Enhanced perception in volume visualization

Due to the nature of scientic data sets, the generation of convenient visualizations may be a difficult task, but crucial to correctly convey the relevant information of the data. When working with complex volume models, such as the anatomical ones, it is important to provide accurate representations, since a misinterpretation can lead to serious mistakes while diagnosing a disease or planning surgery. In these cases, enhancing the perception of the features of interest usually helps to properly understand the data. Throughout years, researchers have focused on different methods to improve the visualization of volume data sets. For instance, the definition of good transfer functions is a key issue in Volume Visualization, since transfer functions determine how materials are classified. Other approaches are based on simulating realistic illumination models to enhance the spatial perception, or using illustrative effects to provide the level of abstraction needed to correctly interpret the data. This thesis contributes with new approaches to enhance the visual and spatial perception in Volume Visualization. Thanks to the new computing capabilities of modern graphics hardware, the proposed algorithms are capable of modifying the illumination model and simulating illustrative motifs in real time. In order to enhance local details, which are useful to better perceive the shape and the surfaces of the volume, our first contribution is an algorithm that employs a common sharpening operator to modify the lighting applied. As a result, the overall contrast of the visualization is enhanced by brightening the salient features and darkening the deeper regions of the volume model. The enhancement of depth perception in Direct Volume Rendering is also covered in the thesis. To do this, we propose two algorithms to simulate ambient occlusion: a screen-space technique based on using depth information to estimate the amount of light occluded, and a view-independent method that uses the density values of the data set to estimate the occlusion. Additionally, depth perception is also enhanced by adding halos around the structures of interest. Maximum Intensity Projection images provide a good understanding of the high intensity features of the data, but lack any contextual information. In order to enhance the depth perception in such a case, we present a novel technique based on changing how intensity is accumulated. Furthermore, the perception of the spatial arrangement of the displayed structures is also enhanced by adding certain colour cues. The last contribution is a new manipulation tool designed for adding contextual information when cutting the volume. Based on traditional illustrative effects, this method allows the user to directly extrude structures from the cross-section of the cut. As a result, the clipped structures are displayed at different heights, preserving the information needed to correctly perceive them.Debido a la naturaleza de los datos científicos, visualizarlos correctamente puede ser una tarea complicada, pero crucial para interpretarlos de forma adecuada. Cuando se trabaja con modelos de volumen complejos, como es el caso de los modelos anatómicos, es importante generar imágenes precisas, ya que una mala interpretación de las mismas puede producir errores graves en el diagnóstico de enfermedades o en la planificación de operaciones quirúrgicas. En estos casos, mejorar la percepción de las zonas de interés, facilita la comprensión de la información inherente a los datos. Durante décadas, los investigadores se han centrado en el desarrollo de técnicas para mejorar la visualización de datos volumétricos. Por ejemplo, los métodos que permiten definir buenas funciones de transferencia son clave, ya que éstas determinan cómo se clasifican los materiales. Otros ejemplos son las técnicas que simulan modelos de iluminación realista, que permiten percibir mejor la distribución espacial de los elementos del volumen, o bien los que imitan efectos ilustrativos, que proporcionan el nivel de abstracción necesario para interpretar correctamente los datos. El trabajo presentado en esta tesis se centra en mejorar la percepción de los elementos del volumen, ya sea modificando el modelo de iluminación aplicado en la visualización, o simulando efectos ilustrativos. Aprovechando la capacidad de cálculo de los nuevos procesadores gráficos, se describen un conjunto de algoritmos que permiten obtener los resultados en tiempo real. Para mejorar la percepción de detalles locales, proponemos modificar el modelo de iluminación utilizando una conocida herramienta de procesado de imágenes (unsharp masking). Iluminando aquellos detalles que sobresalen de las superficies y oscureciendo las zonas profundas, se mejora el contraste local de la imagen, con lo que se consigue realzar los detalles de superficie. También se presentan diferentes técnicas para mejorar la percepción de la profundidad en Direct Volume Rendering. Concretamente, se propone modificar la iluminación teniendo en cuenta la oclusión ambiente de dos maneras diferentes: la primera utiliza los valores de profundidad en espacio imagen para calcular el factor de oclusión del entorno de cada pixel, mientras que la segunda utiliza los valores de densidad del volumen para aproximar dicha oclusión en cada vóxel. Además de estas dos técnicas, también se propone mejorar la percepción espacial y de la profundidad de ciertas estructuras mediante la generación de halos. La técnica conocida como Maximum Intensity Projection (MIP) permite visualizar los elementos de mayor intensidad del volumen, pero no aporta ningún tipo de información contextual. Para mejorar la percepción de la profundidad, proponemos una nueva técnica basada en cambiar la forma en la que se acumula la intensidad en MIP. También se describe un esquema de color para mejorar la percepción espacial de los elementos visualizados. La última contribución de la tesis es una herramienta de manipulación directa de los datos, que permite preservar la información contextual cuando se realizan cortes en el modelo de volumen. Basada en técnicas ilustrativas tradicionales, esta técnica permite al usuario estirar las estructuras visibles en las secciones de los cortes. Como resultado, las estructuras de interés se visualizan a diferentes alturas sobre la sección, lo que permite al observador percibirlas correctamente

