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The only fully opensource software package providing a complete pipeline from medical image data segmentation to patient specific blood flow simulation and analysis.

About SimVascular

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Description

SimVascular is an open source software suite for cardiovascular simulation, providing a complete pipeline from medical image data to 3D model construction, meshing, and blood flow simulation. SimVacular represents the state of the art in cardiovascular simulation, including advanced tools for physiologic boundary conditions, fluid structure interaction, and an accurate and efficient finite element Navier-Stokes solver. SimVascular integrates custom code with best-in-class open source packages to support clinical and basic science research.
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Origins

SimVascular originated in the lab of Charles Taylor at Stanford University, and incorporates flow solver code from the PHASTA project (SCOREC at RPI). The SimVascular revitalization project now aims to provide the first truly open source package for cardiovascular simulation with enhanced functionality for clinical and basic science research. SimVascular is now developed and maintained by an active international group of researchers in academia and industry.
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Purpose

To provide a platform for patient-specific cardiovascular modeling and simulation that enables advances in cardiovascular disease through basic science and clinical research.
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Audience

Biomedical and clinical researchers interested in medical computing, cardiovascular hemodynamics and biomechanics, including medical image segmentation, patient specific model construction, blood flow simulations, vessel biomechanics, and finite element flow simulations.
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Broader Uses

Beyond hemodynamics simulations, SimVascular has been used in simulations of medical devices, respiratory flows, and cardiac development. SimVascular provides a full Navier-Stokes flow solver for complex geometries that can be flexibly applied across a wide range of problems in engineering and medicine.

Funding Sources

The SimVascular project is funded by the NSF SSI program under Program Officers Dan Katz (ACI) and Sumanta Acharya (CBET)

What's New?

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New features in SimVascular 2.0

  • Replacement of all prior commercial components
  • Opensource meshing tools with adaption
  • Efficient linear solver customized for blood flow
  • Solid modeling Boolean operations
  • Multiscale modelling capabilities
  • Coronary boundary conditions
  • Improved image segmentation tools
  • Backflow stabilization

Download SimVascular

Users: download installer packages

Developers: visit our source code repository

License Terms

SimVascular components svModel, svMesh, svPre, and svPost are provided under the full BSD license subject to the terms below:

Copyright © 1998-2007 Stanford University, Charles Taylor, Nathan Wilson, Ken Wang. See SimVascular Acknowledgements file for additional contributors to the source code.

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

The SimVascular solver, including svSolver and svLS, is provided under a modified BSD-license subject to the permissions below:

This software is Copyright © 2014 The Regents of the University of California. All Rights Reserved. Permission to copy, modify, and distribute this software and its documentation for educational, research and non-profit purposes, without fee, and without a written agreement is hereby granted, provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies.

Permission to make commercial use of this software may be obtained by contacting:

Technology Transfer Office
9500 Gilman Drive, Mail Code 0910
University of California
La Jolla, CA 92093-0910
(858) 534-5815
invent@ucsd.edu

This software program and documentation are copyrighted by The Regents of the University of California. The software program and documentation are supplied "as is", without any accompanying services from The Regents. The Regents does not warrant that the operation of the program will be uninterrupted or error-free. The end-user understands that the program was developed for research purposes and is advised not to rely exclusively on the program for any reason.

IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF CALIFORNIA HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.

Licensing terms for external open source packages

ITK: http://www.itk.org/ITK/project/license.html
VTK: http://www.vtk.org/VTK/project/license.html
Tetgen: http://wias-berlin.de/software/tetgen/1.5/agpl-3.0-standalone.html

Commercial components

MeshSim users should contact simmetrix for licensing information.

Additional license information

Please see the additional license information contained in the SimVascular source code.

SimVascular Documentation

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Getting Started


Installing SimVascular
Install SimVascular on your system.

Compile Sources
Compile SimVascular source code on your system.

Code snippets
Unleash the power of SimVascular with console scripts.

SimVascular CDash board
SimVascular automated software testing.

Quick Guide
A quick intro on how to use the main functionalities in SimVascular.

Doxygen Docs
Understand the SimVascular source code. Doxygen documentation for c++, tcl and fortran code (documentation work in progress...).

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User Guides


Image Guide
How to manipulate clinical image data in SimVascular.

Model Building Guide
Walks you through how to build a cardiovascular model from image data.

Meshing Guide
Basic and advanced meshing and model editing in SimVascular.

Simulation Guide
Walks you through the process of generating hemodynamic result with simple examples.

Youtube Tutorials
Follow our Youtube channel for video tutorials.

References
Articles in the literature relevant for the SimVascular project.

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Clinical Case Studies


Aortofemoral Normal - Case 1
From the supraceliac aorta to the femoral and profunda femoris artery bifurcation.

Aortofemoral Normal - Case 2
From the thoracic aorta to the femoral arteries.

Coronary Normal - Case 3
The ascending aorta ostium and the left and right coronary arteries.

Healthy Pulmonary - Case 4
From the main pulmonary artery to various levels of branching in the left and right pulmonary arteries.

