Positioning system for 3D scans inside objects

En este trabajo presentamos un sistema de posicionamiento de visión activa para el escaneo 3D del interior de piezas. El diseño del sistema propuesto consta de dos módulos: un sistema de dimensionamiento 2D de visión activa, y un sistema que posiciona el módulo de visión activa. El sistema de posicionamiento es capaz de determinar la profundidad del sistema de dimensionamiento 2D de visión activa en el interior del objeto a escanear usando varios sensores. Las principales contribuciones de este trabajo son la caracterización del sistema de dimensionamiento 2D, y el desarrollo de algoritmos de posicionamiento de la luz activa con énfasis en el modelado y fusión de sensores. El sistema puede utilizarse como un sistema de dimensionamiento en aplicaciones industriales como la industria metal mecánica, la aeronáutica, la medicina, en el control de calidad y en áreas de visión por computadora.In this work we present an active positioning system for 3D scan of interior parts. The design of the proposed system consists of two modules: an active 2D dimensional system and positional system based on active vision. The active 2D dimensional system is able to determine the depth of the 2D dimensional system inside the object to be scanned using several sensors. The main contributions of this work are the characterization of the 2D dimensional system and the development of active light positioning algorithms with emphasis on the modeling and fusion of the sensors. The system can be used as a dimensional system in industrial applications such as the metal mechanical industry, aeronautics industry, medicine, quality control and computer vision.Peer Reviewe

Three-dimensional anatomical atlas of the human body

A thesis submitted in partial fulfillment of the requirements for the degree of Doctor in Information Management, specialization in Geographic Information SystemsAnatomical atlases allow mapping the anatomical structures of the human body. Early versions of these systems consisted of analogic representations with informative text and labelled images of the human body. With the advent of computer systems, digital versions emerged and the third dimension was introduced. Consequently, these systems increased their efficiency, allowing more realistic visualizations with improved interactivity. The development of anatomical atlases in geographic information systems (GIS) environments allows the development of platforms with a high degree of interactivity and with tools to explore and analyze the human body. In this thesis, a prototype for the human body representation is developed. The system includes a 3D GIS topological model, a graphical user interface and functions to explore and analyze the interior and the surface of the anatomical structures of the human body. The GIS approach relies essentially on the topological characteristics of the model and on the kind of available functions, which include measurement, identification, selection and analysis. With the incorporation of these functions, the final system has the ability to replicate the kind of information provided by the conventional anatomical atlases and also provides a higher level of functionality, since some of the atlases limitations are precisely features offered by GIS, namely, interactive capabilities, multilayer management, measurement tools, edition mode, allowing the expansion of the information contained in the system, and spatial analyzes

Visualization methods for analysis of 3D multi-scale medical data

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Three-Dimensional Biomimetic Patterning to Guide Cellular Migration and Organization

This thesis develops a novel photopatterning strategy for biomimetic scaffolds that enables spatial and biochemical control of engineered cellular architectures, such as the microvasculature. Intricate tools that allow for the three dimensional (3D) manipulation of biomaterial microenvironments will be critical for organizing cellular behavior, directing tissue formation, and ultimately, developing functional therapeutics to treat patients with critical organ failure. Poly(ethylene glycol) (PEG) based hydrogels, which without modification naturally resist protein adsorption and cellular adhesion, were utilized in combination with a two-photon laser patterning approach to covalently immobilize specific biomolecules in custom-designed, three-dimensional (3D) micropatterns. This technique, known as two-photon laser scanning lithography (TP-LSL), was shown in this thesis to possess the capability to micropattern multiple different biomolecules at modular concentrations into a single hydrogel microenvironment over a broad range of size scales with high 3D resolution. 3D cellular adhesion and migration were then explored in detail using time-lapse confocal microscopy to follow cells as they migrated along micropatterned tracks of various 3D size and composition. Further, in a valuable modification of TP-LSL, images from the endogenous microenvironment were converted into instructions to precisely direct the laser patterning of biomolecules within PEG-based hydrogels. 3D images of endogenous microvasculature from various tissues were directly converted into 3D biomolecule patterns within the hydrogel scaffold with precise pattern fidelity. While tissue engineers have previously demonstrated the formation of vessels through the encapsulation of endothelial cells and pericyte precursor cells within PEG-based hydrogels, the vessel structure had been random, uncoordinated, and therefore, ultimately non-functional. This thesis has utilized image guided TP-LSL to pattern biomolecules into a 3D structure that directs the organization of vessels to mimic that of the endogenous tissue vasculature. TP-LSL now stands as a valuable tool to control the microstructure of engineered cellular architectures, thereby providing a critical step in the development of cellularized scaffolds into functional tissues. Ultimately, this thesis develops new technologies that advance the field of regenerative medicine towards the goal of engineering viable organs to therapeutically treat the 18 patients who die every day waiting on the organ transplant list