Generation of 360 Degree Point Cloud for Characterization of Morphological and Chemical Properties of Maize and Sorghum

Recently, imaged-based high-throughput phenotyping methods have gained popularity in plant phenotyping. Imaging projects the 3D space into a 2D grid causing the loss of depth information and thus causes the retrieval of plant morphological traits challenging. In this study, LiDAR was used along with a turntable to generate a 360-degree point cloud of single plants. A LABVIEW program was developed to control and synchronize both the devices. A data processing pipeline was built to recover the digital surface models of the plants. The system was tested with maize and sorghum plants to derive the morphological properties including leaf area, leaf angle and leaf angular distribution. The results showed a high correlation between the manual measurement and the LiDAR measurements of the leaf area (R2\u3e0.91). Also, Structure from Motion (SFM) was used to generate 3D spectral point clouds of single plants at different narrow spectral bands using 2D images acquired by moving the camera completely around the plants. Seven narrow band (band width of 10 nm) optical filters, with center wavelengths at 530 nm, 570 nm, 660 nm, 680 nm, 720 nm, 770 nm and 970 nm were used to obtain the images for generating a spectral point cloud. The possibility of deriving the biochemical properties of the plants: nitrogen, phosphorous, potassium and moisture content using the multispectral information from the 3D point cloud was tested through statistical modeling techniques. The results were optimistic and thus indicated the possibility of generating a 3D spectral point cloud for deriving both the morphological and biochemical properties of the plants in the future. Advisor: Yufeng G

Real-time tissue viability assessment using near-infrared light

Despite significant advances in medical imaging technologies, there currently exist no tools to effectively assist healthcare professionals during surgical procedures. In turn, procedures remain subjective and dependent on experience, resulting in avoidable failure and significant quality of care disparities across hospitals. Optical techniques are gaining popularity in clinical research because they are low cost, non-invasive, portable, and can retrieve both fluorescence and endogenous contrast information, providing physiological information relative to perfusion, oxygenation, metabolism, hydration, and sub-cellular content. Near-infrared (NIR) light is especially well suited for biological tissue and does not cause tissue damage from ionizing radiation or heat. My dissertation has been focused on developing rapid imaging techniques for mapping endogenous tissue constituents to aid surgical guidance. These techniques allow, for the first time, video-rate quantitative acquisition over a large field of view (> 100 cm2) in widefield and endoscopic implementations. The optical system analysis has been focused on the spatial-frequency domain for its ease of quantitative measurements over large fields of view and for its recent development in real-time acquisition, single snapshot of optical properties (SSOP) imaging. Using these methods, this dissertation provides novel improvements and implementations to SSOP, including both widefield and endoscopic instrumentations capable of video-rate acquisition of optical properties and sample surface profile maps. In turn, these measures generate profile-corrected maps of hemoglobin concentration that are highly beneficial for perfusion and overall tissue viability. Also utilizing optical property maps, a novel technique for quantitative fluorescence imaging was also demonstrated, showing large improvement over standard and ratiometric methods. To enable real-time feedback, rapid processing algorithms were designed using lookup tables that provide a 100x improvement in processing speed. Finally, these techniques were demonstrated in vivo to investigate their ability for early detection of tissue failure due to ischemia. Both pre-clinical studies show endogenous contrast imaging can provide early measures of future tissue viability. The goal of this work has been to provide the foundation for real-time imaging systems that provide tissue constituent quantification for tissue viability assessments.2018-01-09T00:00:00

