High-performance geometric vascular modelling

Image-based high-performance geometric vascular modelling and reconstruction is an essential component of computer-assisted surgery on the diagnosis, analysis and treatment of cardiovascular diseases. However, it is an extremely challenging task to efficiently reconstruct the accurate geometric structures of blood vessels out of medical images. For one thing, the shape of an individual section of a blood vessel is highly irregular because of the squeeze of other tissues and the deformation caused by vascular diseases. For another, a vascular system is a very complicated network of blood vessels with different types of branching structures. Although some existing vascular modelling techniques can reconstruct the geometric structure of a vascular system, they are either time-consuming or lacking sufficient accuracy. What is more, these techniques rarely consider the interior tissue of the vascular wall, which consists of complicated layered structures. As a result, it is necessary to develop a better vascular geometric modelling technique, which is not only of high performance and high accuracy in the reconstruction of vascular surfaces, but can also be used to model the interior tissue structures of the vascular walls.This research aims to develop a state-of-the-art patient-specific medical image-based geometric vascular modelling technique to solve the above problems. The main contributions of this research are:- Developed and proposed the Skeleton Marching technique to reconstruct the geometric structures of blood vessels with high performance and high accuracy. With the proposed technique, the highly complicated vascular reconstruction task is reduced to a set of simple localised geometric reconstruction tasks, which can be carried out in a parallel manner. These locally reconstructed vascular geometric segments are then combined together using shape-preserving blending operations to faithfully represent the geometric shape of the whole vascular system.- Developed and proposed the Thin Implicit Patch method to realistically model the interior geometric structures of the vascular tissues. This method allows the multi-layer interior tissue structures to be embedded inside the vascular wall to illustrate the geometric details of the blood vessel in real world

Numerical Simulation in Biomechanics and Biomedical Engineering

In the first contribution, Morbiducci and co-workers discuss the theoretical and methodological bases supporting the Lagrangian- and Euler-based methods, highlighting their application to cardiovascular flows. The second contribution, by the Ansón and van Lenthe groups, proposes an automated virtual bench test for evaluating the stability of custom shoulder implants without the necessity of mechanical testing. Urdeitx and Doweidar, in the third paper, also adopt the finite element method for developing a computational model aim to study cardiac cell behavior under mechano-electric stimulation. In the fourth contribution, Ayensa-Jiménez et al. develop a methodology to approximate the multidimensional probability density function of the parametric analysis obtained developing a mathematical model of the cancer evolution. The fifth paper is oriented to the topological data analysis; the group of Cueto and Chinesta designs a predictive model capable of estimating the state of drivers using the data collected from motion sensors. In the sixth contribution, the Ohayon and Finet group uses wall shear stress-derived descriptors to study the role of recirculation in the arterial restenosis due to different malapposed and overlapping stent conditions. In the seventh contribution, the research group of Antón demonstrates that the simulation time can be reduced for cardiovascular numerical analysis considering an adequate geometry-reduction strategy applicable to truncated patient specific artery. In the eighth paper, Grasa and Calvo present a numerical model based on the finite element method for simulating extraocular muscle dynamics. The ninth paper, authored by Kahla et al., presents a mathematical mechano-pharmaco-biological model for bone remodeling. Martínez, Peña, and co-workers propose in the tenth paper a methodology to calibrate the dissection properties of aorta layer, with the aim of providing useful information for reliable numerical tools. In the eleventh contribution, Martínez-Bocanegra et al. present the structural behavior of a foot model using a detailed finite element model. The twelfth contribution is centered on the methodology to perform a finite, element-based, numerical model of a hydroxyapatite 3D printed bone scaffold. In the thirteenth paper, Talygin and Gorodkov present analytical expressions describing swirling jets for cardiovascular applications. In the fourteenth contribution, Schenkel and Halliday propose a novel non-Newtonian particle transport model for red blood cells. Finally, Zurita et al. propose a parametric numerical tool for analyzing a silicone customized 3D printable trachea-bronchial prosthesis

A computational model of cell viability and proliferation of extrusion-based 3D-bioprinted constructs during tissue maturation process

3D bioprinting is a novel promising solution for living tissue fabrication, with several potential advantages in many different applicative sectors. However, the implementation of complex vascular networks remains as one of the limiting factors for the production of complex tissues and for bioprinting scale-up. In this work, a physics-based computational model is presented to describe nutrients diffusion and consumption phenomena in bioprinted constructs. The model - a system of partial differential equations that is approximated by means of the finite element method - allows for the description of cell viability and proliferation, and it can be easily adapted to different cell types, densities, biomaterials, and 3D-printed geometries, thus allowing a preassessment of cell viability within the bioprinted construct. The experimental validation is performed on bioprinted specimens to assess the ability of the model to predict changes in cell viability. The proposed model constitutes a proof of concept of digital twinning of biofabricated constructs that can be suitably included in the basic toolkit for tissue bioprinting

A Revisit of Shape Editing Techniques: from the Geometric to the Neural Viewpoint

