Meshless Mechanics and Point-Based Visualization Methods for Surgical Simulations

Computer-based modeling and simulation practices have become an integral part of the medical education field. For surgical simulation applications, realistic constitutive modeling of soft tissue is considered to be one of the most challenging aspects of the problem, because biomechanical soft-tissue models need to reflect the correct elastic response, have to be efficient in order to run at interactive simulation rates, and be able to support operations such as cuts and sutures. Mesh-based solutions, where the connections between the individual degrees of freedom (DoF) are defined explicitly, have been the traditional choice to approach these problems. However, when the problem under investigation contains a discontinuity that disrupts the connectivity between the DoFs, the underlying mesh structure has to be reconfigured in order to handle the newly introduced discontinuity correctly. This reconfiguration for mesh-based techniques is typically called dynamic remeshing, and most of the time it causes the performance bottleneck in the simulation. In this dissertation, the efficiency of point-based meshless methods is investigated for both constitutive modeling of elastic soft tissues and visualization of simulation objects, where arbitrary discontinuities/cuts are applied to the objects in the context of surgical simulation. The point-based deformable object modeling problem is examined in three functional aspects: modeling continuous elastic deformations with, handling discontinuities in, and visualizing a point-based object. Algorithmic and implementation details of the presented techniques are discussed in the dissertation. The presented point-based techniques are implemented as separate components and integrated into the open-source software framework SOFA. The presented meshless continuum mechanics model of elastic tissue were verified by comparing it to the Hertzian non-adhesive frictionless contact theory. Virtual experiments were setup with a point-based deformable block and a rigid indenter, and force-displacement curves obtained from the virtual experiments were compared to the theoretical solutions. The meshless mechanics model of soft tissue and the integrated novel discontinuity treatment technique discussed in this dissertation allows handling cuts of arbitrary shape. The implemented enrichment technique not only modifies the internal mechanics of the soft tissue model, but also updates the point-based visual representation in an efficient way preventing the use of costly dynamic remeshing operations

Non-rigid registration of 2-D/3-D dynamic data with feature alignment

In this work, we are computing the matching between 2D manifolds and 3D manifolds with temporal constraints, that is we are computing the matching among a time sequence of 2D/3D manifolds. It is solved by mapping all the manifolds to a common domain, then build their matching by composing the forward mapping and the inverse mapping. At first, we solve the matching problem between 2D manifolds with temporal constraints by using mesh-based registration method. We propose a surface parameterization method to compute the mapping between the 2D manifold and the common 2D planar domain. We can compute the matching among the time sequence of deforming geometry data through this common domain. Compared with previous work, our method is independent of the quality of mesh elements and more efficient for the time sequence data. Then we develop a global intensity-based registration method to solve the matching problem between 3D manifolds with temporal constraints. Our method is based on a 4D(3D+T) free-from B-spline deformation model which has both spatial and temporal smoothness. Compared with previous 4D image registration techniques, our method avoids some local minimum. Thus it can be solved faster and achieve better accuracy of landmark point predication. We demonstrate the efficiency of these works on the real applications. The first one is applied to the dynamic face registering and texture mapping. The second one is applied to lung tumor motion tracking in the medical image analysis. In our future work, we are developing more efficient mesh-based 4D registration method. It can be applied to tumor motion estimation and tracking, which can be used to calculate the read dose delivered to the lung and surrounding tissues. Thus this can support the online treatment of lung cancer radiotherapy

A parallel interaction potential approach coupled with the immersed boundary method for fully resolved simulations of deformable interfaces and membranes

In this paper we show and discuss the use of a versatile interaction potential approach coupled with an immersed boundary method to simulate a variety of flows involving deformable bodies. In particular, we focus on two kinds of problems, namely (i) deformation of liquid-liquid interfaces and (ii) flow in the left ventricle of the heart with either a mechanical or a natural valve. Both examples have in common the two-way interaction of the flow with a deformable interface or a membrane. The interaction potential approach (de Tullio & Pascazio, Jou. Comp. Phys., 2016; Tanaka, Wada and Nakamura, Computational Biomechanics, 2016) with minor modifications can be used to capture the deformation dynamics in both classes of problems. We show that the approach can be used to replicate the deformation dynamics of liquid-liquid interfaces through the use of ad-hoc elastic constants. The results from our simulations agree very well with previous studies on the deformation of drops in standard flow configurations such as deforming drop in a shear flow or a cross flow. We show that the same potential approach can also be used to study the flow in the left ventricle of the heart. The flow imposed into the ventricle interacts dynamically with the mitral valve (mechanical or natural) and the ventricle which are simulated using the same model. Results from these simulations are compared with ad- hoc in-house experimental measurements. Finally, a parallelisation scheme is presented, as parallelisation is unavoidable when studying large scale problems involving several thousands of simultaneously deforming bodies on hundreds of distributed memory computing processors