Observation of mesenteric microcirculatory disturbance in rat by laser oblique scanning optical microscopy

Ischemia-reperfusion (I/R) injury model has been widely applied to the study of microcirculation disturbance. In this work, we used laser oblique scanning optical microscopy (LOSOM) to observe the microcirculation system in the mesentery of rat model. Utilizing a localized point-scanning detection scheme, high-contrast images of leukocytes were obtained. The extended detection capability facilitated both the automatic in vivo cell counting and the accurate measurement of the rolling velocity of leukocytes. Statistical analysis of the different treatment groups suggested that the distinction between I/R and sham groups with time lapse is significant

Visual analytics methods for retinal layers in optical coherence tomography data

Optical coherence tomography is an important imaging technology for the early detection of ocular diseases. Yet, identifying substructural defects in the 3D retinal images is challenging. We therefore present novel visual analytics methods for the exploration of small and localized retinal alterations. Our methods reduce the data complexity and ensure the visibility of relevant information. The results of two cross-sectional studies show that our methods improve the detection of retinal defects, contributing to a deeper understanding of the retinal condition at an early stage of disease.Die optische Kohärenztomographie ist ein wichtiges Bildgebungsverfahren zur Früherkennung von Augenerkrankungen. Die Identifizierung von substrukturellen Defekten in den 3D-Netzhautbildern ist jedoch eine Herausforderung. Wir stellen daher neue Visual-Analytics-Methoden zur Exploration von kleinen und lokalen Netzhautveränderungen vor. Unsere Methoden reduzieren die Datenkomplexität und gewährleisten die Sichtbarkeit relevanter Informationen. Die Ergebnisse zweier Querschnittsstudien zeigen, dass unsere Methoden die Erkennung von Netzhautdefekten in frühen Krankheitsstadien verbessern

Analysis and Development of Augmented Reality Applications for the Dissemination of Cultural Heritage

