Reconstruction active par projection de lumière non structurée

Cette thèse porte sur la reconstruction active de modèles 3D à l’aide d’une caméra et d’un projecteur. Les méthodes de reconstruction standards utilisent des motifs de lumière codée qui ont leurs forces et leurs faiblesses. Nous introduisons de nouveaux motifs basés sur la lumière non structurée afin de pallier aux manques des méthodes existantes. Les travaux présentés s’articulent autour de trois axes : la robustesse, la précision et finalement la comparaison des patrons de lumière non structurée aux autres méthodes. Les patrons de lumière non structurée se différencient en premier lieu par leur robustesse aux interréflexions et aux discontinuités de profondeur. Ils sont conçus de sorte à homogénéiser la quantité d’illumination indirecte causée par la projection sur des surfaces difficiles. En contrepartie, la mise en correspondance des images projetées et capturées est plus complexe qu’avec les méthodes dites structurées. Une méthode d’appariement probabiliste et efficace est proposée afin de résoudre ce problème. Un autre aspect important des reconstructions basées sur la lumière non structurée est la capacité de retrouver des correspondances sous-pixels, c’est-à-dire à un niveau de précision plus fin que le pixel. Nous présentons une méthode de génération de code de très grande longueur à partir des motifs de lumière non structurée. Ces codes ont l’avantage double de permettre l’extraction de correspondances plus précises tout en requérant l’utilisation de moins d’images. Cette contribution place notre méthode parmi les meilleures au niveau de la précision tout en garantissant une très bonne robustesse. Finalement, la dernière partie de cette thèse s’intéresse à la comparaison des méthodes existantes, en particulier sur la relation entre la quantité d’images projetées et la qualité de la reconstruction. Bien que certaines méthodes nécessitent un nombre constant d’images, d’autres, comme la nôtre, peuvent se contenter d’en utiliser moins aux dépens d’une qualité moindre. Nous proposons une méthode simple pour établir une correspondance optimale pouvant servir de référence à des fins de comparaison. Enfin, nous présentons des méthodes hybrides qui donnent de très bons résultats avec peu d’images.

A New Gridding Technique for High Density Microarray Images Using Intensity Projection Profile of Best Sub Image

As the technologies for the fabrication of high quality microarray advances rapidly, quantification of microarray data becomes a major task. Gridding is the first step in the analysis of microarray images for locating the subarrays and individual spots within each subarray. For accurate gridding of high-density microarray images, in the presence of contamination and background noise, precise calculation of parameters is essential. This paper presents an accurate fully automatic gridding method for locating suarrays and individual spots using the intensity projection profile of the most suitable subimage. The method is capable of processing the image without any user intervention and does not demand any input parameters as many other commercial and academic packages. According to results obtained, the accuracy of our algorithm is between 95-100% for microarray images with coefficient of variation less than two. Experimental results show that the method is capable of gridding microarray images with irregular spots, varying surface intensity distribution and with more than 50% contamination

On the relationship between the Method of Least Squares and Gram-Schmidt orthogonalization

The method of Least Squares is due to Carl Friedrich Gauss. The Gram-Schmidt orthogonalization method is of much younger date. A method for solving Least Squares Problems is developed which automatically results in the appearance of the Gram-Schmidt orthogonalizers. Given these orthogonalizers an induction-proof is available for solving Least Squares Problems.

Overview of coded light projection techniques for automatic 3D profiling

Obtaining automatic 3D profile of objects is one of the most important issues in computer vision. With this information, a large number of applications become feasible: from visual inspection of industrial parts to 3D reconstruction of the environment for mobile robots. In order to achieve 3D data, range finders can be used. Coded structured light approach is one of the most widely used techniques to retrieve 3D information of an unknown surface. An overview of the existing techniques as well as a new classification of patterns for structured light sensors is presented. This kind of systems belong to the group of active triangulation method, which are based on projecting a light pattern and imaging the illuminated scene from one or more points of view. Since the patterns are coded, correspondences between points of the image(s) and points of the projected pattern can be easily found. Once correspondences are found, a classical triangulation strategy between camera(s) and projector device leads to the reconstruction of the surface. Advantages and constraints of the different patterns are discussed

An overview of the advantages and constraints of coded pattern projection techniques for autonomous navigation