A multimodal computational pipeline for 3D histology of the human brain

ABSTRACT: Ex vivo imaging enables analysis of the human brain at a level of detail that is not possible in vivo with MRI. In particular, histology can be used to study brain tissue at the microscopic level, using a wide array of different stains that highlight different microanatomical features. Complementing MRI with histology has important applications in ex vivo atlas building and in modeling the link between microstructure and macroscopic MR signal. However, histology requires sectioning tissue, hence distorting its 3D structure, particularly in larger human samples. Here, we present an open-source computational pipeline to produce 3D consistent histology reconstructions of the human brain. The pipeline relies on a volumetric MRI scan that serves as undistorted reference, and on an intermediate imaging modality (blockface photography) that bridges the gap between MRI and histology. We present results on 3D histology reconstruction of whole human hemispheres from two donors

Development of Imaging Mass Spectrometry Analysis of Lipids in Biological and Clinically Relevant Applications

La spectrométrie de masse mesure la masse des ions selon leur rapport masse sur charge. Cette technique est employée dans plusieurs domaines et peut analyser des mélanges complexes. L’imagerie par spectrométrie de masse (Imaging Mass Spectrometry en anglais, IMS), une branche de la spectrométrie de masse, permet l’analyse des ions sur une surface, tout en conservant l’organisation spatiale des ions détectés. Jusqu’à présent, les échantillons les plus étudiés en IMS sont des sections tissulaires végétales ou animales. Parmi les molécules couramment analysées par l’IMS, les lipides ont suscité beaucoup d'intérêt. Les lipides sont impliqués dans les maladies et le fonctionnement normal des cellules; ils forment la membrane cellulaire et ont plusieurs rôles, comme celui de réguler des événements cellulaires. Considérant l’implication des lipides dans la biologie et la capacité du MALDI IMS à les analyser, nous avons développé des stratégies analytiques pour la manipulation des échantillons et l’analyse de larges ensembles de données lipidiques. La dégradation des lipides est très importante dans l’industrie alimentaire. De la même façon, les lipides des sections tissulaires risquent de se dégrader. Leurs produits de dégradation peuvent donc introduire des artefacts dans l’analyse IMS ainsi que la perte d’espèces lipidiques pouvant nuire à la précision des mesures d’abondance. Puisque les lipides oxydés sont aussi des médiateurs importants dans le développement de plusieurs maladies, leur réelle préservation devient donc critique. Dans les études multi-institutionnelles où les échantillons sont souvent transportés d’un emplacement à l’autre, des protocoles adaptés et validés, et des mesures de dégradation sont nécessaires. Nos principaux résultats sont les suivants : un accroissement en fonction du temps des phospholipides oxydés et des lysophospholipides dans des conditions ambiantes, une diminution de la présence des lipides ayant des acides gras insaturés et un effet inhibitoire sur ses phénomènes de la conservation des sections au froid sous N2. A température et atmosphère ambiantes, les phospholipides sont oxydés sur une échelle de temps typique d’une préparation IMS normale (~30 minutes). Les phospholipides sont aussi décomposés en lysophospholipides sur une échelle de temps de plusieurs jours. La validation d’une méthode de manipulation d’échantillon est d’autant plus importante lorsqu’il s’agit d’analyser un plus grand nombre d’échantillons. L’athérosclérose est une maladie cardiovasculaire induite par l’accumulation de matériel cellulaire sur la paroi artérielle. Puisque l’athérosclérose est un phénomène en trois dimension (3D), l'IMS 3D en série devient donc utile, d'une part, car elle a la capacité à localiser les molécules sur la longueur totale d’une plaque athéromateuse et, d'autre part, car elle peut identifier des mécanismes moléculaires du développement ou de la rupture des plaques. l'IMS 3D en série fait face à