Tesis por compendio[ES] La RA consiste en la superposición de elementos virtuales sobre el entorno real, de manera que el usuario percibe estos elementos como si formaran parte de la realidad que está visualizando. Las aplicaciones de RA en dispositivos móviles permiten visualizar el contenido virtual a través de la cámara del dispositivo. La RA es una herramienta de divulgación muy potente ya que permite añadir a la realidad cualquier tipo de información, desde un simple texto informativo a un modelo 3D interactivo. Tiene infinitas utilidades, puede servir de guía en un museo, puede mostrar la recreación de un monumento destruido, o como en el caso de estudio aquí presentado, ayudar a la interpretación de pinturas rupestres. Esta tesis parte de la idea de que la RA puede mejorar mucho la interpretación del arte rupestre sin alterar ni dañar las pinturas. Puede servir para atraer a un público mayor, dar a conocer la historia de las pinturas rupestres y que al mismo tiempo el visitante tenga una experiencia mucho más enriquecedora. A lo largo de la tesis se ha estudiado en profundidad la técnica de visualización de RA mediante dispositivos móviles. Se han analizado las diferentes librerías de programación mediante casos de estudio en entornos reales y examinado los factores que pueden afectar al reconocimiento de las pinturas. Se ha desarrollado una aplicación de RA aplicada a un caso real de pinturas rupestres y posteriormente ha sido evaluada por un grupo de personas. Finalmente, se ha estudiado el efecto de la luz solar y sus cambios a lo largo del día sobre el reconocimiento de imágenes en entornos al aire libre. Este trabajo proporciona un punto de partida para el desarrollo de aplicaciones de RA aplicadas a la difusión del patrimonio cultural, especialmente centrado en el arte rupestre, un entorno que sufre de unas dificultades añadidas debido a su localización, dificultad de reconocimiento de puntos característicos en las pinturas y los cambios en la luz solar, problemas que se han tratado de resolver a lo largo del estudio. Las principales conclusiones han sido muy favorables, partiendo de librerías de programación disponibles y gratuitas. Se han podido desarrollar un conjunto de aplicaciones de RA en diferentes lugares. Las valoraciones han sido muy positivas, los usuarios que han probado las aplicaciones afirman que la interpretación de las pinturas les resulta más fácil y consiguen entender mejor el propósito de las mismas. El principal inconveniente encontrado es la falta de conocimiento sobre esta técnica y la pérdida de realismo en algunos casos debido a la oclusión, es decir, que los objetos virtuales no se posicionen por detrás de los objetos reales. La buena noticia es que esta tecnología evoluciona muy rápido y durante el desarrollo de la tesis ha habido avances muy grandes, entre ellos, el desarrollo de nuevas librerías de programación desarrolladas por Google y Apple, que proporcionan las herramientas necesarias para crear aplicaciones muy potentes e immersivas, donde el usuario se sentirá parte de los entornos creados.[CA] La RA consisteix en la superposició d'elements virtuals sobre l'entorn real, de manera que l'usuari percep aquests elements com si formaren part de la realitat que està visualitzant. Les aplicacions de RA en dispositius mòbils permeten visualitzar el contingut virtual a través de la cambra del dispositiu. La RA és una eina de divulgació molt potent ja que permet afegir a la realitat qualsevol tipus d'informació, des d'un simple text informatiu a un model 3D interactiu. Té infinites utilitats, pot servir de guia en un museu, pot mostrar la recreació d'un monument destruït, o com en el cas d'estudi ací presentat, ajudar a la interpretació de pintures rupestres. Aquesta tesi parteix de la idea que la RA pot millorar molt la interpretació de l'art rupestre sense alterar ni danyar les pintures. Pot servir per a atraure a un públic major, donar a conéixer la història de les pintures rupestres i que al mateix temps el visitant tinga una experiència molt més enriquidora. Al llarg de la tesi s'ha estudiat en profunditat la tècnica de visualització de RA mitjançant dispositius mòbils. S'han analitzat les diferents llibreries de programació mitjançant casos d'estudi en entorns reals i analitzat els factors que poden afectar el reconeixement de les pintures. S'ha desenvolupat una aplicació de RA aplicada a un cas real de pintures rupestres i posteriorment ha sigut avaluada per un grup de persones. Finalment, s'ha estudiat l'efecte de la llum solar i els seus canvis al llarg del dia sobre el reconeixement d'imatges en entorns a l'aire lliure. Aquest treball proporciona un punt de partida per al desenvolupament d'aplicacions de RA aplicades a la difusió del patrimoni cultural, especialment centrat en l'art rupestre, un entorn que pateix d'unes dificultats afegides a causa de la seua localització, dificultat de reconeixement de punts característics en les pintures i els canvis en la llum solar, problemes que s'han tractat de resoldre al llarg de l'estudi. Les principals conclusions han sigut molt favorables, partint de llibreries de programació disponibles i gratuïtes. S'han pogut desenvolupar un conjunt d'aplicacions de RA en diferents llocs. Les valoracions han sigut molt positives, els usuaris que han provat les aplicacions afirmen que la interpretació de les pintures els resulta més fàcil i aconsegueixen entendre millor el propòsit d'aquestes. El principal inconvenient trobat és la falta de coneixement sobre aquesta tècnica i la perduda de realisme en alguns casos a causa de l'oclusió, és a dir, que els objectes virtuals no es posicionen per darrere dels objectes reals. La bona notícia és que aquesta tecnologia evoluciona molt ràpid i durant el desenvolupament de la tesi hi ha hagut avanços molt grans, entre ells, el desenvolupament de noves llibreries de programació per Google i Apple, que proporcionen les eines necessàries per a crear aplicacions molt potents i immersives, on l'usuari se sentirà part dels entorns creats.[EN] AR consists of superimposing virtual elements on the real environment, so that the user perceives these elements as if they were part of the reality they are looking at. AR applications on smartphones allow virtual content to be visualised through the device's camera. AR is a very powerful tool for dissemination as it allows any type of information to be added to reality, from a simple informative text to an interactive 3D model. It can be used as a guide in a museum, it can show the recreation of a destroyed monument, or, as in the case study presented here, it can help in the interpretation of cave paintings. This thesis is based on the idea that AR can greatly enhance the interpretation of rock art without affecting or damaging the paintings. It can be used to attract a wider audience, to introduce the history of the rock art paintings and at the same time provide the visitor with a much more enriching experience. Throughout the thesis, the technique of AR visualisation using mobile devices has been studied in-depth. The different programming libraries have been analysed by means of case studies in real environments as well as the factors that can affect the paintings recognition. An AR application applied to a real case of rock art paintings has been developed and subsequently evaluated by a group of people. Finally, the effect of sunlight and its changes throughout the day on image recognition in outdoor environments has been studied. This work provides a starting point for the AR applications development applied to the dissemination of cultural heritage, especially focused on rock art, an environment that suffers from additional difficulties due to its location, the difficulty of characteristic points recognition and changes in sunlight, problems that have been tried to solve throughout the study. The main outcomes have been very favourable, using freely available programming libraries, and it has been possible to develop a set of AR applications in different places. The evaluations have been very positive, with users who have tested the applications confirming that the interpretation of the paintings is easier for them and they can better understand the purpose of the paintings. The major drawback is the lack of knowledge about this technique and the loss of realism in some cases due to occlusion, i.e. the virtual objects are not positioned behind the real objects. The good news is that this technology is evolving very fast and during the development of the thesis there have been great advances, among them, the development of new programming libraries developed by Google and Apple, which provide the necessary tools to create very powerful and immersive applications, where the user will feel part of the virtual environments created.Blanco Pons, S. (2021). Analysis and Development of Augmented Reality Applications for the Dissemination of Cultural Heritage [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/178895TESISCompendi

