Three-Dimensional Biplanar Reconstruction of the Scoliotic Spine for Standard Clinical Setup

Tese de Doutoramento. Engenharia Informática. Faculdade de Engenharia. Universidade do Porto. 201

Deformable and articulated 3D reconstruction from monocular video sequences

PhDThis thesis addresses the problem of deformable and articulated structure from motion from monocular uncalibrated video sequences. Structure from motion is defined as the problem of recovering information about the 3D structure of scenes imaged by a camera in a video sequence. Our study aims at the challenging problem of non-rigid shapes (e.g. a beating heart or a smiling face). Non-rigid structures appear constantly in our everyday life, think of a bicep curling, a torso twisting or a smiling face. Our research seeks a general method to perform 3D shape recovery purely from data, without having to rely on a pre-computed model or training data. Open problems in the field are the difficulty of the non-linear estimation, the lack of a real-time system, large amounts of missing data in real-world video sequences, measurement noise and strong deformations. Solving these problems would take us far beyond the current state of the art in non-rigid structure from motion. This dissertation presents our contributions in the field of non-rigid structure from motion, detailing a novel algorithm that enforces the exact metric structure of the problem at each step of the minimisation by projecting the motion matrices onto the correct deformable or articulated metric motion manifolds respectively. An important advantage of this new algorithm is its ability to handle missing data which becomes crucial when dealing with real video sequences. We present a generic bilinear estimation framework, which improves convergence and makes use of the manifold constraints. Finally, we demonstrate a sequential, frame-by-frame estimation algorithm, which provides a 3D model and camera parameters for each video frame, while simultaneously building a model of object deformation

Computationally efficient deformable 3D object tracking with a monocular RGB camera

182 p.Monocular RGB cameras are present in most scopes and devices, including embedded environments like robots, cars and home automation. Most of these environments have in common a significant presence of human operators with whom the system has to interact. This context provides the motivation to use the captured monocular images to improve the understanding of the operator and the surrounding scene for more accurate results and applications.However, monocular images do not have depth information, which is a crucial element in understanding the 3D scene correctly. Estimating the three-dimensional information of an object in the scene using a single two-dimensional image is already a challenge. The challenge grows if the object is deformable (e.g., a human body or a human face) and there is a need to track its movements and interactions in the scene.Several methods attempt to solve this task, including modern regression methods based on Deep NeuralNetworks. However, despite the great results, most are computationally demanding and therefore unsuitable for several environments. Computational efficiency is a critical feature for computationally constrained setups like embedded or onboard systems present in robotics and automotive applications, among others.This study proposes computationally efficient methodologies to reconstruct and track three-dimensional deformable objects, such as human faces and human bodies, using a single monocular RGB camera. To model the deformability of faces and bodies, it considers two types of deformations: non-rigid deformations for face tracking, and rigid multi-body deformations for body pose tracking. Furthermore, it studies their performance on computationally restricted devices like smartphones and onboard systems used in the automotive industry. The information extracted from such devices gives valuable insight into human behaviour a crucial element in improving human-machine interaction.We tested the proposed approaches in different challenging application fields like onboard driver monitoring systems, human behaviour analysis from monocular videos, and human face tracking on embedded devices

Computationally efficient deformable 3D object tracking with a monocular RGB camera

182 p.Monocular RGB cameras are present in most scopes and devices, including embedded environments like robots, cars and home automation. Most of these environments have in common a significant presence of human operators with whom the system has to interact. This context provides the motivation to use the captured monocular images to improve the understanding of the operator and the surrounding scene for more accurate results and applications.However, monocular images do not have depth information, which is a crucial element in understanding the 3D scene correctly. Estimating the three-dimensional information of an object in the scene using a single two-dimensional image is already a challenge. The challenge grows if the object is deformable (e.g., a human body or a human face) and there is a need to track its movements and interactions in the scene.Several methods attempt to solve this task, including modern regression methods based on Deep NeuralNetworks. However, despite the great results, most are computationally demanding and therefore unsuitable for several environments. Computational efficiency is a critical feature for computationally constrained setups like embedded or onboard systems present in robotics and automotive applications, among others.This study proposes computationally efficient methodologies to reconstruct and track three-dimensional deformable objects, such as human faces and human bodies, using a single monocular RGB camera. To model the deformability of faces and bodies, it considers two types of deformations: non-rigid deformations for face tracking, and rigid multi-body deformations for body pose tracking. Furthermore, it studies their performance on computationally restricted devices like smartphones and onboard systems used in the automotive industry. The information extracted from such devices gives valuable insight into human behaviour a crucial element in improving human-machine interaction.We tested the proposed approaches in different challenging application fields like onboard driver monitoring systems, human behaviour analysis from monocular videos, and human face tracking on embedded devices