The absolute necessity of obtaining 3D information of structured and unknown environments in autonomous navigation reduce considerably the set of sensors that can be used. The necessity to know, at each time, the position of the mobile robot with respect to the scene is indispensable. Furthermore, this information must be obtained in the least computing time. Stereo vision is an attractive and widely used method, but, it is rather limited to make fast 3D surface maps, due to the correspondence problem. The spatial and temporal correspondence among images can be alleviated using a method based on structured light. This relationship can be directly found codifying the projected light; then each imaged region of the projected pattern carries the needed information to solve the correspondence problem. We present the most significant techniques, used in recent years, concerning the coded structured light method

Immersive Projection for biochemical pattern matching

In all biological processes, protein molecules and other small molecules interact to function and form transient macromolecular complexes. This interaction of two or more molecules can be described by a docking event. Docking is an important phase for structure-based drug design strategies, as it can be used as a method to simulate protein-ligand interactions. Various docking programs exist that allow automated docking, but most of them have limited visualization and user interaction. It would be advantageous if scientists could visualize the molecules participating in the docking process, manipulate their structures and manually dock them before submitting the new conformations to an automated docking process in an immersive environment, which can help stimulate the design/docking process. This also could greatly reduce docking time and resources. To achieve this, we propose a new virtual modelling/docking program, whereby the advantages of virtual modelling programs and the efficiency of the algorithms in existing docking programs will be merged.

Near threshold vibrational excitation of molecules by positron impact: A projection operator approach

We report vibrational excitation (v(i) = 0 -> v(f) = 1) cross-sections for positron scattering by H(2) and model calculations for the (v(i) = 0 -> v(f) = 1) excitation of the C-C symmetric stretch mode of C(2)H(2). The Feshbach projection operator formalism was employed to vibrationally resolve the fixed-nuclei phase shifts obtained with the Schwinger multichannel method. The near threshold behavior of H(2) and C(2)H(2) significantly differ in the sense that no low lying singularity (either virtual or bound state) was found for the former, while a e(+)-acetylene virtual state was found at the equilibrium geometry (this virtual state becomes a bound state upon stretching the molecule). For C(2)H(2), we also performed model calculations comparing excitation cross-sections arising from virtual (-i kappa(0)) and bound (+i kappa(0)) states symmetrically located around the origin of the complex momentum plane (i.e. having the same kappa(0)). The virtual state is seen to significantly couple to vibrations, and similar cross-sections were obtained for shallow bound and virtual states. (c) 2007 Elsevier B.V. All rights reserved.

New class of spin projection operators for 3D models

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Surface reconstruction using multiple light sources and perspective projection

This paper presents a method to recover 3D geometry of Lambertian surfaces by using multiple images taken from the same view point and with the scene illuminated from different positions. This approach differs from Stereo Photometry in that it considers the light source at a finite distance from the object and the perspective projection in image formation. The proposed model allows local solution and recovery of 3D coordinates, in addition to surface orientation. A procedure to calibrate the light sources is also presented. Results of the application of the algorithm to synthetic images are shown.

A method for the geometric standardization of intraoral radiographs for long-term follow up of replanted teeth: A case report

The interpretation of the set of radiographs taken during the follow-up period after tooth replantation might pose several difficulties, especially the inability to adequately reproduce the projection geometry of the exposures. This article describes a method for the geometric standardization of intraoral radiographs using a custom-made apparatus comprising a film-holder attached to an occlusal splint for the long-term follow up of dentoalveolar trauma. The method was applied in a patient who suffered an avulsion of the maxillary central incisors and had the teeth replanted after 4 h in saline storage. Endodontic treatment started 7 days after the trauma with changes of a calcium hydroxide intracanal medication every 15 days in the first 2 months and thereafter at 30-day intervals for 8 months. Root canal filling was carried out after this period. The radiographic exposures taken at the follow-up visits were standardized to identify the possible alterations during the repair process, such as root resorptions. A maxillary arch impression was made with alginate, and the model was cast in stone for fabrication of an acetate occlusal splint. The custom-made apparatus used for standardization of the radiographic exposures was fabricated by fixing a Rinn X-C-P film-holder and a 5-mm-long piece of 0.7-mm orthodontic wire to the occlusal splint with autopolymerized acrylic resin. Radiographs were taken at 4-month intervals, starting 10 months after replantation up to 76 months. The images were digitized and analysed using the Digora system. The length of the central incisors was determined to verify the reproduction of the projection geometry of the exposures and the orthodontic wire served to assess accuracy during length estimations in the radiographs. The method described in this article for geometric standardization of intraoral radiographs provided a consistent reproduction of the geometric exposure parameters, being indicated for use in the radiographic follow up of cases of dentoalveolar trauma. © 2012 John Wiley & Sons A/S.

