Photo repair and 3d structure from flatbed scanners

We introduce a technique that allows 3D information to be captured from a conventional flatbed scanner. The technique requires no hardware modification and allows untrained users to easily capture 3D datasets. Once captured, these datasets can be used for interactive relighting and enhancement of surface detail on physical objects. We have also found that the method can be used to scan and repair damaged photographs. Since the only 3D structure on these photographs will typically be surface tears and creases, our method provides an accurate procedure for automatically detecting these flaws without any user intervention. Once detected, automatic techniques, such as infilling and texture synthesis, can be leveraged to seamlessly repair such damaged areas. We first present a method that is able to repair damaged photographs with minimal user interaction and then show how we can achieve similar results using a fully automatic process

A Survey of Geometric Analysis in Cultural Heritage

We present a review of recent techniques for performing geometric analysis in cultural heritage (CH) applications. The survey is aimed at researchers in the areas of computer graphics, computer vision and CH computing, as well as to scholars and practitioners in the CH field. The problems considered include shape perception enhancement, restoration and preservation support, monitoring over time, object interpretation and collection analysis. All of these problems typically rely on an understanding of the structure of the shapes in question at both a local and global level. In this survey, we discuss the different problem forms and review the main solution methods, aided by classification criteria based on the geometric scale at which the analysis is performed and the cardinality of the relationships among object parts exploited during the analysis. We finalize the report by discussing open problems and future perspectives

Investigation and Evaluation of Methods for Measuring Surface Texture on Worktops and Kitchen Fronts

In this Master Thesis different methods for measuring and evaluating surface textures have been investigated and evaluated. A method for digitizing textures called photometric stereo have also been studied. The purpose has been to find methods that can replace or supplement the current method of visual inspection used for surface texture studies by IKEA of Sweden. The suggested methods are going to be used by the company for securing that the surface textures on laminate worktops and pigment lacquered kitchen fronts are both consistent between different suppliers and matching the original reference sample. The thesis work has been written in three phases. First a background study of surface texture measurement methods has been carried out as well as a market research about what instruments are used for surface texture measurements. The next step has been an investigation of what problems IKEA is experiencing and finding the cause of these problems. This includes studies of the manufacturing process for laminates, the tools used for giving texture to laminates and how textures patterns are developed. The manufacturing process of the kitchen front has been also studied. In the last step the different methods have been tested and evaluated based on the needs of IKEA of Sweden

Preclinical evaluation of nanoparticle enhanced breast cancer diagnosis and radiation therapy

Triple negative breast cancer (TNBC) is an aggressive type of cancer which makes up 15-20% of all newly diagnosed cases, lacking the main target molecules for tumor specific treatment. Surgery or systemic therapy by chemotherapy are frequently used in the clinic and combined with radiation therapy to improve locoregional control in breast cancer patients after surgery. With a poor prognosis, there is a clear need to explore new treatment options for TNBC. The aim of the here presented PhD project was to evaluate the feasibility to enhance the biological effect of radiation therapy and increase tumor contrast for diagnosis by applying an in vivo microCT imaging system in combination with barium nanoparticles (BaNPs) in a pH8N8 WAP-T-NP8 mouse model for TNBC. Characterization of the BaNPs revealed strong x-ray attenuation and no toxic effects in different cancer and normal cell lines. Furthermore, irradiation of cancer cells using low energy x-rays in the keV range by a microCT resulted in a significant reduction on colony formation capability. In vitro, this low energy irradiation effect on clonogenic tumor cell survival was enhanced in the presence of BaNPs. Next, a subcutaneous lung cancer mouse model in immunodeficient mice and an orthotopic syngeneic mouse model for breast cancer was applied for further in vivo evaluation. Once the treatment plan was optimized regarding the applied x-ray doses and the frequency of irradiation, low energy radiation therapy within a classical in vivo microCT significantly reduced tumor growth or even resulted in shrinkage of the tumors without visible side effects and weight loss in comparison to untreated controls. However, the intratumoral application of BaNPs was not able to increase the irradiation effect on tumor growth kinetics. This might be in part due to inhomogeneous distribution of BaNPs within the tumor observed by microCT imaging. K-edge subtraction imaging as well as x-ray fluorescence of explanted tumor samples confirmed these findings. To localize the BaNPs in 3D to specific sites within the tumor environment and to detect morphological alterations within the tumor due to irradiation in proximity to BaNPs an ex-vivo imaging based analytic platform was established, utilizing co-registration of microCT and histology data. This imaging approach co-localized BaNPs with CD68 positive phagocytic cells and revealed a non-uniform distribution of the BaNPs within the tumor, however with no signs of locally enhanced radiation effects. Furthermore, antibody functionalized BaNPs were generated for systemic application. Analysis of biodistribution revealed that EpCAM labeled BaNPs did not reach the tumor after intra-venous administration, but accumulated in liver and spleen, demonstrated by a strong CT contrast within these organs. In summary, I showed that low energy radiation therapy by applying an in vivo microCT significantly reduced tumor volumes in comparison to untreated tumors in a syngeneic breast cancer tumor mouse model resembling TNBC. However, BaNPs while enhancing the effectiveness of irradiation on tumor cells in vitro, did not improve the irradiation effect on tumor growth in vivo.2021-07-1

