Fluid-electro-mechanical model of the human heart for supercomputers

The heart is a complex system. From the transmembrane cell activity to the spatial organization in helicoidal fibers, it includes several spatial and temporal scales. The heart muscle is surrounded by two main tissues that modulate how it deforms: the pericardium and the blood. The former constrains the epicardial surface and the latter exerts a force in the endocardium. The main function of this peculiar muscle is to pump blood to the pulmonary and systemic circulations. In this way, solid dynamics of the heart is as important as the induced fluid dynamics. Despite the work done in computational research of multiphysics heart modelling, there is no reference of a tightly-coupled scheme that includes electrophysiology, solid and fluid mechanics in a whole human heart. In this work, we propose, develop and test a fluid-electro-mechanical model of the human heart. To start, the heartbeat phenomenon is disassembled in the different composing problems. The first building block is the electrical activity of the myocytes, that induces the mechanical deformation of the myocardium. The contraction of the muscle reduces the intracavitary space, that pushes out the contained blood. At the same time, the inertia, pressure and viscous stresses in this fluid exerts a force on the solid wall. In this way, we can understand the heart as a fluid-electro-mechanical problem. All the models are implemented in Alya, the Barcelona Supercomputing Center simulation software. A multi-code approach is used, splitting the problem in a solid and a fluid domain. In the former, electrophysiology coupled with solid mechanics are solved. In the later, fluid dynamics in an arbitrary Lagrangian-Eulerian domain are computed. The equations are spatially discretized using the finite element method and temporally discretized using finite differences. Facilitated by the multi-code approach, a novel high performance quasi-Newton method is developed to deal with the intrinsic issues of fluid-structure interaction problems in iomechanics. All the schemes are optimized to run in massively parallel computers. A wide range of experiments are shown to validate, test and tune the numerical model. The different hypothesis proposed — as the critical effect of the atrium or the presence of pericardium — are also tested in these experiments. Finally, a normal heartbeat is simulated and deeply analyzed. This healthy computational heart is first diseased with a left bundle branch block. After this, its function is restored simulating a cardiac resynchronization therapy. Then, a third grade atrioventricular block is simulated in the healthy heart. In this case, the pathologic model is treated with a minimally invasive leadless intracardiac pacemaker. This requires to include the device in the geometrical description of the problem, solve the structural problem with the tissue, and the fluid-structure interaction problem with the blood. As final experiment, we test the parallel performance of the coupled solver. In the cases mentioned above, the results are qualitatively compared against experimental measurements, when possible. Finally, a first glance in a coupled fluid-electro-mechanical cardiovascular system is shown. This model is build adding a one dimensional model of the arterial network created by the Laboratório Nacional de Computação Científica in Petropolis, Brasil. Despite the artificial geometries used, the outflow curves are comparable with physiological observations. The model presented in this thesis is a step towards the virtual human heart. In a near future computational models like the presented in this thesis will change how pathologies are understood and treated, and the way