3D SEM Surface Reconstruction: An Optimized, Adaptive, and Intelligent Approach

Structural analysis of microscopic objects is a longstanding topic in several scientific disciplines, including biological, mechanical, and material sciences. The scanning electron microscope (SEM), as a promising imaging equipment has been around to determine the surface properties (e.g., compositions or geometries) of specimens by achieving increased magnification, contrast, and resolution greater than one nanometer. Whereas SEM micrographs still remain two-dimensional (2D), many research and educational questions truly require knowledge and information about their three-dimensional (3D) surface structures. Having 3D surfaces from SEM images would provide true anatomic shapes of micro samples which would allow for quantitative measurements and informative visualization of the systems being investigated. In this research project, we novel design and develop an optimized, adaptive, and intelligent multi-view approach named 3DSEM++ for 3D surface reconstruction of SEM images, making a 3D SEM dataset publicly and freely available to the research community. The work is expected to stimulate more interest and draw attention from the computer vision and multimedia communities to the fast-growing SEM application area

Non-Rigid Structure from Motion

This thesis revisits a challenging classical problem in geometric computer vision known as "Non-Rigid Structure-from-Motion" (NRSfM). It is a well-known problem where the task is to recover the 3D shape and motion of a non-rigidly moving object from image data. A reliable solution to this problem is valuable in several industrial applications such as virtual reality, medical surgery, animation movies etc. Nevertheless, to date, there does not exist any algorithm that can solve NRSfM for all kinds of conceivable motion. As a result, additional constraints and assumptions are often employed to solve NRSfM. The task is challenging due to the inherent unconstrained nature of the problem itself as many 3D varying configurations can have similar image projections. The problem becomes even more challenging if the camera is moving along with the object. The thesis takes on a modern view to this challenging problem and proposes a few algorithms that have set a new performance benchmark to solve NRSfM. The thesis not only discusses the classical work in NRSfM but also proposes some powerful elementary modification to it. The foundation of this thesis surpass the traditional single object NRSFM and for the first time provides an effective formulation to realise multi-body NRSfM. Most techniques for NRSfM under factorisation can only handle sparse feature correspondences. These sparse features are then used to construct a scene using the organisation of points, lines, planes or other elementary geometric primitive. Nevertheless, sparse representation of the scene provides an incomplete information about the scene. This thesis goes from sparse NRSfM to dense NRSfM for a single object, and then slowly lifts the intuition to realise dense 3D reconstruction of the entire dynamic scene as a global as rigid as possible deformation problem. The core of this work goes beyond the traditional approach to deal with deformation. It shows that relative scales for multiple deforming objects can be recovered under some mild assumption about the scene. The work proposes a new approach for dense detailed 3D reconstruction of a complex dynamic scene from two perspective frames. Since the method does not need any depth information nor it assumes a template prior, or per-object segmentation, or knowledge about the rigidity of the dynamic scene, it is applicable to a wide range of scenarios including YouTube Videos. Lastly, this thesis provides a new way to perceive the depth of a dynamic scene which essentially trivialises the notion of motion estimation as a compulsory step to solve this problem. Conventional geometric methods to address depth estimation requires a reliable estimate of motion parameters for each moving object, which is difficult to obtain and validate. In contrast, this thesis introduces a new motion-free approach to estimate the dense depth map of a complex dynamic scene for successive/multiple frames. The work show that given per-pixel optical flow correspondences between two consecutive frames and the sparse depth prior for the reference frame, we can recover the dense depth map for the successive frames without solving for motion parameters. By assigning the locally rigid structure to the piece-wise planar approximation of a dynamic scene which transforms as rigid as possible over frames, we can bypass the motion estimation step. Experiments results and MATLAB codes on relevant examples are provided to validate the motion-free idea

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

Three-dimensional modeling of the human jaw/teeth using optics and statistics.