3D Non-Rigid Reconstruction with Prior Shape Constraints

3D non-rigid shape recovery from a single uncalibrated camera is a challenging, under-constrained problem in computer vision. Although tremendous progress has been achieved towards solving the problem, two main limitations still exist in most previous solutions. First, current methods focus on non-incremental solutions, that is, the algorithms require collection of all the measurement data before the reconstruction takes place. This methodology is inherently unsuitable for applications requiring real-time solutions. At the same time, most of the existing approaches assume that 3D shapes can be accurately modelled in a linear subspace. These methods are simple and have been proven effective for reconstructions of objects with relatively small deformations, but have considerable limitations when the deformations are large or complex. The non-linear deformations are often observed in highly flexible objects for which the use of the linear model is impractical. Note that specific types of shape variation might be governed by only a small number of parameters and therefore can be well-represented in a low dimensional manifold. The methods proposed in this thesis aim to estimate the non-rigid shapes and the corresponding camera trajectories, based on both the observations and the prior learned manifold. Firstly, an incremental approach is proposed for estimating the deformable objects. An important advantage of this method is the ability to reconstruct the 3D shape from a newly observed image and update the parameters in 3D shape space. However, this recursive method assumes the deformable shapes only have small variations from a mean shape, thus is still not feasible for objects subject to large scale deformations. To address this problem, a series of approaches are proposed, all based on non-linear manifold learning techniques. Such manifold is used as a shape prior, with the reconstructed shapes constrained to lie within the manifold. Those non-linear manifold based approaches significantly improve the quality of reconstructed results and are well-adapted to different types of shapes undergoing significant and complex deformations. Throughout the thesis, methods are validated quantitatively on 2D points sequences projected from the 3D motion capture data for a ground truth comparison, and are qualitatively demonstrated on real example of 2D video sequences. Comparisons are made for the proposed methods against several state-of-the-art techniques, with results shown for a variety of challenging deformable objects. Extensive experiments also demonstrate the robustness of the proposed algorithms with respect to measurement noise and missing data

Automatic registration of 3D models to laparoscopic video images for guidance during liver surgery

Laparoscopic liver interventions offer significant advantages over open surgery, such as less pain and trauma, and shorter recovery time for the patient. However, they also bring challenges for the surgeons such as the lack of tactile feedback, limited field of view and occluded anatomy. Augmented reality (AR) can potentially help during laparoscopic liver interventions by displaying sub-surface structures (such as tumours or vasculature). The initial registration between the 3D model extracted from the CT scan and the laparoscopic video feed is essential for an AR system which should be efficient, robust, intuitive to use and with minimal disruption to the surgical procedure. Several challenges of registration methods in laparoscopic interventions include the deformation of the liver due to gas insufflation in the abdomen, partial visibility of the organ and lack of prominent geometrical or texture-wise landmarks. These challenges are discussed in detail and an overview of the state of the art is provided. This research project aims to provide the tools to move towards a completely automatic registration. Firstly, the importance of pre-operative planning is discussed along with the characteristics of the liver that can be used in order to constrain a registration method. Secondly, maximising the amount of information obtained before the surgery, a semi-automatic surface based method is proposed to recover the initial rigid registration irrespective of the position of the shapes. Finally, a fully automatic 3D-2D rigid global registration is proposed which estimates a global alignment of the pre-operative 3D model using a single intra-operative image. Moving towards incorporating the different liver contours can help constrain the registration, especially for partial surfaces. Having a robust, efficient AR system which requires no manual interaction from the surgeon will aid in the translation of such approaches to the clinics