biomedical devices are designed.El corazón es un sistema complejo. Desde la actividad celular hasta la organización espacial en fibras helicoidales, incluye gran cantidad de escalas espaciales y temporales. El corazón está rodeado principalmente por dos tejidos que modulan su deformación: el pericardio y la sangre. El primero restringe el movimiento del epicardio, mientras el segundo ejerce fuerza sobre el endocardio. La función principal de este músculo es bombear sangre a la circulación sistémica y a la pulmonar. Así, la deformación del miocardio es tan importante como la fluidodinámica inducida. Al día de hoy, solo se han propuesto modelos parciales del corazón. Ninguno de los modelos publicados resuelve electrofisiología, mecánica del sólido, y dinámica de fluidos en una geometría completa del corazón. En esta tesis, proponemos, desarrollamos y probamos un modelo fluido -electro -mecánico del corazón. Primero, el problema del latido cardíaco es descompuesto en los distintos subproblemas. El primer bloque componente es la actividad eléctrica de los miocitos, que inducen la deformación mecánica del miocardio. La contratación de este músculo, reduce el espacio intracavitario, que empuja la sangre contenida. Al mismo tiempo, la inercia, presión y fuerzas viscosas del fluido inducen una presión sobre la pared del sólido. De esta manera, podemos entender el latido cardíaco como un problema fluido-electro-mecánico. Los modelos son implementados en Alya, el software de simulación del Barcelona Supercomputing Center. Se utiliza un diseño multi-código, separando el problema según el dominio en sólido y fluido. En el primero, se resuelve electrofisiología acoplado con mecánica del sólido. En el segundo, fluido dinámica en un dominio arbitrario Lagrangiano-Euleriano. Las ecuaciones son discretizadas espacial y temporalmente utilizando elementos finitos y diferencias finitas respectivamente. Facilitado por el diseño multi-codigo, se desarrolló un novedoso método quasi-Newton de alta performance, pensado específicamente para lidiar con los problemas intrínsecos de interacción fluido-estructura en biomecánica. Todos los esquemas fueron optimizados para correr en ordenadores masivamente paralelos.Se presenta un amplio espectro de experimentos con el fin de validar, probar y ajustar el modelo numérico. Las diferentes hipótesis propuestas tales como el efecto producido por la presencia de las aurículas o el pericardio son también demostradas en estos experimentos. Finalmente un latido normal es simulado y sus resultados son analizados con profundidad. El corazón computacional sano es, primeramente enfermado de un bloqueo de rama izquierda. Posteriormente se restaura la función normal mediante la terapia de resincronización cardíaca. Luego se afecta al corazón de un bloqueo atrioventricular de tercer grado. Esta patología es tratada mediante la implantación de un marcapasos intracardíaco. Para esto, se requiere incluir el dispositivo en la descripción geométrica, resolver el problema estructural con el tejido y la interacción fluido-estructura con la sangre. Como experimento numérico final, se prueba el desempeño paralelo del modelo acoplado.Finalmente, se muestran resultados preliminares para un modelo fluido-electro-mecánico del sistema cardiovascular. Este modelo se construye agregando un modelo unidimensional del árbol arterial. A pesar de las geometrías artificiales usadas, la curva de flujo en la raíz aórtica es comparable con observaciones experimentales. El modelo presentado aquí representa un avance hacia el humano virtual. En un futuro, modelos similares, cambiarán la forma en la que se entienden y tratan las enfermedades y la forma en la que los dispositivos biomédicos son diseñados.Postprint (published version