Isothermal-based DNA biosensors for application in pharmacogenetics

Tesis por compendio[EN] The determination of genetic biomarkers is progressively becoming more extended and popular, being commercialized even in kits for personalized medicine. Establishing specific genotype variations for each patient, such as single nucleotide polymorphisms (SNPs), could be a fundamental tool in the field of diagnosis, prognosis and therapy selection. However, the use of DNA testing is not fully implemented in general healthcare, mainly due to technical and economic barriers associated to the current technologies, which are limited only to specialized centers and large hospitals. In this thesis, the main goal was to overcome these obstacles by developing simpler, faster and more affordable point-of-care (POC) genotyping systems. Allele discrimination was achieved by employing isothermal enzymatic reactions, like recombinase polymerase amplification (RPA), ligation of oligonucleotides and loop-mediated isothermal amplification (LAMP). These processes were integrated to colorimetric indicators and immunoenzymatic assays, in a microarray format. Using compact discs and polycarbonate chips as platforms, the detection was achieved through widespread electronics, like disc-reader, flatbed scanner and smartphone. To demonstrate their capacities, the resulting systems were applied for identifying SNPs in human samples, associated to therapies for tobacco smoking cessation, major depression disorder and blood clotting-related diseases. After selecting the proper conditions, all studied strategies discriminated SNPs in samples containing as low as 100 copies of genomic DNA, with an error rate below 15%. Most importantly, the developed methods have reduced assays times varying between 70 and 140 minutes, at a cost similar to a conventional PCR-based analog, but maintaining or raising amplification efficiency and eliminating the need of specialized temperature cyclers and fluorescence scanners. In conclusion, the biosensors based in isothermal reactions and consumer electronics devices greatly improve the competitivity of POC DNA analysis. It was demonstrated that the technologies developed in this thesis could support genotyping assays in low-resource areas, such as primary healthcare centers and emerging countries. Through this democratization of genetic testing and by performing adequate association studies, molecular diagnostics and personalized medicine practices could have their application extended to the clinical routine.[ES] La determinación de biomarcadores genéticos es cada vez más extensa y popular, estando incluso comercializándose kits para medicina personalizada. Establecer las variaciones específicas en el genotipo de cada paciente, como los polimorfismos de un solo nucleótido (SNP) podría ser una herramienta fundamental en el campo del diagnóstico, pronóstico y selección de la terapia. Sin embargo, el uso de pruebas de ADN no se encuentra completamente implementado en la atención médica general, principalmente debido a las barreras técnicas y económicas asociadas a las tecnologías actuales, limitadas solamente a centros especializados y grandes hospitales. En esta tesis, el objetivo principal fue superar estos obstáculos mediante el desarrollo de sistemas de genotipado point-of-care (POC), más simples, rápidos y asequibles. La discriminación alélica se logró mediante el uso de reacciones enzimáticas isotermas, como la amplificación de la recombinasa polimerasa (RPA), la ligación de oligonucleótidos y la amplificación isotérmica mediada por bucle (LAMP). Estos procesos se integraron a indicadores colorimétricos y ensayos inmunoenzimáticos en formato de micromatriz. Utilizando discos compactos y chips de policarbonato como plataforma de ensayo, se ha logrado la detección mediante dispositivos electrónicos de consumo, como un lector de discos, escáner documental y teléfono móvil. Para demostrar sus capacidades, los sistemas resultantes se aplicaron a la identificación de SNPs en muestras humanas, asociados a terapias antitabaquismo, para depresión y enfermedades relacionadas con la coagulación de la sangre. Tras seleccionar las condiciones adecuadas, todas las estrategias estudiadas discriminaron SNPs en muestras conteniendo tan solo 100 copias de ADN genómico, con una tasa de error inferior al 15%. Más importante, los métodos desarrollados han reducido los tiempos de ensayo a valores entre 70 y 140 minutos, a un coste similar a un análogo convencional basado en la reacción en cadena de la polimerasa (PCR), pero manteniendo o aumentando la eficiencia de amplificación y eliminando la necesidad de termocicladores y escáneres de fluorescencia. En conclusión, los biosensores basados en reacciones isotérmicas y dispositivos de electrónica de consumo mejoran en gran medida la competitividad del análisis POC de ADN. Se ha demostrado que las tecnologías desarrolladas en esta tesis podrían apoyar los ensayos de genotipado en áreas de recursos escasos, como centros de atención primaria y países emergentes. A través de esta democratización de las pruebas genéticas y realización estudios de asociación adecuados, el diagnóstico molecular y las prácticas en medicina personalizada podrían extender su aplicación a la rutina clínica.