Object modeling is a fundamental problem in engineering, involving talents from computer-aided design, computational geometry, computer vision and advanced manufacturing. The process of object modeling takes three stages: sensing, representation, and analysis. Various sensors may be used to capture information about objects; optical cameras and laser scanners are common with rigid objects, while X-ray, CT and MRI are common with biological organs. These sensors may provide a direct or an indirect inference about the object, requiring a geometric representation in the computer that is suitable for subsequent usage. Geometric representations that are compact, i.e., capture the main features of the objects with a minimal number of data points or vertices, fall into the domain of computational geometry. Once a compact object representation is in the computer, various analysis steps can be conducted, including recognition, coding, transmission, etc. The subject matter of this dissertation is object reconstruction from a sequence of optical images using shape from shading (SFS) and SFS with shape priors. The application domain is dentistry. Most of the SFS approaches focus on the computational part of the SFS problem, i.e. the numerical solution. As a result, the imaging model in most conventional SFS algorithms has been simplified under three simple, but restrictive assumptions: (1) the camera performs an orthographic projection of the scene, (2) the surface has a Lambertian reflectance and (3) the light source is a single point source at infinity. Unfortunately, such assumptions are no longer held in the case of reconstruction of real objects as intra-oral imaging environment for human teeth. In this work, we introduce a more realistic formulation of the SFS problem by considering the image formation components: the camera, the light source, and the surface reflectance. This dissertation proposes a non-Lambertian SFS algorithm under perspective projection which benefits from camera calibration parameters. The attenuation of illumination is taken account due to near-field imaging. The surface reflectance is modeled using the Oren-Nayar-Wolff model which accounts for the retro-reflection case. In this context, a new variational formulation is proposed that relates an evolving surface model with image information, taking into consideration that the image is taken by a perspective camera with known parameters. A new energy functional is formulated to incorporate brightness, smoothness and integrability constraints. In addition, to further improve the accuracy and practicality of the results, 3D shape priors are incorporated in the proposed SFS formulation. This strategy is motivated by the fact that humans rely on strong prior information about the 3D world around us in order to perceive 3D shape information. Such information is statistically extracted from training 3D models of the human teeth. The proposed SFS algorithms have been used in two different frameworks in this dissertation: a) holistic, which stitches a sequence of images in order to cover the entire jaw, and then apply the SFS, and b) piece-wise, which focuses on a specific tooth or a segment of the human jaw, and applies SFS using physical teeth illumination characteristics. To augment the visible portion, and in order to have the entire jaw reconstructed without the use of CT or MRI or even X-rays, prior information were added which gathered from a database of human jaws. This database has been constructed from an adult population with variations in teeth size, degradation and alignments. The database contains both shape and albedo information for the population. Using this database, a novel statistical shape from shading (SSFS) approach has been created. Extending the work on human teeth analysis, Finite Element Analysis (FEA) is adapted for analyzing and calculating stresses and strains of dental structures. Previous Finite Element (FE) studies used approximate 2D models. In this dissertation, an accurate three-dimensional CAD model is proposed. 3D stress and displacements of different teeth type are successfully carried out. A newly developed open-source finite element solver, Finite Elements for Biomechanics (FEBio), has been used. The limitations of the experimental and analytical approaches used for stress and displacement analysis are overcome by using FEA tool benefits such as dealing with complex geometry and complex loading conditions