Utilization of fringe projection technique for evaluation of wound dimensions and of healing progress.

Background: The methods used for evaluating wound dimensions, especially the chronic ones, are invasive and inaccurate. The fringe projection technique with phase shift is a non-invasive, accurate and low-cost optical method. Objective: The aim is to validate the technique through the determination of dimensions of objects of known topography and with different geometries and colors to simulate the wounds and tones of skin color. Taking into account the influence of skin wound optical factors, the technique will be used to evaluate actual patients’ wound dimensions and to study its limitations in this application. Methods: Four sinusoidal fringe patterns, displaced ¼ of period each, were projected onto the objects surface. The object dimensions were obtained from the unwrapped phase map through the observation of the fringe deformations caused by the object topography and using phase shift analysis. An object with simple geometry was used for dimensional calibration and the topographic dimensions of the others were determined from it. After observing the compatibility with the data and validating the method, it was used for measuring the dimensions of real patients’ wounds. Results and Conclusions: The discrepancies between actual topography and dimensions determined with Fringe Projection Technique and for the known object were lower than 0.50 cm. The method was successful in obtaining the topography of real patient’s wounds. Objects and wounds with sharp topographies or causing shadow or reflection are difficult to be evaluated with this technique.

Fast and accurate numerical solutions in some problems of particle and radiation transport: synthetic acceleration for the method of short characteristics, Doppler-broadened scattering kernel, remote sensing of the cryosphere

The aim of this work is to present various aspects of numerical simulation of particle and radiation transport for industrial and environmental protection applications, to enable the analysis of complex physical processes in a fast, reliable, and efficient way. In the first part we deal with speed-up of numerical simulation of neutron transport for nuclear reactor core analysis. The convergence properties of the source iteration scheme of the Method of Characteristics applied to be heterogeneous structured geometries has been enhanced by means of Boundary Projection Acceleration, enabling the study of 2D and 3D geometries with transport theory without spatial homogenization. The computational performances have been verified with the C5G7 2D and 3D benchmarks, showing a sensible reduction of iterations and CPU time. The second part is devoted to the study of temperature-dependent elastic scattering of neutrons for heavy isotopes near to the thermal zone. A numerical computation of the Doppler convolution of the elastic scattering kernel based on the gas model is presented, for a general energy dependent cross section and scattering law in the center of mass system. The range of integration has been optimized employing a numerical cutoff, allowing a faster numerical evaluation of the convolution integral. Legendre moments of the transfer kernel are subsequently obtained by direct quadrature and a numerical analysis of the convergence is presented. In the third part we focus our attention to remote sensing applications of radiative transfer employed to investigate the Earth's cryosphere. The photon transport equation is applied to simulate reflectivity of glaciers varying the age of the layer of snow or ice, its thickness, the presence or not other underlying layers, the degree of dust included in the snow, creating a framework able to decipher spectral signals collected by orbiting detectors.

Study of the sensitivity of the XENON1T experiment with the profile likelihood method

Oggi sappiamo che la materia ordinaria rappresenta solo una piccola parte dell'intero contenuto in massa dell'Universo. L'ipotesi dell'esistenza della Materia Oscura, un nuovo tipo di materia che interagisce solo gravitazionalmente e, forse, tramite la forza debole, è stata avvalorata da numerose evidenze su scala sia galattica che cosmologica. Gli sforzi rivolti alla ricerca delle cosiddette WIMPs (Weakly Interacting Massive Particles), il generico nome dato alle particelle di Materia Oscura, si sono moltiplicati nel corso degli ultimi anni. L'esperimento XENON1T, attualmente in costruzione presso i Laboratori Nazionali del Gran Sasso (LNGS) e che sarà in presa dati entro la fine del 2015, segnerà un significativo passo in avanti nella ricerca diretta di Materia Oscura, che si basa sulla rivelazione di collisioni elastiche su nuclei bersaglio. XENON1T rappresenta la fase attuale del progetto XENON, che ha già realizzato gli esperimenti XENON10 (2005) e XENON100 (2008 e tuttora in funzione) e che prevede anche un ulteriore sviluppo, chiamato XENONnT. Il rivelatore XENON1T sfrutta circa 3 tonnellate di xeno liquido (LXe) e si basa su una Time Projection Chamber (TPC) a doppia fase. Dettagliate simulazioni Monte Carlo della geometria del rivelatore, assieme a specifiche misure della radioattività dei materiali e stime della purezza dello xeno utilizzato, hanno permesso di predire con accuratezza il fondo atteso. In questo lavoro di tesi, presentiamo lo studio della sensibilità attesa per XENON1T effettuato tramite il metodo statistico chiamato Profile Likelihood (PL) Ratio, il quale nell'ambito di un approccio frequentista permette un'appropriata trattazione delle incertezze sistematiche. In un primo momento è stata stimata la sensibilità usando il metodo semplificato Likelihood Ratio che non tiene conto di alcuna sistematica. In questo modo si è potuto valutare l'impatto della principale incertezza sistematica per XENON1T, ovvero quella sulla emissione di luce di scintillazione dello xeno per rinculi nucleari di bassa energia. I risultati conclusivi ottenuti con il metodo PL indicano che XENON1T sarà in grado di migliorare significativamente gli attuali limiti di esclusione di WIMPs; la massima sensibilità raggiunge una sezione d'urto σ=1.2∙10-47 cm2 per una massa di WIMP di 50 GeV/c2 e per una esposizione nominale di 2 tonnellate∙anno. I risultati ottenuti sono in linea con l'ambizioso obiettivo di XENON1T di abbassare gli attuali limiti sulla sezione d'urto, σ, delle WIMPs di due ordini di grandezza. Con tali prestazioni, e considerando 1 tonnellata di LXe come massa fiduciale, XENON1T sarà in grado di superare gli attuali limiti (esperimento LUX, 2013) dopo soli 5 giorni di acquisizione dati.

