 and 16 pots corresponding to two and four cultivars in the first and second experiments, respectively. Root samples were scanned up to the completeness of the root system and the root area and length were estimated. Scanning a root sample demanded 21 minutes, and scanning the entire root system demanded 4 hours and 53 minutes. In the first experiment, root area and length estimated with two samples showed, respectively, a correlation of 0.977 and 0.860, with these traits measured in the entire root. In the second experiment, the correlation was 0.889 and 0.915. The increase in the correlation with more than two samples was negligible. The two samples corresponded to 13.4% and 16.9% of total root mass (excluding taproot and nodules) in the first and second experiments. Taproot stands for a high proportion of root mass and must be deducted on root trait estimations. Samples with nearly 15% of total root mass produce reliable root trait estimates.