certains défis spécifiques, dont beaucoup se rapportent simplement à la reconstruction en 3D et à l’interprétation de la reconstruction moléculaire en temps réel. En tenant compte de ces objectifs et en utilisant l’IMS des lipides pour l’étude des plaques d’athérosclérose d’une carotide humaine et d’un modèle murin d’athérosclérose, nous avons élaboré des méthodes «open-source» pour la reconstruction des données de l’IMS en 3D. Notre méthodologie fournit un moyen d’obtenir des visualisations de haute qualité et démontre une stratégie pour l’interprétation rapide des données de l’IMS 3D par la segmentation multivariée. L’analyse d’aortes d’un modèle murin a été le point de départ pour le développement des méthodes car ce sont des échantillons mieux contrôlés. En corrélant les données acquises en mode d’ionisation positive et négative, l’IMS en 3D a permis de démontrer une accumulation des phospholipides dans les sinus aortiques. De plus, l’IMS par AgLDI a mis en évidence une localisation différentielle des acides gras libres, du cholestérol, des esters du cholestérol et des triglycérides. La segmentation multivariée des signaux lipidiques suite à l’analyse par IMS d’une carotide humaine démontre une histologie moléculaire corrélée avec le degré de sténose de l’artère. Ces recherches aident à mieux comprendre la complexité biologique de l’athérosclérose et peuvent possiblement prédire le développement de certains cas cliniques. La métastase au foie du cancer colorectal (Colorectal cancer liver metastasis en anglais, CRCLM) est la maladie métastatique du cancer colorectal primaire, un des cancers le plus fréquent au monde. L’évaluation et le pronostic des tumeurs CRCLM sont effectués avec l’histopathologie avec une marge d’erreur. Nous avons utilisé l’IMS des lipides pour identifier les compartiments histologiques du CRCLM et extraire leurs signatures lipidiques. En exploitant ces signatures moléculaires, nous avons pu déterminer un score histopathologique quantitatif et objectif et qui corrèle avec le pronostic. De plus, par la dissection des signatures lipidiques, nous avons identifié des espèces lipidiques individuelles qui sont discriminants des différentes histologies du CRCLM et qui peuvent potentiellement être utilisées comme des biomarqueurs pour la détermination de la réponse à la thérapie. Plus spécifiquement, nous avons trouvé une série de plasmalogènes et sphingolipides qui permettent de distinguer deux différents types de nécrose (infarct-like necrosis et usual necrosis en anglais, ILN et UN, respectivement). L’ILN est associé avec la réponse aux traitements chimiothérapiques, alors que l’UN est associé au fonctionnement normal de la tumeur.Mass spectrometry is the measurement of the mass over charge ratio of ions. It is broadly applicable and capable of analyzing complex mixtures. Imaging mass spectrometry (IMS) is a branch of mass spectrometry that analyses ions across a surface while conserving their spatial organization on said surface. At this juncture, the most studied IMS samples are thin tissue sections from plants and animals. Among the molecules routinely imaged by IMS, lipids have generated significant interest. Lipids are important in disease and normal cell function as they form cell membranes and act as signaling molecules for cellular events among many other roles. Considering the potential of lipids in biological and clinical applications and the capability of MALDI to ionize lipids, we developed analytical strategies for the handling of samples and analysis of large lipid MALDI IMS datasets. Lipid degradation is massively important in the food industry with oxidized products producing a bad smell and taste. Similarly, lipids in thin tissue sections cut from whole tissues are subject to degradation, and their degradation products can introduce IMS artifacts and the loss of normally occurring species to degradation can skew accuracy in IMS measures of abundance. Oxidized lipids are also known to be important mediators in the progression of several diseases and their accurate preservation is critical. As IMS studies become multi-institutional and collaborations