Physically-based 6-DoF Nodes Deformable Models: Application to Connective Tissues Simulation and Soft-Robots Control

The medical simulation is an increasingly active research field. Yet, despite the promising advance observed over the past years, the complete virtual patient’s model is yet to come. There are still many avenues for improvements, especially concerning the mechanical modeling of boundary conditions on anatomical structures.So far, most of the work has been dedicated to organs simulation, which are generally simulated alone. This raises a real problem as the role of the surrounding organs in the boundary conditions is neglected. However, these interactions can be complex, involving contacts but also mechanical links provided by layers of soft tissues. The latter are known as connective tissues or fasciae. As a consequence, the mutual influences between the anatomical structures are generally simplified, weakening the realism of the simulations.This thesis aims at studying the importance of the connective tissues, and especially of a proper modeling of the boundary conditions. To this end, the role of the ligaments during laparoscopic liver surgery has been investigated. In order to enhance the simulations’ realism, a mechanical model dedicated to the connective tissues has been worked out. This has led to the development of a physically-based method relying on material points that can, not only translate, but also rotate themselves. The goal of this model is to enable the simulation of multiple organs linked by complex interactions.In addition, the work on the connective tissues model has been derived to be used in soft robotics. Indeed, the principle of relying on orientable material points has been used to developed a reduced model that can reproduce the behavior of more complex structures. The objective of this work is to provide the means to control – in real-time – a soft robot made of a deformable arm.La simulation médicale est un domaine de recherche de plus en plus actif. Cependant, malgré les avancées prometteuses observées ces dernières années, le modèle complet du patient virtuel reste un objectif ambitieux. Il existe encore de nombreuses opportunités de recherche, notamment concernant la modélisation mécanique des conditions aux limites des organes.Jusqu'à présent, la majorité des travaux était consacrée à la simulation d'organes, ces derniers étant généralement simulés seuls. Cette situation pose un réel problème car l'influence qu'ont les organes environnants sur les conditions aux limites est négligée. Ces interactions peuvent être complexes, impliquant des contacts mais aussi des liaisons mécaniques dues à des couches de tissus connus sous le nom de tissus conjonctifs ou fasciae. Pour cette raison, les influences mutuelles entre les structures anatomiques sont généralement simplifiées, diminuant le réalisme des simulations.Cette thèse visé à étudier l'importance des tissus conjonctifs, et plus particulièrement d'une bonne modélisation des conditions aux limites. Dans ce but, le rôle des ligaments lors d'une intervention chirurgicale sur la foie par laparoscopie a été étudié. Afin d'améliorer le réalisme des simulations, un modèle mécanique dédié aux tissus conjonctifs a été mis au point. Ainsi, une méthode basée sur la mécanique des milieux continus et un ensemble de nœuds à 6 degrés de liberté a été développée. L'objectif de ce modèle étant de permettre la simulation simultanée de plusieurs organes liés par des interaction complexes.En outre, les travaux sur les tissus conjonctifs ont donné lieu à la mise au point d'une méthode de modélisation utilisée dans le cadre des robots déformables. Cette méthode permet un contrôle précis, et temps-réel, d'un bras robotisé déformable. En effet, l'utilisation de nœuds orientables a permis de développer un modèle a nombre de degrés de liberté réduit, qui permet de reproduire le comportement de structures plus complexes

Research on real-time physics-based deformation for haptic-enabled medical simulation

This study developed a multiple effective visuo-haptic surgical engine to handle a variety of surgical manipulations in real-time. Soft tissue models are based on biomechanical experiment and continuum mechanics for greater accuracy. Such models will increase the realism of future training systems and the VR/AR/MR implementations for the operating room

