<p> Advances in robotics and information technology are leading to the development of virtual reality-based surgical simulators as an alternative to the conventional means of medical training. Modeling and simulation of medical procedures also have numerous applications in pre-operative and intra-operative surgical planning as well as robotic (semi)-autonomous execution of surgical tasks. </p> <p> Surgical simulation requires modeling of human soft-tissue organs. Soft-tissues exhibit geometrical and material nonlinearities that should be taken into account for realistic modeling of the deformations and interaction forces between the surgical tool and tissues during medical procedures. However, most existing work in the literature, particularly for modeling of cutting, use linear deformation models. In this thesis, modeling of two common surgical tasks, i.e. palpation and cutting, using nonlinear modeling techniques has been studied. The complicated mechanical behavior of soft-tissue deformation is modeled by considering both geometrical and material nonlinearities. Large deformations are modeled by employing a nonlinear strain measure, the Green-Lagrange strain tensor, and a nonlinear stress-strain curve is employed by using an Ogden-based hyperelastic constitutive equation. The incompressible property of soft-tissue material during the deformation is enforced by modifying the strain energy function to include a term that penalizes changes in the object's area/volume. The problem of simulating the tool-tissue interactions using nonlinear dynamic analysis is formulated within a total Lagrangian framework. The finite element method is utilized to discretize the deformable object model in space and an explicit time integration is employed to solve for the resulting deformations. </p> <p> In this thesis, the nonlinear finite element analysis with the Ogden-based constitutive equation has also been applied to the modeling of soft-tissue cutting. Element separation and node snapping are used to create a cut in the mesh that is close to the tool trajectory. The external force applied on the object along the tool direction is used as a physical cutting criterion. The possibility of producing degenerated elements by node snapping that can cause numerical instability in the simulation is eliminated by remeshing the local elements when badly shaped elements are generated. The remeshing process involves retriangulation of the local elements using the Delaunay function and/ or moving a node depending on what is needed in order to generate elements with the required quality. </p> <p> Extensive simulations have been carried out in order to evaluate and demonstrate the effectiveness of the proposed modeling techniques and the results are reported in the thesis. A two-dimensional object with a concentrated external force has been considered in the simulations. </p> / Thesis / Master of Applied Science (MASc)

Esta dissertação de mestrado propõe o estudo e a implementação de um método de deformação usando modelos tridimensionais sem o uso de malhas baseado na técnica Smoothed Particles Hydrodynamics (SPH), que consiste num sistema de resolução de equações diferenciais para aplicação de conceitos físicos para simular deformação de tecidos moles. A opção pelo método sem malha para processo de deformação é apresentado nesta dissertação como alternativa a um dos métodos mais comuns em simulação de deformação de tecidos, o método massa-mola, explorando questões referentes ao uso de recursos computacionais. Para chegada a definição do método foram analisados os temas envolvendo métodos de deformação, modelos baseados em pontos e o SPH como plataformas para alcançar o desenvolvimento do método proposto pela dissertação. Como forma de comprovar as propriedades do método desenvolvido foi realizada a implementação e testes levando em consideração os modelos de deformação e a interação em tempo real num ambiente de simulação que contempla a deformação de uma mama, levando em conta a comparação com o método massa-mola, o uso de recursos do próprio método em função do aumento de detalhe e do uso de objeto com múltiplas propriedades / This master thesis proposes a study and implementation of deformation method using tridimensional models without edge composed meshes based on Smoothed Particles Hydrodynamics (SPH) technique, that consists on diferential equation solving system to reproduce physical concepts to simulate soft tissue deformation. The option for a meshless method to deformation process is shown in this thesis as an alternative to a very common method in tissue deform simulation, the mass-spring method, reviewing a comparison based on computational resources. To achieve a method definition were analyzed fields of study involving deformation methods, point-based models and SPH as platforms to build and deploy the proposed method for this thesis. To show the characteristics for this developed deformation method was realized the implementation and tests based on deformation models and real time interaction on a simulation environment that includes a breast deformation, taking in account the comparison to mass-spring, number of points of the cloud model and multiple properties