[CA] La determinació de biomarcadors genètics és cada vegada més extensa i popular, estant fins i tot comercialitzant-se kits per a medicina personalitzada. Establir les variacions específiques en el genotip de cada pacient, com els polimorfismes d'un sol nucleòtid (SNP) podria ser una eina fonamental en el camp del diagnòstic, pronòstic i selecció de la teràpia. No obstant això, l'ús de proves d'ADN no es troba completament implementat en l'atenció mèdica general, principalment a causa de les barreres tècniques i econòmiques associades a les tecnologies actuals, limitades solament a centres especialitzats i grans hospitals. En aquesta tesi, l'objectiu principal va ser superar aquests obstacles mitjançant el desenvolupament de sistemes de genotipat point-of-care (POC), més simples, ràpids i assequibles. La discriminació al·lèlica es va aconseguir mitjançant l'ús de reaccions enzimàtiques isotermes, com l'amplificació de la recombinasa polimerasa (RPA), la lligació de oligonucleòtids i l'amplificació isotèrmica mediada per bucle (LAMP). Aquests processos es van integrar a indicadors colorimètrics i assajos inmunoenzimàtics en format de micromatriu. Utilitzant discos compactes i xips de policarbonat com a plataforma d'assaig, s'ha conseguit la detecció mitjançant dispositius electrònics de consum, com un lector de discos, escàner documental i telèfon mòbil. Per a demostrar les seues capacitats, els sistemes resultants es van aplicar a la identificació de polimorfismes en mostres humanes, associats a teràpies antitabaquisme, per a depressió i malalties relacionades amb la coagulació de la sang. Després de seleccionar les condicions adequades, totes les estratègies estudiades van ser capaces de discriminar SNPs en mostres contenint tan sols 100 còpies d'ADN genòmic, amb una taxa d'error inferior al 15%. Més important, els mètodes desenvolupats han reduït els temps d'assaig a valors entre 70 i 140 minuts, a un cost similar a un anàleg convencional basat en la reacció en cadena de la polimerasa (PCR), però mantenint o augmentant l'eficiència d'amplificació i eliminant la necessitat de termocicladors i escàners de fluorescència. En conclusió, els biosensors basats en reaccions isotèrmiques i dispositius d'electrònica de consum milloren en gran manera la competitivitat de l'anàlisi POC del ADN. S'ha demostrat que les tecnologies desenvolupades en aquesta tesi podrien donar suport als assajos de genotipat en àrees de recursos escassos, com a centres d'atenció primària i països emergents. A través d'aquesta democratització de les proves genètiques i realització estudis d'associació adequats, el diagnòstic molecular i les pràctiques en medicina personalitzada podrien estendre la seua aplicació a la rutina clínica.[PT] A determinação de biomarcadores genéticos está tornando-se cada vez mais extensa e popular, sendo comercializada até em kits para medicina personalizada. O estabelecimento de variações específicas de genotipo para cada paciente, tais como os polimorfismo de nucleotídeo único, pode ser uma ferramenta fundamental no campo do diagnóstico, prognóstico e seleção de terapias. No entanto, o uso de testes de DNA ainda não encontra-se totalmente implementado na área de saúde geral, principalmente devido às barreiras técnicas e econômicas associadas às tecnologias atuais, limitadas apenas a centros especializados e grandes hospitais. Nesta tese, o principal objetivo foi superar esses obstáculos desenvolvendo sistemas de genotipagem point-of-care (POC) de DNA, mais simples, rápidos e acessíveis. A discriminação de alelos foi alcançada empregando reações enzimáticas isotérmicas, como amplificação por recombinase polimerase (RPA), ligação de oligonucleotídeos e amplificação isotérmica mediada por loop (LAMP). Tais processos foram integrados a indicadores colorimétricos e ensaios imunoenzimáticos, em formato micromatriz. Usando discos compactos e chips de policarbonato como plataforma de ensaio, os analitos foram detectados através de dispositivos eletrônicos de consumo, como leitor de disco, scanner de mesa e smartphone. Para demonstrar suas capacidades, os sistemas resultantes foram aplicados para identificação de polimorfismos em amostras de DNA humano, associados a terapias antitabagismo, para depressão e doenças relacionadas à coagulação do sangue. Após a seleção das condições adequadas, todas as estratégias estudadas foram capazes de discriminar SNPs em amostras contendo até 100 cópias de DNA genômico, com uma taxa de erro inferior a 15%. Mais importante, os métodos desenvolvidos reduziram o tempo de ensaio a valores entre 70 e 140 minutos, com um custo similar a um método análogo baseado em reação em cadeia da polimerase (PCR), mas mantendo ou aumentando a eficiência da amplificação e eliminando a necessidade de cicladores de temperatura e scanners de fluorescência especializados. Em conclusão, os biosensores baseados em reações enzimáticas isotérmicas e dispositivos eletrônicos de consumo incrementam grandemente a competitividade da análise POC de DNA. Foi demonstrado que as tecnologias desenvolvidas nesta tese poderiam dar suporte a ensaios de genotipagem em lugares com poucos recursos, como centros de atenção primária e países emergentes. Através desta democratização dos testes genéticos e com a realização de estudos de associação adequados, o diagnóstico molecular e as práticas de medicina personalizada poderiam ter sua aplicação extendida à rotina clínica.The authors acknowledge the financial support received from the Generalitat Valenciana (GVA-PROMETEOII/2014/040 Project and GRISOLIA/2014/024 PhD grant) and the Spanish Ministry of Economy and Competitiveness (MINECO CTQ2013-45875-R project)Yamanaka, ES. (2020). Isothermal-based DNA biosensors for application in pharmacogenetics [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/148366TESISCompendi