lead to sample exchange, the need for validated protocols and measures of degradation are necessary. We observed the products of lipid degradation in tissue sections from multiple mouse organs and reported on the conditions promoting and inhibiting their presence as well as the timeline of degradation. Our key findings were the increase in oxidized phospholipids and lysophospholipids from degradation at ambient conditions, the decrease in the presence of lipids containing unsaturations on their fatty acyl chains, and the inhibition of degradation by matrix coating and cold storage of sections under N2 atmosphere. At ambient atmospheric and temperature, lipids degraded into oxidized phospholipids on the time-scale of a normal IMS experiment sample preparation (within 30 min). Lipids then degraded into lysophospholipids’ on a time scale on the order of several days. Validation of sample handling is especially important when a greater number of samples are to be analyzed either through a cohort of samples, or analysis of multiple sections from a single tissue as in serial 3D IMS. Atherosclerosis is disease caused by accumulation of cellular material at the arterial wall. The accumulation implanted in the cell wall grows and eventually occludes the blood vessel, or causes a stroke. Atherosclerosis is a 3D phenomenon and serial 3D IMS is useful for its ability to localize molecules throughout the length of a plaque and help to define the molecular mechanisms of plaque development and rupture. Serial 3D IMS has many challenges, many of which are simply a matter of producing 3D reconstructions and interpreting them in a timely fashion. In this aim and using analysis of lipids from atherosclerotic plaques from a human carotid and mouse aortic sinuses, we described 3D reconstruction methods using open-source software. Our methodology provides means to obtain high quality visualizations and demonstrates strategies for rapid interpretation of 3D IMS datasets through multivariate segmentation. Mouse aorta from model animals provided a springboard for developing the methods on lower risk samples with less variation with interesting molecular results. 3D MALDI IMS showed localized phospholipid accumulation in the mouse aortic sinuses with correlation between separate positive and negative ionization datasets. Silver-assisted LDI imaging presented differential localization of free fatty acids, cholesterol / cholesterol esters, and triglycerides. The human carotid’s 3D segmentation shows molecular histologies (spatial groupings of imaging pixels with similar spectral fingerprints) correlating to the degree of arterial stenosis. Our results outline the potential for 3D IMS in atherosclerotic research. Molecular histologies and their 3D spatial organization, obtained from the IMS techniques used herein, may predict high-risk features, and particularly identify areas of plaque that have higher-risk of rupture. These investigations would help further unravel the biological complexities of atherosclerosis, and predict clinical outcomes. Colorectal cancer liver metastasis (CRCLM) is the metastatic disease of primary colorectal cancer, one of the most common cancers worldwide. CRC is a cancer of the endothelial lining of the colon or rectum. CRC itself is often cured with surgery, while CRCLM is more deadly and treated with chemotherapy with more limited efficacy. Prognosticating and assessment of tumors is performed using classical histopathology with a margin of error. We have used lipid IMS to identify the histological compartments and extract their signatures. Using these IMS signatures we obtained a quantitative and objective histopathological score that correlates with prognosis. Additionally, by dissecting out the lipid signatures we have identified single lipid moieties that are unique to different histologies that could potentially be used as new biomarkers for assessing response to therapy. Particularly, we found a series of plasmalogen and sphingolipid species that differentiate infarct-like and usual necrosis, typical of chemotherapeutic response and normal tumor function, respectively