Deep Learning for 3D Visual Perception

La percepción visual 3D se refiere al conjunto de problemas que engloban la reunión de información a través de un sensor visual y la estimación la posición tridimensional y estructura de los objetos y formaciones al rededor del sensor. Algunas funcionalidades como la estimación de la ego moción o construcción de mapas are esenciales para otras tareas de más alto nivel como conducción autónoma o realidad aumentada. En esta tesis se han atacado varios desafíos en la percepción 3D, todos ellos útiles desde la perspectiva de SLAM (Localización y Mapeo Simultáneos) que en si es un problema de percepción 3D.Localización y Mapeo Simultáneos –SLAM– busca realizar el seguimiento de la posición de un dispositivo (por ejemplo de un robot, un teléfono o unas gafas de realidad virtual) con respecto al mapa que está construyendo simultáneamente mientras la plataforma explora el entorno. SLAM es una tecnología muy relevante en distintas aplicaciones como realidad virtual, realidad aumentada o conducción autónoma. SLAM Visual es el termino utilizado para referirse al problema de SLAM resuelto utilizando unicamente sensores visuales. Muchas de las piezas del sistema ideal de SLAM son, hoy en día, bien conocidas, maduras y en muchos casos presentes en aplicaciones. Sin embargo, hay otras piezas que todavía presentan desafíos de investigación significantes. En particular, en los que hemos trabajado en esta tesis son la estimación de la estructura 3D al rededor de una cámara a partir de una sola imagen, reconocimiento de lugares ya visitados bajo cambios de apariencia drásticos, reconstrucción de alto nivel o SLAM en entornos dinámicos; todos ellos utilizando redes neuronales profundas.Estimación de profundidad monocular is la tarea de percibir la distancia a la cámara de cada uno de los pixeles en la imagen, utilizando solo la información que obtenemos de una única imagen. Este es un problema mal condicionado, y por lo tanto es muy difícil de inferir la profundidad exacta de los puntos en una sola imagen. Requiere conocimiento de lo que se ve y del sensor que utilizamos. Por ejemplo, si podemos saber que un modelo de coche tiene cierta altura y también sabemos el tipo de cámara que hemos utilizado (distancia focal, tamaño de pixel...); podemos decir que si ese coche tiene cierta altura en la imagen, por ejemplo 50 pixeles, esta a cierta distancia de la cámara. Para ello nosotros presentamos el primer trabajo capaz de estimar profundidad a partir de una sola vista que es capaz de obtener un funcionamiento razonable con múltiples tipos de cámara; como un teléfono o una cámara de video.También presentamos como estimar, utilizando una sola imagen, la estructura de una habitación o el plan de la habitación. Para este segundo trabajo, aprovechamos imágenes esféricas tomadas por una cámara panorámica utilizando una representación equirectangular. Utilizando estas imágenes recuperamos el plan de la habitación, nuestro objetivo es reconocer las pistas en la imagen que definen la estructura de una habitación. Nos centramos en recuperar la versión más simple, que son las lineas que separan suelo, paredes y techo.Localización y mapeo a largo plazo requiere dar solución a los cambios de apariencia en el entorno; el efecto que puede tener en una imagen tomarla en invierno o verano puede ser muy grande. Introducimos un modelo multivista invariante a cambios de apariencia que resuelve el problema de reconocimiento de lugares de forma robusta. El reconocimiento de lugares visual trata de identificar un lugar que ya hemos visitado asociando pistas visuales que se ven en las imágenes; la tomada en el pasado y la tomada en el presente. Lo preferible es ser invariante a cambios en punto de vista, iluminación, objetos dinámicos y cambios de apariencia a largo plazo como el día y la noche, las estaciones o el clima.Para tener funcionalidad a largo plazo también presentamos DynaSLAM, un sistema de SLAM que distingue las partes estáticas y dinámicas de la escena. Se asegura de estimar su posición unicamente basándose en las partes estáticas y solo reconstruye el mapa de las partes estáticas. De forma que si visitamos una escena de nuevo, nuestro mapa no se ve afectado por la presencia de nuevos objetos dinámicos o la desaparición de los anteriores.En resumen, en esta tesis contribuimos a diferentes problemas de percepción 3D; todos ellos resuelven problemas del SLAM Visual.<br /

Virtual anthropology? Reliability of three-dimensional photogrammetry as a forensic anthropology measurement and documentation technique

