PM3 SimVascular: Haemodynamic Risk Assessment in Human Blood Vessels.

SimVascular is a sophisticated computational platform for the physiologically accurate study of blood flow, vessel wall mechanics, and their interaction. In this project, we will customize the platform to enable high impact research in multiple teams. Together, we will use it to implement an in silico methodology that advances our diagnostics.
Clinical requirement to fully exploit imaging data: Our London Ontario Hospitals and basic science departments perform extensive imaging that guides their vascular treatment planning. The imaging provides crucial structural information such as blood vessel size and geometric abnormalities, which is currently the most widely used diagnostics method. However, imaging alone is incapable of fully guiding clinical decision making objectively, leading to an unacceptably high number of patients not receiving proper treatment. In addition, multiple imaging examinations are required to construct a strategy, prolonging time to treatment. The avoidable patient examinations and current subjective diagnostics deficiencies are a significant economic burden to our health care system. There is a clear need to improve diagnostic accuracy to both augment patient care and reduce ineffective expenditure.

To address the knowledge gap, we will extend a spectrum of available imaging data to obtain dynamic insights into how structural defects hinder blood flow. Such a quantitative approach will enable the medical practitioner to implement the optimal treatment plan option. To do so, we will construct 3D geometries of affected blood vessels using clinical images and mathematically model blood flow through them. A whole-body blood flow model will be developed to ascertain the effects of dialysis on body organs. As a new development, we will test new methods simulating contrast agent movement through blood vessel networks which can improve clinical imaging protocols. The modeling is designed to generate hemodynamic risk indices to enable improved diagnoses. The underlying mathematics, physics, and computing of blood flow are complex and require sophisticated computational platforms. We will use a platform called SimVascular which provides an integrated solution for performing imaging data driven hemodynamics modeling.

SimVascular provides an integrated research functionality: The platform is an all inclusive research instrument suitable for use in diverse research teams. Its major components are comprised of an easy to use artificial intelligence based image processing, dynamic blood flow calculation methods, and advanced data processing capabilities. The image processing component is encoded in a graphical user interface. Using subject specific images, it facilitates interactive generation of structural models using intelligent algorithms. The algorithms use sophisticated image intensity and in-depth machine learning methods, among others. The image processing also encompasses blood vessel network analysis which can provide crucial disease information useful in diagnostics.

Blood flow in diseased vessels is undesirably uneven and often exerts pathological forces, or shear, on the vessel walls. To accurately calculate blood flow, the platform has integrated highly sophisticated flow simulators. They use an advanced numerical method called finite elements to solve intricate hemodynamics (Navier-Stokes) and solid mechanics (elasto-dynamics) equations. The numerical simulations must be performed using powerful supercomputers to achieve results in a reasonable time. SimVascular has the capability to efficiently use large supercomputers, which stems from its uses of powerful numerical methods. Sophisticated programming called message passing interface allows SimVascular to use multiple computer processors (CPUs) simultaneously. Repetitive calculations are performed using graphical processing units (GPUs) that further accelerate the calculations. The outcomes of the numerical simulations permit a functional assessment of the severity of vascular structural abnormalities. The user is provided with methods to combine the estimated hemodynamic quantities (e.g. pressure gradients, flow velocities, and wall shear) to construct clinically measurable signals such as pulse wave velocities, mean arterial pressures, and other risk indices.

An important part of scientific investigations is to post-process the intricate simulated data for visualization and metrics calculation. SimVascular integrates sophisticated scientific visualization methods. Visualization enables the results to be presented in a way that is understandable. It is also capable of using representations of blood flow patterns and their derived quantities to construct clinically interpretable risk indices.

SimVascular is user friendly: The platform is designed for use by interdisciplinary researchers in diverse fields such as medicine, physics, computing, and mathematics. A straightforward high level simulation and visualization mechanism is provided for rapid model setup. It also permits image processing and generation of results, without having to manipulate the underlying platform modules. The user friendly nature of the platform also permits training of highly qualified personnel from a wide range of backgrounds.

SimVascular is versatile: SimVascular has been designed and tested to work on multiple operating systems including Windows, Mac OS, and Linux. This feature is extremely useful in an educational-research-clinical application context. The Windows and Mac OS versions are suitable for clinically oriented researchers undertaking interactive image processing. The Windows versions are useful to our teaching members who will use it with routine audiovisual setups available in our institutions. SimVascular is also capable of being configured on developer systems such as those used by our national supercomputers, as scientists who create new platform functionality use Unix/Unix like (e.g. Linux) systems.

Current application and features of the platform: 1600 teams worldwide. It is being used in a wide range of bio-medical research such as the study of aneurysms and blood rheology abnormalities. The platform's feature called modular extensibility makes it SimVascular is currently being used by over attractive for uptake by future users and developers.

This project will maximally deploy the platform in multiple research teams with significant benefit to Canadian research. Reuse will minimize time to application and accelerate vital research into improving the quality of lives of our critically ill patients. This collaborative project will enhance research and train future biomedical scientists and innovators.

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August 5th, 2020. Dr. Sanjay R. Kharche. The contents of the PM3 SimVascular pages are owned by the PM3 lab. and investigators: Drs. Sanjay R Kharche, Daniel Goldman, and CW McIntyre. External links are not gaurenteed to work. Source codes provided in this portal are distributed under GNU GPL lincence unless otherwise stated. You may use, modify, and share the distributions without any charges or permissions. You may use the PM3 generated models upon agreement with authors and developers. Please cite our publications if you use our codes and models.