Fluid-electro-mechanical model of the human heart for supercomputers

The heart is a complex system. From the transmembrane cell activity to the spatial organization in helicoidal fibers, it includes several spatial and temporal scales. The heart muscle is surrounded by two main tissues that modulate how it deforms: the pericardium and the blood. The former constrains the epicardial surface and the latter exerts a force in the endocardium. The main function of this peculiar muscle is to pump blood to the pulmonary and systemic circulations. In this way, solid dynamics of the heart is as important as the induced fluid dynamics. Despite the work done in computational research of multiphysics heart modelling, there is no reference of a tightly-coupled scheme that includes electrophysiology, solid and fluid mechanics in a whole human heart. In this work, we propose, develop and test a fluid-electro-mechanical model of the human heart. To start, the heartbeat phenomenon is disassembled in the different composing problems. The first building block is the electrical activity of the myocytes, that induces the mechanical deformation of the myocardium. The contraction of the muscle reduces the intracavitary space, that pushes out the contained blood. At the same time, the inertia, pressure and viscous stresses in this fluid exerts a force on the solid wall. In this way, we can understand the heart as a fluid-electro-mechanical problem. All the models are implemented in Alya, the Barcelona Supercomputing Center simulation software. A multi-code approach is used, splitting the problem in a solid and a fluid domain. In the former, electrophysiology coupled with solid mechanics are solved. In the later, fluid dynamics in an arbitrary Lagrangian-Eulerian domain are computed. The equations are spatially discretized using the finite element method and temporally discretized using finite differences. Facilitated by the multi-code approach, a novel high performance quasi-Newton method is developed to deal with the intrinsic issues of fluid-structure interaction problems in iomechanics. All the schemes are optimized to run in massively parallel computers. A wide range of experiments are shown to validate, test and tune the numerical model. The different hypothesis proposed — as the critical effect of the atrium or the presence of pericardium — are also tested in these experiments. Finally, a normal heartbeat is simulated and deeply analyzed. This healthy computational heart is first diseased with a left bundle branch block. After this, its function is restored simulating a cardiac resynchronization therapy. Then, a third grade atrioventricular block is simulated in the healthy heart. In this case, the pathologic model is treated with a minimally invasive leadless intracardiac pacemaker. This requires to include the device in the geometrical description of the problem, solve the structural problem with the tissue, and the fluid-structure interaction problem with the blood. As final experiment, we test the parallel performance of the coupled solver. In the cases mentioned above, the results are qualitatively compared against experimental measurements, when possible. Finally, a first glance in a coupled fluid-electro-mechanical cardiovascular system is shown. This model is build adding a one dimensional model of the arterial network created by the Laboratório Nacional de Computação Científica in Petropolis, Brasil. Despite the artificial geometries used, the outflow curves are comparable with physiological observations. The model presented in this thesis is a step towards the virtual human heart. In a near future computational models like the presented in this thesis will change how pathologies are understood and treated, and the way biomedical devices are designed.El corazón es un sistema complejo. Desde la actividad celular hasta la organización espacial en fibras helicoidales, incluye gran cantidad de escalas espaciales y temporales. El corazón está rodeado principalmente por dos tejidos que modulan su deformación: el pericardio y la sangre. El primero restringe el movimiento del epicardio, mientras el segundo ejerce fuerza sobre el endocardio. La función principal de este músculo es bombear sangre a la circulación sistémica y a la pulmonar. Así, la deformación del miocardio es tan importante como la fluidodinámica inducida. Al día de hoy, solo se han propuesto modelos parciales del corazón. Ninguno de los modelos publicados resuelve electrofisiología, mecánica del sólido, y dinámica de fluidos en una geometría completa del corazón. En esta tesis, proponemos, desarrollamos y probamos un modelo fluido -electro -mecánico del corazón. Primero, el problema del latido cardíaco es descompuesto en los distintos subproblemas. El primer bloque componente es la actividad eléctrica de los miocitos, que inducen la deformación mecánica del miocardio. La contratación de este músculo, reduce el espacio intracavitario, que empuja la sangre contenida. Al mismo tiempo, la inercia, presión y fuerzas viscosas del fluido inducen una presión sobre la pared del sólido. De esta manera, podemos entender el latido cardíaco como un problema fluido-electro-mecánico. Los modelos son implementados en Alya, el software de simulación del Barcelona Supercomputing Center. Se utiliza un diseño multi-código, separando el problema según el dominio en sólido y fluido. En el primero, se resuelve electrofisiología acoplado con mecánica del sólido. En el segundo, fluido dinámica en un dominio arbitrario Lagrangiano-Euleriano. Las ecuaciones son discretizadas espacial y temporalmente utilizando elementos finitos y diferencias finitas respectivamente. Facilitado por el diseño multi-codigo, se desarrolló un novedoso método quasi-Newton de alta performance, pensado específicamente para lidiar con los problemas intrínsecos de interacción fluido-estructura en biomecánica. Todos los esquemas fueron optimizados para correr en ordenadores masivamente paralelos.Se presenta un amplio espectro de experimentos con el fin de validar, probar y ajustar el modelo numérico. Las diferentes hipótesis propuestas tales como el efecto producido por la presencia de las aurículas o el pericardio son también demostradas en estos experimentos. Finalmente un latido normal es simulado y sus resultados son analizados con profundidad. El corazón computacional sano es, primeramente enfermado de un bloqueo de rama izquierda. Posteriormente se restaura la función normal mediante la terapia de resincronización cardíaca. Luego se afecta al corazón de un bloqueo atrioventricular de tercer grado. Esta patología es tratada mediante la implantación de un marcapasos intracardíaco. Para esto, se requiere incluir el dispositivo en la descripción geométrica, resolver el problema estructural con el tejido y la interacción fluido-estructura con la sangre. Como experimento numérico final, se prueba el desempeño paralelo del modelo acoplado.Finalmente, se muestran resultados preliminares para un modelo fluido-electro-mecánico del sistema cardiovascular. Este modelo se construye agregando un modelo unidimensional del árbol arterial. A pesar de las geometrías artificiales usadas, la curva de flujo en la raíz aórtica es comparable con observaciones experimentales. El modelo presentado aquí representa un avance hacia el humano virtual. En un futuro, modelos similares, cambiarán la forma en la que se entienden y tratan las enfermedades y la forma en la que los dispositivos biomédicos son diseñados