A tool for the qualitative comparison of membrane-embedded and detergent-solubilized membrane protein structures in projection

The calculation of projection structures (PSs) from Protein Data Bank (PDB)-coordinate files of membrane proteins is not well-established. Reports on such attempts exist but are rare. In addition, the different procedures are barely described and thus difficult if not impossible to reproduce. Here we present a simple, fast and well-documented method for the calculation and visualization of PSs from PDB-coordinate files of membrane proteins: the projection structure visualization (PSV)-method. The PSV-method was successfully validated using the PS of aquaporin-1 (AQP1) from 2D crystals and cryo-transmission electron microscopy, and the PDB-coordinate file of AQP1 determined from 3D crystals and X-ray crystallography. Besides AQP1, which is a relatively rigid protein, we also studied a flexible membrane transport protein, i.e. the L-arginine/agmatine antiporter AdiC. Comparison of PSs calculated from the existing PDB-coordinate files of substrate-free and L-arginine-bound AdiC indicated that conformational changes are detected in projection. Importantly, structural differences were found between the PSV-method calculated PSs of the detergent-solubilized AdiC proteins and the PS from cryo-TEM of membrane-embedded AdiC. These differences are particularly exciting since they may reflect a different conformation of AdiC induced by the lateral pressure in the lipid bilayer.

Thoracic target volume delineation using various maximum-intensity projection computed tomography image sets for stereotactic body radiation therapy

The motion of lung tumors during respiration makes the accurate delivery of radiation therapy to the thorax difficult because it increases the uncertainty of target position. The adoption of four-dimensional computed tomography (4D-CT) has allowed us to determine how a tumor moves with respiration for each individual patient. Using information acquired during a 4D-CT scan, we can define the target, visualize motion, and calculate dose during the planning phase of the radiotherapy process. One image data set that can be created from the 4D-CT acquisition is the maximum-intensity projection (MIP). The MIP can be used as a starting point to define the volume that encompasses the motion envelope of the moving gross target volume (GTV). Because of the close relationship that exists between the MIP and the final target volume, we investigated four MIP data sets created with different methodologies (3 using various 4D-CT sorting implementations, and one using all available cine CT images) to compare target delineation. It has been observed that changing the 4D-CT sorting method will lead to the selection of a different collection of images; however, the clinical implications of changing the constituent images on the resultant MIP data set are not clear. There has not been a comprehensive study that compares target delineation based on different 4D-CT sorting methodologies in a patient population. We selected a collection of patients who had previously undergone thoracic 4D-CT scans at our institution, and who had lung tumors that moved at least 1 cm. We then generated the four MIP data sets and automatically contoured the target volumes. In doing so, we identified cases in which the MIP generated from a 4D-CT sorting process under-represented the motion envelope of the target volume by more than 10% than when measured on the MIP generated from all of the cine CT images. The 4D-CT methods suffered from duplicate image selection and might not choose maximum extent images. Based on our results, we suggest utilization of a MIP generated from the full cine CT data set to ensure a representative inclusive tumor extent, and to avoid geometric miss.