Modelling human pose and shape based on a database of human 3D scans

Generating realistic human shapes and motion is an important task both in the motion picture industry and in computer games. In feature films, high quality and believability are the most important characteristics. Additionally, when creating virtual doubles the generated charactes have to match as closely as possible to given real persons. In contrast, in computer games the level of realism does not need to be as high but real-time performance is essential. It is desirable to meet all these requirements with a general model of human pose and shape. In addition, many markerless human tracking methods applied, e.g., in biomedicine or sports science can benefit greatly from the availability of such a model because most methods require a 3D model of the tracked subject as input, which can be generated on-the-fly given a suitable shape and pose model. In this thesis, a comprehensive procedure is presented to generate different general models of human pose. A database of 3D scans spanning the space of human pose and shape variations is introduced. Then, four different approaches for transforming the database into a general model of human pose and shape are presented, which improve the current state of the art. Experiments are performed to evaluate and compare the proposed models on real-world problems, i.e., characters are generated given semantic constraints and the underlying shape and pose of humans given 3D scans, multi-view video, or uncalibrated monocular images is estimated.Die Erzeugung realistischer Menschenmodelle ist eine wichtige Anwendung in der Filmindustrie und bei Computerspielen. In Spielen ist Echtzeitsynthese unabdingbar aber der Detailgrad muß nicht so hoch sein wie in Filmen. Für virtuelle Doubles, wie sie z.B. in Filmen eingesetzt werden, muss der generierte Charakter dem gegebenen realen Menschen möglichst ähnlich sein. Mit einem generellen Modell für menschliche Pose und Körperform ist es möglich alle diese Anforderungen zu erfüllen. Zusätzlich können viele Verfahren zur markerlosen Bewegungserfassung, wie sie z.B. in der Biomedizin oder in den Sportwissenschaften eingesetzt werden, von einem generellen Modell für Pose und Körperform profitieren. Da diese ein 3D Modell der erfassten Person benötigen, das jetzt zur Laufzeit generiert werden kann. In dieser Doktorarbeit wird ein umfassender Ansatz vorgestellt, um verschiedene Modelle für Pose und Körperform zu berechnen. Zunächst wird eine Datenbank von 3D Scans aufgebaut, die Pose- und Körperformvariationen von Menschen umfasst. Dann werden vier verschiedene Verfahren eingeführt, die daraus generelle Modelle für Pose und Körperform berechnen und Probleme beim Stand der Technik beheben. Die vorgestellten Modelle werden auf realistischen Problemstellungen getestet. So werden Menschenmodelle aus einigen wenigen Randbedingungen erzeugt und Pose und Körperform von Probanden wird aus 3D Scans, Multi-Kamera Videodaten und Einzelbildern der bekleideten Personen geschätzt

Editing faces in videos

Editing faces in movies is of interest in the special effects industry. We aim at producing effects such as the addition of accessories interacting correctly with the face or replacing the face of a stuntman with the face of the main actor. The system introduced in this thesis is based on a 3D generative face model. Using a 3D model makes it possible to edit the face in the semantic space of pose, expression, and identity instead of pixel space, and due to its 3D nature allows a modelling of the light interaction. In our system we first reconstruct the 3D face, which is deforming because of expressions and speech, the lighting, and the camera in all frames of a monocular input video. The face is then edited by substituting expressions or identities with those of another video sequence or by adding virtual objects into the scene. The manipulated 3D scene is rendered back into the original video, correctly simulating the interaction of the light with the deformed face and virtual objects. We describe all steps necessary to build and apply the system. This includes registration of training faces to learn a generative face model, semi-automatic annotation of the input video, fitting of the face model to the input video, editing of the fit, and rendering of the resulting scene. While describing the application we introduce a host of new methods, each of which is of interest on its own. We start with a new method to register 3D face scans to use as training data for the face model. For video preprocessing a new interest point tracking and 2D Active Appearance Model fitting technique is proposed. For robust fitting we introduce background modelling, model-based stereo techniques, and a more accurate light model

Foetal echocardiographic segmentation

Congenital heart disease affects just under one percentage of all live births [1]. Those defects that manifest themselves as changes to the cardiac chamber volumes are the motivation for the research presented in this thesis. Blood volume measurements in vivo require delineation of the cardiac chambers and manual tracing of foetal cardiac chambers is very time consuming and operator dependent. This thesis presents a multi region based level set snake deformable model applied in both 2D and 3D which can automatically adapt to some extent towards ultrasound noise such as attenuation, speckle and partial occlusion artefacts. The algorithm presented is named Mumford Shah Sarti Collision Detection (MSSCD). The level set methods presented in this thesis have an optional shape prior term for constraining the segmentation by a template registered to the image in the presence of shadowing and heavy noise. When applied to real data in the absence of the template the MSSCD algorithm is initialised from seed primitives placed at the centre of each cardiac chamber. The voxel statistics inside the chamber is determined before evolution. The MSSCD stops at open boundaries between two chambers as the two approaching level set fronts meet. This has significance when determining volumes for all cardiac compartments since cardiac indices assume that each chamber is treated in isolation. Comparison of the segmentation results from the implemented snakes including a previous level set method in the foetal cardiac literature show that in both 2D and 3D on both real and synthetic data, the MSSCD formulation is better suited to these types of data. All the algorithms tested in this thesis are within 2mm error to manually traced segmentation of the foetal cardiac datasets. This corresponds to less than 10% of the length of a foetal heart. In addition to comparison with manual tracings all the amorphous deformable model segmentations in this thesis are validated using a physical phantom. The volume estimation of the phantom by the MSSCD segmentation is to within 13% of the physically determined volume