Registration of serial sections: An evaluation method based on distortions of the ground truths

Registration of histological serial sections is a challenging task. Serial sections exhibit distortions and damage from sectioning. Missing information on how the tissue looked before cutting makes a realistic validation of 2D registrations extremely difficult. This work proposes methods for ground-truth-based evaluation of registrations. Firstly, we present a methodology to generate test data for registrations. We distort an innately registered image stack in the manner similar to the cutting distortion of serial sections. Test cases are generated from existing 3D data sets, thus the ground truth is known. Secondly, our test case generation premises evaluation of the registrations with known ground truths. Our methodology for such an evaluation technique distinguishes this work from other approaches. Both under- and over-registration become evident in our evaluations. We also survey existing validation efforts. We present a full-series evaluation across six different registration methods applied to our distorted 3D data sets of animal lungs. Our distorted and ground truth data sets are made publicly available.Comment: Supplemental data available under https://zenodo.org/record/428244

Proceedings of the second "international Traveling Workshop on Interactions between Sparse models and Technology" (iTWIST'14)

The implicit objective of the biennial "international - Traveling Workshop on Interactions between Sparse models and Technology" (iTWIST) is to foster collaboration between international scientific teams by disseminating ideas through both specific oral/poster presentations and free discussions. For its second edition, the iTWIST workshop took place in the medieval and picturesque town of Namur in Belgium, from Wednesday August 27th till Friday August 29th, 2014. The workshop was conveniently located in "The Arsenal" building within walking distance of both hotels and town center. iTWIST'14 has gathered about 70 international participants and has featured 9 invited talks, 10 oral presentations, and 14 posters on the following themes, all related to the theory, application and generalization of the "sparsity paradigm": Sparsity-driven data sensing and processing; Union of low dimensional subspaces; Beyond linear and convex inverse problem; Matrix/manifold/graph sensing/processing; Blind inverse problems and dictionary learning; Sparsity and computational neuroscience; Information theory, geometry and randomness; Complexity/accuracy tradeoffs in numerical methods; Sparsity? What's next?; Sparse machine learning and inference.Comment: 69 pages, 24 extended abstracts, iTWIST'14 website: http://sites.google.com/site/itwist1

Prostate biopsy tracking with deformation estimation

Transrectal biopsies under 2D ultrasound (US) control are the current clinical standard for prostate cancer diagnosis. The isoechogenic nature of prostate carcinoma makes it necessary to sample the gland systematically, resulting in a low sensitivity. Also, it is difficult for the clinician to follow the sampling protocol accurately under 2D US control and the exact anatomical location of the biopsy cores is unknown after the intervention. Tracking systems for prostate biopsies make it possible to generate biopsy distribution maps for intra- and post-interventional quality control and 3D visualisation of histological results for diagnosis and treatment planning. They can also guide the clinician toward non-ultrasound targets. In this paper, a volume-swept 3D US based tracking system for fast and accurate estimation of prostate tissue motion is proposed. The entirely image-based system solves the patient motion problem with an a priori model of rectal probe kinematics. Prostate deformations are estimated with elastic registration to maximize accuracy. The system is robust with only 17 registration failures out of 786 (2%) biopsy volumes acquired from 47 patients during biopsy sessions. Accuracy was evaluated to 0.76$\pm$0.52mm using manually segmented fiducials on 687 registered volumes stemming from 40 patients. A clinical protocol for assisted biopsy acquisition was designed and implemented as a biopsy assistance system, which allows to overcome the draw-backs of the standard biopsy procedure.Comment: Medical Image Analysis (2011) epub ahead of prin