Establishing the identity of unknown remains is a vital role of forensic anthropology. While establishing identity is generally straightforward due to conventional methods of identification like DNA analysis, sometimes these methods are not applicable in the case of remains that are heavily skeletonized, severely decomposed or severely charred. In such instances, a forensic anthropologist will be called upon. The role of the forensic anthropologist is to aid in the identification of remains when conventional methods such as DNA and fingerprinting are not applicable. They may also be required to collaborate with other experts like forensic odontologists in order to attain a positive identification. A number of methods are available to the anthropologist that can aid in achieving identification: comparative radiography, nonimaged records, craniofacial superimposition, dental comparison and craniofacial reconstruction. All the methods except nonimaged records require imaging, either in two dimensions or three dimensions. Three-dimensional imaging is quickly becoming a vital tool for reconstruction, comparison, and analysis in forensic science. It has found applications in road accident reconstruction, facial reconstruction, comparison of patterned injuries to the injury-inflicting instruments, and anthropometry. The main three-dimensional imaging methods utilized in the forensic field are photogrammetry, laser scanning and radiological scanning (computed tomography (CT) and magnetic resonance imaging (MRI)), with forensic three-dimensional/computer aided design (3D/CAD)-supported photogrammetry being the method that is primarily used due to its low cost, rapid results, does not need expertise to operate, has no radiation risks and, above all, the record is permanent. Regardless of this, CT and MRI are more established methods and are widely used in a variety of industries. The purpose of this paper is to compare and contrast the three-dimensional imaging methods currently employed in forensic science on the basis of reliability, reproducibility, and accuracy; with an ultimate aim of validating photogrammetry as an analytical and documentation method of forensic science

Towards Visual Localization, Mapping and Moving Objects Tracking by a Mobile Robot: a Geometric and Probabilistic Approach

Dans cette thèse, nous résolvons le problème de reconstruire simultanément une représentation de la géométrie du monde, de la trajectoire de l'observateur, et de la trajectoire des objets mobiles, à l'aide de la vision. Nous divisons le problème en trois étapes : D'abord, nous donnons une solution au problème de la cartographie et localisation simultanées pour la vision monoculaire qui fonctionne dans les situations les moins bien conditionnées géométriquement. Ensuite, nous incorporons l'observabilité 3D instantanée en dupliquant le matériel de vision avec traitement monoculaire. Ceci élimine les inconvénients inhérents aux systèmes stéréo classiques. Nous ajoutons enfin la détection et suivi des objets mobiles proches en nous servant de cette observabilité 3D. Nous choisissons une représentation éparse et ponctuelle du monde et ses objets. La charge calculatoire des algorithmes de perception est allégée en focalisant activement l'attention aux régions de l'image avec plus d'intérêt. ABSTRACT : In this thesis we give new means for a machine to understand complex and dynamic visual scenes in real time. In particular, we solve the problem of simultaneously reconstructing a certain representation of the world's geometry, the observer's trajectory, and the moving objects' structures and trajectories, with the aid of vision exteroceptive sensors. We proceeded by dividing the problem into three main steps: First, we give a solution to the Simultaneous Localization And Mapping problem (SLAM) for monocular vision that is able to adequately perform in the most ill-conditioned situations: those where the observer approaches the scene in straight line. Second, we incorporate full 3D instantaneous observability by duplicating vision hardware with monocular algorithms. This permits us to avoid some of the inherent drawbacks of classic stereo systems, notably their limited range of 3D observability and the necessity of frequent mechanical calibration. Third, we add detection and tracking of moving objects by making use of this full 3D observability, whose necessity we judge almost inevitable. We choose a sparse, punctual representation of both the world and the moving objects in order to alleviate the computational payload of the image processing algorithms, which are required to extract the necessary geometrical information out of the images. This alleviation is additionally supported by active feature detection and search mechanisms which focus the attention to those image regions with the highest interest. This focusing is achieved by an extensive exploitation of the current knowledge available on the system (all the mapped information), something that we finally highlight to be the ultimate key to success

Cultural Heritage in Marker-Less Augmented Reality: A Survey

Augmented Reality (AR) is considered as one of the most significant technologies in the field of computer graphics and is utilized for many applications. In this paper, we have presented a comprehensive survey for cultural heritage using Augmented Reality systems. This survey describes the main objectives and characteristics of Marker-less Augmented Reality Systems through presenting up-to-date research results in this area. We describe the marker-less technologies in the area of AR, indoor marker-less AR, outdoor marker-less AR, real-time solutions to the tracking problem, real-time registration, cultural heritage in AR, 3D remonstration techniques, as well as presenting the problems in each research