Automatic Generation of Urban Road 3D Models for Pedestrian Studies From LiDAR Data

[Abstract] The point clouds acquired with a mobile LiDAR scanner (MLS) have high density and accuracy, which allows one to identify different elements of the road in them, as can be found in many scientific references, especially in the last decade. This study presents a methodology to characterize the urban space available for walking, by segmenting point clouds from data acquired with MLS and automatically generating impedance surfaces to be used in pedestrian accessibility studies. Common problems in the automatic segmentation of the LiDAR point cloud were corrected, achieving a very accurate segmentation of the points belonging to the ground. In addition, problems caused by occlusions caused mainly by parked vehicles and that prevent the availability of LiDAR points in spaces normally intended for pedestrian circulation, such as sidewalks, were solved in the proposed methodology. The innovation of this method lies, therefore, in the high definition of the generated 3D model of the pedestrian space to model pedestrian mobility, which allowed us to apply it in the search for shorter and safer pedestrian paths between the homes and schools of students in urban areas within the Big-Geomove project. Both the developed algorithms and the LiDAR data used are freely licensed for their use in further research.This research study was funded by the Directorate-General for Traffic of Spain, grant number SPIP2017-0234

A high-resolution photogrammetric workflow based on focus stacking for the 3D modeling of small Aegean inscriptions

Any attempt of decipherment and language identification of the scripts from the Aegean dating to the second millennium BCE (namely Cretan Hieroglyphic, Linear A, and Cypro-Minoan) has relied, until today, on traditional catalogues of inscriptions, consisting of incomplete or subjective 2D representations, such as photographs and hand-drawn copies, which are not suitable for documenting such three-dimensional writing systems. In contrast, 3D models of the inscribed media allow for an accurate and objective “autopsy” of the entire surface of the inscriptions. In this context, this work presents an efficient, accurate, high-resolution, and high-quality texture photogrammetric workflow based on focus-stacked macro images, designed for the 3D modeling of small Aegean inscriptions, to properly reconstruct their geometry and to enhance the identification of their signs, making their transcription as unbiased as possible. The pipeline we propose also benefits from a pre-processing stage to remove any coloration difference from the images, and a reliable and simple 3D scaling procedure. We tested this workflow on six inscribed artifacts (two in Cretan Hieroglyphic, three in Linear A, one of uncertain affiliation), whose average size ranges approximately from 1 to 3 cm. Our results show that this workflow achieved an accuracy of a few hundredths of mm, comparable to the technical specifications of standard commercial 3D scanners. Moreover, the high 3D density we obtained (corresponding to the edge average length of the 3D model mesh), up to ≈ 30 µm, allowed us to reconstruct even the smallest details of the inscriptions, both in the mesh and in the texture layer of the 3D models