SimVascular Model Repository

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What is it

The vascular model repository, a sister project of SimVascular, is a library of computational models of normal and diseased human cardiovascular and pulmonary anatomy and input and output boundary conditions for various physiologic states. These models can be used to simulate cardiovascular and pulmonary solid and fluid mechanics and will provide spatially and temporally-resolved benchmark solutions that can be used by academic, government and industry researchers to verify their computational methods. Most models in the repository were created with SimVascular. The SimVascular project provides an open source package for simulation to accompany the data provided in the model repository.
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Our Team

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Alison Marsden

Bio notes

Alison Marsden is an associate professor in the Mechanical and Aerospace Engineering Department at the University of California San Diego. She graduated with a bachelor’s degree in Mechanical Engineering from Princeton University in 1998, and a PhD in Mechanical Engineering from Stanford in 2005 working with Prof. Parviz Moin. She was a postdoctoral fellow at Stanford University in Bioengineering and Pediatric Cardiology from 2005-07 working with Charles Taylor and Jeffrey Feinstein. She was the recipient of an American Heart Association postdoctoral fellowship, an AHA beginning grant in aid award, a Burroughs Wellcome Fund Career Award at the Scientific Interface, an NSF CAREER award, and is a member of an international Leducq Foundation Network of Excellence. She has published over 60 peer reviewed journal papers, and her lab has received funding from the NSF, NIH, and several private foundations. Her work focuses on the development of numerical methods for simulation of cardiovascular blood flow problems, medical device design, application of optimization to large-scale fluid mechanics simulations, and use of engineering tools to impact patient care in cardiovascular surgery and congenital heart disease.

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Shawn Shadden

Bio notes

Shawn Shadden is an Assistant Professor of Mechanical Engineering at the University of California, Berkeley. His research focuses on the advancement of theoretical and computational methods to quantify complex fluid flow. He received a BS in Aerospace Engineering from The University of Texas at Austin (2001), and PhD in Control and Dynamical Systems from the California Institute of Technology (2006). From 2006-2009 he carried out an NSF Mathematical Sciences Postdoctoral Research Fellowship to translate his work in dynamical systems to research on cardiovascular biomechanics at Stanford University. From 2009-2013 he served as an Assistant Professor at the Illinois Institute of Technology in Chicago, IL, before joining the faculty at UC Berkeley.

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Nathan Wilson

Bio notes

Dr. Nathan Wilson has started two medical-related software companies, served as a Principal Investigator on two SBIR research grants, co-authored over thirty peer-reviewed journal and conference publications, and teaches introductory classes in entrepreneurship, business plan development, and technology and science commercialization at UCLA. Nathan has a PhD in Mechanical Engineering from Stanford University and an MBA from UCLA Anderson.

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Daniele Schiavazzi

Bio notes

Daniele Schiavazzi is a post-doctoral researcher at the University of California, San Diego. He graduated with honors from the University of Padova and pursued a Ph.D. degree in applied mathematics from the same University. He was awarded a visiting researcher appointment from the Uncertainty Quantification Lab at Stanford University during his Ph.D. and, more recently, an AHA post-doctoral fellowship. His main research interests are in numerical simulation and finite element analysis, forward uncertainty propagation using sparse multi-resolution representations, inverse Bayesian estimation and use of computational models to inform clinical decision making under uncertainty. He is a keen tennis player and cross-country ski enthusiast.

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Jameson Merkow

Bio notes

Jameson Merkow is a PhD student in the Electrical and Computer Engineering Department and University of California, San Diego. He graduated with a BSE in Computer Engineering at Tulane University in New Orleans, LA. Jameson has received prestigious awards such as the Distinguished Scholar Award, and Excellence in Mathematics for Outside Majors. Jameson continued his education at Carnegie Mellon University where he received an MS in Electrical and Computer Engineering with a concentration in machine learning and computer vision. He is currently a co-member of the Cardiovascular Biomechanics Computations Laboratory and Computer Vision Laboratory at UCSD.

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Hongzhi Lan

Bio notes

Hongzhi Lan is a postdoctoral scholar in the Mechanical and Aerospace Engineering Department at the University of California San Diego. He received a bachelor degree(1999) in Mechanical Engineering from Tsinghua University, a master degree(2007) in Mechanical Engineering and a PhD(2013) in Biomedical Engineering from Tulane University. His research experiences include modeling/simulation of indentation on alloys and piezoelectric materials, biotransport of nutrients between cells in the bone matrix, and leukocyte deformation/migration using viscoelastic models. His current research interests focus on flow solver for cardiovascular simulation, development of the open source project SimVascular, and simulation for cardiovascular diseases and surgery.

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Adam Updegrove

Bio notes

Adam Updegrove is a second year PhD student in the department of Mechanical Engineering at the University of California, Berkeley. He graduated with a BS in Mechanical Engineering at Rensselaer Polytechnic Institute in Troy, NY. At RPI, Adam received prestigious awards such as the Founder’s Award of Excellence and the Living W. Houston Citizenship Award. This past year, Adam was awarded the National Science Foundation Graduate Research Fellowship to help promote scientific innovation and teaching. Amongst other things, Adam loves playing soccer and volunteering in the Community.

Other Contributors

  • Charles A. Taylor, Ph.D., Founder, CTO, and Member of the Board of Directors, HeartFlow Inc.
  • Mahdi Esmaily Moghadam, Ph.D., Postdoctoral Fellow, CTR, Stanford University
  • C. Alberto Figueroa, Ph.D., Edward B. Diethrich Associate Professor of Surgery and Biomedical Engineering, University of Michigan
  • Kenneth Jansen, Ph.D., Professor of Aerospace Engineering, University of Colorado, Boulder
  • Weiguang Yang, Ph.D., Research Scientist, Pediatrics, Stanford University
  • Irene Vignon-Clementel, Ph.D., Permanent Research Scientist, INRIA Paris Rocquencourt
  • Kenneth Wang, M.D., Ph.D., Department of Radiology, Johns Hopkins School of Medicine

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