3D shape editing is widely used in a range of applications such as movie production, computer games and computer aided design. It is also a popular research topic in computer graphics and computer vision. In past decades, researchers have developed a series of editing methods to make the editing process faster, more robust, and more reliable. Traditionally, the deformed shape is determined by the optimal transformation and weights for an energy term. With increasing availability of 3D shapes on the Internet, data-driven methods were proposed to improve the editing results. More recently as the deep neural networks became popular, many deep learning based editing methods have been developed in this field, which is naturally data-driven. We mainly survey recent research works from the geometric viewpoint to those emerging neural deformation techniques and categorize them into organic shape editing methods and man-made model editing methods. Both traditional methods and recent neural network based methods are reviewed

Simulation of the spatial structure and cellular organization evolution of cell aggregates arranged in various simple geometries, using a kinetic monte carlo method applied to a lattice model

ilustraciones, graficasEsta tesis trata los modelos de morfogénesis, en particular los modelos de evolución guiada por contacto que son coherentes con la hipótesis de la adhesión diferencial. Se presenta una revisión de algunos modelos, sus principios biológicos subyacentes, la relevancia y aplicaciones en el marco de la bioimpresión, la ingeniería de tejidos y la bioconvergencia. Luego, se presentan los detalles de los modelos basados en métodos de Monte Carlo para profundizar más adelante en el modelo basados en algoritmos Kinetic Monte Carlo (KMC) , más específicamente, se describe en detalle un modelo KMC de autoaprendizaje (SL-KMC). Se presenta y explica la estructura algorítmica del código implementado, se evalúa el rendimiento del modelo y se compara con un modelo KMC tradicional. Finalmente, se realizan los procesos de calibración y validación, se observó que el modelo es capaz de replicar la evolución del sistema multicelular cuando las condiciones de energía interfacial del sistema simulado son similares a las del sistema de calibraciones. (Texto tomado de la fuente)This thesis treats the models for morphogenesis, in particular the contact-guided evolution models that are coherent with the differential adhesion hypothesis. A review of some models, their biological underpinning principles, the relevance and applications in the framework of bioprinting, tissue engineering and bioconvergence are presented. Then the details for the Monte Carlo methods-based models are presented to later deep dive into the Kinetic Monte Carlo (KMC) based model, and more specifically a Self-Learning KMC (SL-KMC) model is described to detail. The algorithmic structure of the implemented code is presented and explained, the model performance is assessed and compared with a traditional KMC model. Finally, the calibration and validation processes have been carried out, it was observed that the model is able to replicate the multicellular system evolution when the interfacial energy conditions of the simulated system are similar to those of the calibrations system.MaestríaMagíster en Ingeniería - Ingeniería Químic

Translating computational modelling tools for clinical practice in congenital heart disease

Increasingly large numbers of medical centres worldwide are equipped with the means to acquire 3D images of patients by utilising magnetic resonance (MR) or computed tomography (CT) scanners. The interpretation of patient 3D image data has significant implications on clinical decision-making and treatment planning. In their raw form, MR and CT images have become critical in routine practice. However, in congenital heart disease (CHD), lesions are often anatomically and physiologically complex. In many cases, 3D imaging alone can fail to provide conclusive information for the clinical team. In the past 20-30 years, several image-derived modelling applications have shown major advancements. Tools such as computational fluid dynamics (CFD) and virtual reality (VR) have successfully demonstrated valuable uses in the management of CHD. However, due to current software limitations, these applications have remained largely isolated to research settings, and have yet to become part of clinical practice. The overall aim of this project was to explore new routes for making conventional computational modelling software more accessible for CHD clinics. The first objective was to create an automatic and fast pipeline for performing vascular CFD simulations. By leveraging machine learning, a solution was built using synthetically generated aortic anatomies, and was seen to be able to predict 3D aortic pressure and velocity flow fields with comparable accuracy to conventional CFD. The second objective was to design a virtual reality (VR) application tailored for supporting the surgical planning and teaching of CHD. The solution was a Unity-based application which included numerous specialised tools, such as mesh-editing features and online networking for group learning. Overall, the outcomes of this ongoing project showed strong indications that the integration of VR and CFD into clinical settings is possible, and has potential for extending 3D imaging and supporting the diagnosis, management and teaching of CHD

Titanium Lattice Structures Produced via Additive Manufacturing for a Bone Scaffold: A Review

The progress in additive manufacturing has remarkably increased the application of lattice materials in the biomedical field for the fabrication of scaffolds used as bone substitutes. Ti6Al4V alloy is widely adopted for bone implant application as it combines both biological and mechanical properties. Recent breakthroughs in biomaterials and tissue engineering have allowed the regeneration of massive bone defects, which require external intervention to be bridged. However, the repair of such critical bone defects remains a challenge. The present review collected the most significant findings in the literature of the last ten years on Ti6Al4V porous scaffolds to provide a comprehensive summary of the mechanical and morphological requirements for the osteointegration process. Particular attention was given on the effects of pore size, surface roughness and the elastic modulus on bone scaffold performances. The application of the Gibson-Ashby model allowed for a comparison of the mechanical performance of the lattice materials with that of human bone. This allows for an evaluation of the suitability of different lattice materials for biomedical applications