Comparative Analysis of Tissue Reconstruction Algorithms for 3D Histology

Motivation: Digital pathology enables new approaches that expand beyond storage, visualization or analysis of histological samples in digital format. One novel opportunity is 3D histology, where a three-dimensional reconstruction of the sample is formed computationally based on serial tissue sections. This allows examining tissue architecture in 3D, for example, for diagnostic purposes. Importantly, 3D histology enables joint mapping of cellular morphology with spatially resolved omics data in the true 3D context of the tissue at microscopic resolution. Several algorithms have been proposed for the reconstruction task, but a quantitative comparison of their accuracy is lacking. Results: We developed a benchmarking framework to evaluate the accuracy of several free and commercial 3D reconstruction methods using two whole slide image datasets. The results provide a solid basis for further development and application of 3D histology algorithms and indicate that methods capable of compensating for local tissue deformation are superior to simpler approaches.publishedVersionPeer reviewe

Carotid plaque stress analysis by fluid structure interaction based on in-vivo MRI: Implications to plaque vulnerability assessment

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University, 2010.Stroke is one of the leading causes of death in the world, resulting mostly from the sudden rupture of atherosclerotic plaques. From a biomechanical view, plaque rupture can be considered as a mechanical failure caused by extremely high plaque stress. In this PhD project, we are aiming to predict 3D plaque stress based on in-vivo MRI by using fluid structure interaction (FSI) method, and provide information for plaque rupture risk assessment. Fluid structure interaction was implemented with ANSYS 11.0, followed by a parameter study on fibrous cap thickness and lipid core size with realistic carotid plaque geometry. Twenty patients with carotid plaques imaged by in-vivo MRI were provided in the project. A framework of reconstructing 3D plaque geometry from in-vivo multispectral MRI was designed. The followed reproducibility study on plaque geometry reconstruction procedure and its effect on plaque stress analysis filled the gap in the literature on imaging based plaque stress modeling. The results demonstrated that current MRI technology can provide sufficient information for plaque structure characterization; however stress analysis result is highly affected by MRI resolution and quality. The application of FSI stress analysis to 4 patients with different plaque burdens has showed that the whole procedure from plaque geometry reconstruction to FSI stress analysis was applicable. In the study, plaque geometries from three patients with recent transient ischemic attack were reconstructed by repairing ruptured fibrous cap. The well correlated relationship between local stress concentrations and plaque rupture sites indicated that extremely high plaque stress could be a factor responsible for plaque rupture. Based on the 20 reconstructed carotid plaques from two groups (symptomatic and asymptomatic), fully coupled fluid structure interaction was performed. It was found that there is a significant difference between symptomatic and asymptomatic patients in plaque stress levels, indicating plaque stress could be used as one of the factors for plaque vulnerability assessment. A corresponding plaque morphological feature study showed that plaque stress is significantly affected by fibrous cap thickness, lipid core size and fibrous cap surface irregularities (curvedness). A procedure was proposed for predicting plaque stress by using fibrous cap thickness and curvedness, which requires much less computational time, and has the potential for clinical routine application. The effects of residual stress on plaque stress analysis and arterial wall material property characterization by using in-vivo MRI data were also discussed for patient specific modeling. As the further development, histological study of plaque sample has been combined with conventional plaque stress analysis by assigning material properties to each computational element, based on the data from histological analysis. This method could bridge the gap between biochemistry and biomechanical study of atherosclerosis plaques. In conclusion, extreme stress distributions in the plaque region can be predicted by modern numerical methods, and used for plaque rupture risk assessment, which will be helpful in clinical practice. The combination of plaque MR imaging analysis, computational modelling, and clinical study/ validation would advance our understandings of plaque rupture, prediction of future rupture, and establish new procedures for patient diagnose, management, and treatment.Financial Support was obtained from British Heart Foundation, Brunel Institute for Bioengineering and Brunel Graduate School