Esta dissertação de mestrado propõe o estudo e a implementação de um método de deformação usando modelos tridimensionais sem o uso de malhas baseado na técnica Smoothed Particles Hydrodynamics (SPH), que consiste num sistema de resolução de equações diferenciais para aplicação de conceitos físicos para simular deformação de tecidos moles. A opção pelo método sem malha para processo de deformação é apresentado nesta dissertação como alternativa a um dos métodos mais comuns em simulação de deformação de tecidos, o método massa-mola, explorando questões referentes ao uso de recursos computacionais. Para chegada a definição do método foram analisados os temas envolvendo métodos de deformação, modelos baseados em pontos e o SPH como plataformas para alcançar o desenvolvimento do método proposto pela dissertação. Como forma de comprovar as propriedades do método desenvolvido foi realizada a implementação e testes levando em consideração os modelos de deformação e a interação em tempo real num ambiente de simulação que contempla a deformação de uma mama, levando em conta a comparação com o método massa-mola, o uso de recursos do próprio método em função do aumento de detalhe e do uso de objeto com múltiplas propriedades / This master thesis proposes a study and implementation of deformation method using tridimensional models without edge composed meshes based on Smoothed Particles Hydrodynamics (SPH) technique, that consists on diferential equation solving system to reproduce physical concepts to simulate soft tissue deformation. The option for a meshless method to deformation process is shown in this thesis as an alternative to a very common method in tissue deform simulation, the mass-spring method, reviewing a comparison based on computational resources. To achieve a method definition were analyzed fields of study involving deformation methods, point-based models and SPH as platforms to build and deploy the proposed method for this thesis. To show the characteristics for this developed deformation method was realized the implementation and tests based on deformation models and real time interaction on a simulation environment that includes a breast deformation, taking in account the comparison to mass-spring, number of points of the cloud model and multiple properties

Biomechanical imaging (BMI) is the process of non-invasively measuring the spatial distribution of mechanical properties of biological tissues. The most common approach uses ultrasound to non-invasively measure soft tissue deformations. The measured deformations are then used in an inverse problem to infer local tissue mechanical properties. Thus quantifying local tissue mechanical properties can enable better medical diagnosis, treatment, and understanding of various diseases. A major difficulty with ultrasound biomechanical imaging is getting accurate measurements of all components of the tissue displacement vector field. One component of the displacement field, that parallel to the direction of sound propagation, is typically measured accurately and precisely; the others are available at such low precision that they may be disregarded in the first instance. If all components were available at high precision, the inverse problem for mechanical properties could be solved directly, and very efficiently. When only one component is available, the inverse problem solution is necessarily iterative, and relatively speaking, computationally inefficient. The goal of this thesis, therefore, is to develop a processing method that can be used to recover the missing displacement data with sufficient precision to allow the direct reconstruction of the linear elastic modulus distribution in tissue. This goal was achieved by using a novel spatial regularization to adaptively enforce and locally relax a special form of momentum conservation on the measured deformation field. The new processing method was implemented with the Finite Element Method (FEM). The processing method was tested with simulated data, measured data from a tissue mimicking phantom, and in-vivo clinical data of breast masses, and in all cases it was able to recover precise estimates the full 2D displacement and strain fields. The recovered strains were then used to calculate the material property distribution directly.

Depth information of tissue surfaces and laparoscope poses are crucial for accurate surgical guidance and navigation in Computer Assisted Surgeries (CAS). Intra-operative Three Dimensional (3D) reconstruction and laparoscope localization are therefore two fundamental tasks in CAS. This dissertation focuses on the abdominal Minimally Invasive Surgeries (MIS) and presents laparoscopic-video-based methods for these two tasks. Different kinds of methods have been presented to recover 3D surface structures of surgical scenes in MIS. Those methods are mainly based on laser, structured light, time-of-flight cameras, and video cameras. Among them, laparoscopic-video-based surface reconstruction techniques have many significant advantages. Specifically, they are non-invasive, provide intra-operative information, and do not introduce extra-hardware to the current surgical platform. On the other side, laparoscopic-video-based 3D reconstruction and laparoscope localization are challenging tasks due to the specialties of the abdominal imaging environment. The well-known difficulties include: low texture, homogeneous areas, tissue deformations, and so on. The goal of this dissertation is to design novel 3D reconstruction and laparoscope localization methods and overcome those challenges from the abdominal imaging environment. Two novel methods are proposed to achieve accurate 3D reconstruction for MIS. The first method is based on the detection of distinctive image features, which is difficult in MIS images due to the low-texture and homogeneous tissue surfaces. To overcome this problem, this dissertation first introduces new types of image features for MIS images based on blood vessels on tissue surfaces and designs novel methods to efficiently detect them. After vessel features have been detected, novel methods are presented to match them in stereo images and 3D vessels can be recovered for each frame. Those 3D vessels from different views are integrated together to obtain a global 3D vessel network and Poisson reconstruction is applied to achieve large-area dense surface reconstruction. The second method is texture-independent and does not rely on the detection of image features. Instead, it proposes to mount a single-point light source on the abdominal wall. Shadows are cast on tissue surfaces when surgical instruments are waving in front of the light. Shadow boundaries are detected and matched in stereo images to recover the depth information. The recovered 3D shadow curves are interpolated to achieve dense reconstruction of tissue surfaces. One novel stereoscope localization method is designed specifically for the abdominal environment. The method relies on RANdom SAmple Consensus (RANSAC) to differentiate rigid points and deforming points. Since no assumption is made on the tissue deformations, the proposed methods is able to handle general tissue deformations and achieve accurate laparoscope localization results in the abdominal MIS environment. With the stereoscope localization results and the large-area dense surface reconstruction, a new scene visualization system, periphery augmented system, is designed to augment the peripheral areas of the original video so that surgeons can have a larger field of view. A user-evaluation system is designed to compare the periphery augmented system with the original MIS video. 30 subjects including 4 surgeons specialized in abdominal MIS participate the evaluation and a numerical measure is defined to represent their understanding of surgical scenes. T-test is performed on the numerical errors and the null hypothesis that the periphery augmented system and the original video have the same mean of errors is rejected. In other words, the results validate that the periphery augmented system improves users' understanding and awareness of surgical scenes.