Autofluorescence endoscopic spectro-imaging and 2D-cartography for in situ localisation and diagnosis of cancerous lesions

Early diagnosis is the most efficient way to struggle against cancer. Among all the existing techniques, optical methods (photodiagnosis from NUV to NIR) show important characteristics required by the physicians : high sensitivity, non-ionising radiations and non-traumatic measurements. They are particularly well suited to the detection of cancers in hollow organs, that are usually superficial and hardly visible with classical endoscopy. This paper describes a methodological approach based on the use of tissue autofluorescence, applicable in clinical endoscopy, and leading to the definition of diagnosis indicators from the spectral parameters. Following a state-of-the-art on autofluorescence spectroscopic (LIFS) and endoscopic imaging methods, we present the efficiency of fibered LIFS in terms of sensitivity and specificity for the diagnosis of esophagus cancerous lesions (clinical study over 25 patients). We then present the technological characteristics of an autofluorescence endoscopic imaging prototype developed in our labs as well as its calibration. A second part is devoted to endoscopic image registration and mosaicing and to optics aberration correction in perspective of the automatic construction of a panoramic image (cartography) of the organ’s explored areas. Finally, exploiting the fluorescence data provided by the imager, the feasibility of the superimposition of spatial and spectral information is validated with a phantom.Le diagnostic précoce est le moyen le plus efficace de lutte contre le cancer. Parmi toutes les techniques possibles, les méthodes optiques (photodiagnostic du proche UV au proche IR) présentent des caractéristiques importantes recherchées par les médecins : grande sensibilité, radiations non ionisantes et mesures atraumatiques. Elles sont particulièrement bien adaptées à la détection des cancers des organes creux, par nature superficiels et difficilement décelables en endoscopie classique. Cet article décrit une approche méthodologique fondée sur l’exploitation de l’autofluorescence tissulaire, applicable en endoscopie clinique, et conduisant à l’élaboration d’indicateurs diagnostiques issus des paramètres spectraux. Après un état de l’art sur les méthodes spectroscopiques (LIFS) et d’imagerie endoscopique d’autofluorescence, nous montrons l’efficacité de la LIFS fibrée en terme de sensibilité et de spécificité pour le diagnostic de lésions cancéreuses de l’oesophage (étude clinique sur 25 patients). Nous présentons ensuite les caractéristiques technologiques et le calibrage du prototype d’imageur endoscopique d’autofluorescence développé. Une seconde partie traite du pré-traitement, du recalage et du mosaïquage des images endoscopiques appliqués à la construction automatique d’une image panoramique (cartographie) à partir de séquences vidéos des zones explorées de l’organe. Finalement, en exploitant les informations de fluorescence fournies par l’imageur, la faisabilité d’une superposition des informations spatiale et spectrale est validée sur fantôme

Atlas of sensations - on sensibilities in a computational design practice

The driving force behind the body of work of SPAN is defined by the application of advanced computational design methodologies. This dissertation can be understood as a cartography (in the best tradition of an atlas) of the work of the practice from its founding year 2003 until 2017 - a period profoundly shaped by the progress made in technological advances. These technological means allow SPAN to discuss architectural project through a series of different lenses such as conceptualization, planning, fabrication to the maintenance of the designed objects, through the use of emerging technical opportunities wither this be the interrogation of novel geometries (Blocks, Ore, Barcelona Recursion), computational methods of rationalization (Expo Façade) or advanced methods of fabrication (Robots, as for example in Plato's Columns). In a parallel move between the necessities and desires of the practice and the ambitious studios and seminars in academia, novel toolsets and design concepts are developed to address contemporary architectural problems. These areas can be understood as different territories of interrogation, forming a landscape of opportunities, or as we describe it internally in our office: a design ecology. The interrogation of these distinct territories, and the unique way in which SPAN assembles those various elements to something larger than its parts, is what constitutes part of SPAN's contribution to the discipline. Apart from projects and visual work, SPAN´s contribution to discourse started early with papers to conferences such as IASS (International Association for Shell and Spatial Structures) in 2007, Design Modeling Symposium in 2008, and ACADIA (Association for Computer Aided Design in Architecture) in 2008, which included ideas such as the application of tissue engineering in architecture, aspects of artifact and affect, fabrication, and considerations on architectural details in complex curved geometries. Within the Atlas of Sensations, a second ecology is defined by the contribution to the paradigm shift in the discourse from the continuous to the hyper-articulated surface, which contains an additional level of information. A surface, which describes architectural properties through the deep pochés, folds, joints, niches, and arches it generates.  The question is: How does this shift in the conception of architecture affect the qualities of the design, and by extension the context these objects construct? To further investigate this question the work focuses on one part of the practice's design ecology: design sensibilities. In order to interrogate this question, the presented work observes these moments in SPAN's practice through the lens of geometrical properties. Ultimately resulting in thoughts on Postdigital design ecologies that discuss aspects of design agency in our contemporary age