Towards the Control of Electrophotographic-based 3-Dimensional Printing: Image-Based Sensing and Modeling of Surface Defects

Electro-Photography (EP) has been used for decades for fast, cheap, and reliable printing in offices and homes around the world. It has been shown that extending the use of EP for 3D printing is feasible; multiple layered prints are already commercially available (color laser printers) but only for a very limited number of layers. Many of the advantages of laser printing make EP 3D printing desirable including: speed, reliability, selective coloring, ability to print a thermoplastic, possibilities for multi-material printing, ability to print materials not amenable to liquid ink formulations. However, many challenges remain before EP-based 3D printing can be commercially viable. A limiting factor in using the same system architecture as a traditional laser printer is that as the thickness of the part increases, material deposition becomes more difficult with each layer since the increased thickness reduces the field strength. Different system configurations have been proposed where the layer is printed on intermediate stations and are subsequently transferred to the work piece. Layer registration and uniform transfer from the intermediate station become crucial factors in this architecture. At the Print Research and Imaging Systems Modeling (PRISM) Lab preliminary tests have confirmed the feasibility of using EP for Additive Manufacturing (AM). However, similar issues were encountered to those reported in literature as the number of layers increased, resulting in non-uniform brittle 3D structures. The defects were present but not obvious at each layer, and as the part built up, the defects add up and became more obvious. The process, as in many printers, did not include a control system for the ultimate system output (print), and the actuation method (electrostatic charge) is not entirely well characterized or sensed to be used in a control system. This research intends to help the development of a model and an image-based sensing system that can be used for control of material deposition defects for an EP 3D printing process. This research leverages from the expertise at RIT and the Rochester area in Printing, Electrophotography, Rapid Prototyping, Control, and Imaging Sciences

Uses of uncalibrated images to enrich 3D models information

The decrease in costs of semi-professional digital cameras has led to the possibility for everyone to acquire a very detailed description of a scene in a very short time. Unfortunately, the interpretation of the images is usually quite hard, due to the amount of data and the lack of robust and generic image analysis methods. Nevertheless, if a geometric description of the depicted scene is available, it gets much easier to extract information from 2D data. This information can be used to enrich the quality of the 3D data in several ways. In this thesis, several uses of sets of unregistered images for the enrichment of 3D models are shown. In particular, two possible fields of application are presented: the color acquisition, projection and visualization and the geometry modification. Regarding color management, several practical and cheap solutions to overcome the main issues in this field are presented. Moreover, some real applications, mainly related to Cultural Heritage, show that provided methods are robust and effective. In the context of geometry modification, two approaches are presented to modify already existing 3D models. In the first one, information extracted from images is used to deform a dummy model to obtain accurate 3D head models, used for simulation in the context of three-dimensional audio rendering. The second approach presents a method to fill holes in 3D models, with the use of registered images depicting a pattern projected on the real object. Finally, some useful indications about the possible future work in all the presented fields are given, in order to delineate the developments of this promising direction of research