Collaborative Research: SI2-SSI: A Sustainable Open Source Software Pipeline for Patient Specific Blood Flow Simulation and Analysis

SimVascular软件包是心血管建模和仿真的重要研究工具，并为个性化医疗，手术计划和医疗设备设计的许多进步做出了贡献。SimVascular是目前唯一的综合性软件包，提供了从医学图像数据分割到患者特定血流模拟和分析的完整管道。该软件目前在国内和国际学术实验室的一个小而活跃的小组中形成了心血管模拟研究的骨干。然而，自从它最初发布以来，有几个关键的障碍阻碍了新用户的广泛采用、大规模研究的应用和教育访问。这些包括1)与嵌入式商业组件相关的成本和复杂性，2)对更有效的几何模型构建工具的需求，3)缺乏可持续的架构和基础设施，以及4)缺乏有组织的维护。该项目旨在通过以下目标解决上述障碍：1)创建一个可持续的模块化开源SimVascular 2.0项目，该项目位于斯坦福Simbios？simtk.org提供文档，基准测试和测试套件，2)在SimVascular的第一个真正开源版本中提供所有商业组件的替代方案，3)改进图像分割方法和模型构建效率，以实现高通量研究，4)通过合并优化，流分析和多尺度建模方面的最新研究来增强功能。该项目利用了simtk.org上现有的资源和基础设施，并建立在支持SimVascular最初开源版本的重要前期投资的基础上。通过与美国国立卫生研究院资助的血管模型库交联，访问进一步增强。该项目将增加用户基础，并建立一个由活跃的开源社区支持的可持续软件平台。发布第一个完全开源的SimVascular版本将使心血管医学取得更大的进步，为教育目的提供最先进的模拟工具的开放访问，并促进年轻研究人员的培训。这些努力还将进一步促进多样性，并通过利用该软件使高中学生能够到加州大学圣地亚哥分校的StarCAVE实地考察，使用虚拟现实查看模拟数据，从而吸引学生学习科学和工程。

The SimVascular package is a crucial research tool for cardiovascular modeling and simulation, and has contributed to numerous advances in personalized medicine, surgical planning and medical device design. SimVascular is currently the only comprehensive software package that provides a complete pipeline from medical image data segmentation to patient specific blood flow simulation and analysis. This software now forms the backbone in cardiovascular simulation research in a small but active group of domestic and international academic labs. However, since its original release there have been several critical barriers preventing wider adoption by new users, application to large-scale research studies, and educational access. These include 1) the cost and complications associated with embedded commercial components, 2) the need for more efficient geometric model construction tools, 3) lack of sustainable architecture and infrastructure, and 4) a lack of organized maintenance. This project is addressing the above roadblocks through the following aims: 1) create a sustainable and modular open source SimVascular 2.0 project housed at Stanford Simbios? simtk.org, with documentation, benchmarking and test suites, 2) provide alternatives to all commercial components in the first truly open source release of SimVascular, 3) improve the image segmentation methods and efficiency of model construction to enable high-throughput studies, and 4) enhance functionality by merging state of the art research in optimization, flow analysis, and multiscale modeling. The project leverages existing resources and infrastructure at simtk.org, and builds upon the significant previous investment that enabled the initial open source release of SimVascular. Access is further enhanced by cross-linking with the NIH funded Vascular Model Repository. This project will increase the user base and build a sustainable software platform supported by an active open source community. Releasing the first fully open source version of SimVascular will enable greater advances in cardiovascular medicine, provide open access to state of the art simulation tools for educational purposes, and facilitate training of young investigators. These efforts will also further promote diversity and attract students to science and engineering by leveraging this software to enable high school field trips to the UCSD StarCAVE to view simulation data using virtual reality.