The long-term consequences of repetitive mild traumatic brain injuries (mTBIs), or concussions, as well as the immediate acute dangers of head collisions in sport have become of growing concern in the field of medicine, research and athletics. An estimated 3.8 million sports-related concussions occur in the United States annually, with the highest incidence having been documented in football, hockey, soccer, basketball and rugby (Harmon et al., 2013). The incidence of concussion in the National Rugby League (NRL) corresponds to approximately 8.0-17.5 injuries per 1000 playing hours, with tackling having been identified as the most common cause (Gardner et al., 2014; King et al., 2014). The highest incidence of rugby concussive impacts is a result of shoulder-to-head collisions (35%) during tackles and game play (Gardner et al., 2014). Shoulder-to-head concussive events occur primarily on the ball carrier and secondarily on the tacklers (Hendricks et al., 2014; Quarrie & Hopkins, 2008). While some studies report that the ball carrier is at a greater risk of sustaining a concussion (Gardner et al., 2015; King et al., 2010, 2014), others have demonstrated a greater incidence of tacklers being removed from play for sideline concussion evaluation (Gardner et al., 2014). Given this discrepancy, the purpose of this study was to compare dynamic response and brain tissue deformation metrics for ball carriers and defensive tacklers in professional rugby during shoulder-to-head concussive impacts using in-laboratory reconstructions. Ten cases with an injured defensive tackler and ten cases with an injured ball carrier were reconstructed using a pneumatic linear impactor striking a 50th percentile Hybrid III headform to calculate dynamic response and maximum principal strain values. There was no significant difference between the two impact conditions for peak resultant linear and rotational accelerations, as well as brain tissue deformation. Differences between metrics in this research and past research where the impacting system was not reported were discussed. These differences reflect the importance of accounting for impact compliance when describing the risk associated with collisions in professional rugby.

<p> The simulation of soft tissue deformations has many practical uses in the medical field such as diagnosing medical conditions, training medical professionals and surgical planning. While there are many good computational models that are used in these simulations, carrying out the simulations is time consuming especially for large systems. This is because most simulators are based on software, which are run on general-purpose computers (GPC) that are not optimized to carry out the operations needed for simulation. In order to improve the performance of these simulators, field-programmable-gate-arrays (FPGA) based accelerators for carrying out Matrix-by-Vector multiplications (MVM) have been implemented by Ramachandran in 1998 and Zhuo et. al. in 2005. Zhuo et. al. also looked at the best ways to store a matrix in memory, and how this is affected by certain properties of the matrix.</p> <p> A better approach is to implement an accelerator for carrying out all operations required for simulation on hardware. In this study we propose a hardware accelerator for simulating soft-tissue deformation using finite-difference approximation of elastodynamics equations based on conjugate-gradient inversion of sparse matrices. We designed and implemented the accelerator, which is optimized for use with sparse matrices, on FPGA. We also conducted performance and resource requirements analysis for the accelerator. Our results show this approach is capable of achieving sufficiently high computational rate for carrying out real-time simulation; even with large grids or meshes. Finally, we developed computational models for carrying out real-time simulation of tissue deformation.</p> / Thesis / Master of Applied Science (MASc)

Many preterm infants require mechanical ventilation as life-saving therapy. However, ventilation-induced overpressure can result in lung diseases. Considering the lung as a viscoelastic material, positive pressure inside the lung results in increased hydrostatic pressure and tissue compression. To elucidate the effect of positive pressure on lung tissue mechanics and cell behavior, we mimic the effect of overpressure by employing an uniaxial load onto fetal and adult rat lungs with different deformation rates. Additionally, tissue expansion during tidal breathing due to a negative intrathoracic pressure was addressed by uniaxial tension. We found a hyperelastic deformation behavior of fetal tissues under compression and tension with a remarkable strain stiffening. In contrast, adult lungs exhibited a similar response only during compression. Young’s moduli were always larger during tension compared to compression, while only during compression a strong deformation-rate dependency was found. In fact, fetal lung tissue under compression showed clear viscoelastic features even for small strains. Thus, we propose that the fetal lung is much more vulnerable during inflation by mechanical ventilation compared to normal inspiration. Electrophysiological experiments with different hydrostatic pressure gradients acting on primary fetal distal lung epithelial cells revealed that the activity of the epithelial sodium channel (ENaC) and the sodium-potassium pump (Na,K-ATPase) dropped during pressures of 30 cmH2O. Thus, pressures used during mechanical ventilation might impair alveolar fluid clearance important for normal lung function.