Physics-Based Probabilistic Motion Compensation of Elastically Deformable Objects

A predictive tracking approach and a novel method for visual motion compensation are introduced, which accurately reconstruct and compensate the deformation of the elastic object, even in the case of complete measurement information loss. The core of the methods involves a probabilistic physical model of the object, from which all other mathematical models are systematically derived. Due to flexible adaptation of the models, the balance between their complexity and their accuracy is achieved

Doctor of Philosophy in Computing

dissertationPhysics-based animation has proven to be a powerful tool for creating compelling animations for film and games. Most techniques in graphics are based on methods developed for predictive simulation for engineering applications; however, the goals for graphics applications are dramatically different than the goals of engineering applications. As a result, most physics-based animation tools are difficult for artists to work with, providing little direct control over simulation results. In this thesis, we describe tools for physics-based animation designed with artist needs and expertise in mind. Most materials can be modeled as elastoplastic: they recover from small deformations, but large deformations permanently alter their rest shape. Unfortunately, large plastic deformations, common in graphical applications, cause simulation instabilities if not addressed. Most elastoplastic simulation techniques in graphics rely on a finite-element approach where objects are discretized into a tetrahedral mesh. Using these approaches, maintaining simulation stability during large plastic flows requires remeshing, a complex and computationally expensive process. We introduce a new point-based approach that does not rely on an explicit mesh and avoids the expense of remeshing. Our approach produces comparable results with much lower implementation complexity. Points are a ubiquitous primitive for many effects, so our approach also integrates well with existing artist pipelines. Next, we introduce a new technique for animating stylized images which we call Dynamic Sprites. Artists can use our tool to create digital assets that interact in a natural, but stylized, way in virtual environments. In order to support the types of nonphysical, exaggerated motions often desired by artists, our approach relies on a heavily modified deformable body simulator, equipped with a set of new intuitive controls and an example-based deformation model. Our approach allows artists to specify how the shape of the object should change as it moves and collides in interactive virtual environments. Finally, we introduce a new technique for animating destructive scenes. Our approach is built on the insight that the most important visual aspects of destruction are plastic deformation and fracture. Like with Dynamic Sprites, we use an example-based model of deformation for intuitive artist control. Our simulator treats objects as rigid when computing dynamics but allows them to deform plastically and fracture in between timesteps based on interactions with the other objects. We demonstrate that our approach can efficiently animate the types of destructive scenes common in film and games. These animation techniques are designed to exploit artist expertise to ease creation of complex animations. By using artist-friendly primitives and allowing artists to provide characteristic deformations as input, our techniques enable artists to create more compelling animations, more easily

Investigation of the use of meshfree methods for haptic thermal management of design and simulation of MEMS

This thesis presents a novel approach of using haptic sensing technology combined with virtual environment (VE) for the thermal management of Micro-Electro-Mechanical-Systems (MEMS) design. The goal is to reduce the development cycle by avoiding the costly iterative prototyping procedure. In this regard, we use haptic feedback with virtua lprototyping along with an immersing environment. We also aim to improve the productivity and capability of the designer to better grasp the phenomena operating at the micro-scale level, as well as to augment computational steering through haptic channels. To validate the concept of haptic thermal management, we have implemented a demonstrator with a user friendly interface which allows to intuitively "feel" the temperature field through our concept of haptic texturing. The temperature field in a simple MEMS component is modeled using finite element methods (FEM) or finite difference method (FDM) and the user is able to feel thermal expansion using a combination of different haptic feedback. In haptic application, the force rendering loop needs to be updated at a frequency of 1Khz in order to maintain continuity in the user perception. When using FEM or FDM for our three-dimensional model, the computational cost increases rapidly as the mesh size is reduced to ensure accuracy. Hence, it constrains the complexity of the physical model to approximate temperature or stress field solution. It would also be difficult to generate or refine the mesh in real time for CAD process. In order to circumvent the limitations due to the use of conventional mesh-based techniques and to avoid the bothersome task of generating and refining the mesh, we investigate the potential of meshfree methods in the context of our haptic application. We review and compare the different meshfree formulations against FEM mesh based technique. We have implemented the different methods for benchmarking thermal conduction and elastic problems. The main work of this thesis is to determine the relevance of the meshfree option in terms of flexibility of design and computational charge for haptic physical model