Registration of histology and magnetic resonance imaging of the brain

Combining histology and non-invasive imaging has been attracting the attention of the medical imaging community for a long time, due to its potential to correlate macroscopic information with the underlying microscopic properties of tissues. Histology is an invasive procedure that disrupts the spatial arrangement of the tissue components but enables visualisation and characterisation at a cellular level. In contrast, macroscopic imaging allows non-invasive acquisition of volumetric information but does not provide any microscopic details. Through the establishment of spatial correspondences obtained via image registration, it is possible to compare micro- and macroscopic information and to recover the original histological arrangement in three dimensions. In this thesis, I present: (i) a survey of the literature relative to methods for histology reconstruction with and without the help of 3D medical imaging; (ii) a graph-theoretic method for histology volume reconstruction from sets of 2D sections, without external information; (iii) a method for multimodal 2D linear registration between histology and MRI based on partial matching of shape-informative boundaries

Interactive Medical Image Registration With Multigrid Methods and Bounded Biharmonic Functions

Interactive image registration is important in some medical applications since automatic image registration is often slow and sometimes error-prone. We consider interactive registration methods that incorporate user-specified local transforms around control handles. The deformation between handles is interpolated by some smooth functions, minimizing some variational energies. Besides smoothness, we expect the impact of a control handle to be local. Therefore we choose bounded biharmonic weight functions to blend local transforms, a cutting-edge technique in computer graphics. However, medical images are usually huge, and this technique takes a lot of time that makes itself impracticable for interactive image registration. To expedite this process, we use a multigrid active set method to solve bounded biharmonic functions (BBF). The multigrid approach is for two scenarios, refining the active set from coarse to fine resolutions, and solving the linear systems constrained by working active sets. We\u27ve implemented both weighted Jacobi method and successive over-relaxation (SOR) in the multigrid solver. Since the problem has box constraints, we cannot directly use regular updates in Jacobi and SOR methods. Instead, we choose a descent step size and clamp the update to satisfy the box constraints. We explore the ways to choose step sizes and discuss their relation to the spectral radii of the iteration matrices. The relaxation factors, which are closely related to step sizes, are estimated by analyzing the eigenvalues of the bilaplacian matrices. We give a proof about the termination of our algorithm and provide some theoretical error bounds. Another minor problem we address is to register big images on GPU with limited memory. We\u27ve implemented an image registration algorithm with virtual image slices on GPU. An image slice is treated similarly to a page in virtual memory. We execute a wavefront of subtasks together to reduce the number of data transfers. Our main contribution is a fast multigrid method for interactive medical image registration that uses bounded biharmonic functions to blend local transforms. We report a novel multigrid approach to refine active set quickly and use clamped updates based on weighted Jacobi and SOR. This multigrid method can be used to efficiently solve other quadratic programs that have active sets distributed over continuous regions

Modeling and Simulation in Engineering

This book provides an open platform to establish and share knowledge developed by scholars, scientists, and engineers from all over the world, about various applications of the modeling and simulation in the design process of products, in various engineering fields. The book consists of 12 chapters arranged in two sections (3D Modeling and Virtual Prototyping), reflecting the multidimensionality of applications related to modeling and simulation. Some of the most recent modeling and simulation techniques, as well as some of the most accurate and sophisticated software in treating complex systems, are applied. All the original contributions in this book are jointed by the basic principle of a successful modeling and simulation process: as complex as necessary, and as simple as possible. The idea is to manipulate the simplifying assumptions in a way that reduces the complexity of the model (in order to make a real-time simulation), but without altering the precision of the results