BIOPSE

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 CIBC软件小组最初的重点是生物医学问题解决环境BioPSE。这 环境提供了丰富多样的一组模块和功能，旨在做出设计和实现 建模、仿真和可视化都非常灵活和强大。这种环境背后的想法是提供一个 基础设施，将科学家从与大多数现有的 软件工具。通过掌握一套模块化的、可扩展的、交互式的软件工具，科学家可以自由地应用他们的 为手头的科学提供专业知识。 传统方法 研究生物医学应用的传统方法通常使用多个非集成的计算机程序。为 例如，一位科学家使用计算机模拟来检查电极贴片放置对经心脏的影响 除颤中的电流密度需要几何建模、数值模拟和科学的可视化工具 来完成这项任务。一个程序可以用来根据医学图像定义胸部表面，另一个程序可以用来 创建曲面中包含的体积的离散网格。需要另一个应用程序来运行 电极电流在胸腔内分布的有限元模拟。每个人 程序就是这样一种场景，通常是独立的，可能来自不同的来源，并且是以不同的方式编写的 语言。它几乎肯定会有不同的用户界面布局和结构。这样的分离和差异 形成了仿真集成和快速开发与评估的障碍。 BioPSE是集成模拟步骤的一种方法，从而简化了开发和 模型的执行。这样的简化又促进了评估模型所需的快速迭代 它生成的结果并探索底层系统的行为。 基于工作流的项目组织 在过去的几年里，CIBC已经将软件环境的方法扩展到开发较小的应用程序 虽然通过通用格式和接口进行集成，但它们实际上是独立的程序。最初，我们建立了 这类应用程序如具有定制接口的BioPSE实例，但发现数据流范例固有于 BioPSE在某种程度上是有限的。因此，我们现在组织这些应用程序以与其共享代码和算法 BioPSE(和底层SCIRun体系结构)，但将它们组合到与假定的使用相匹配的工作流中 这些节目。我们选择了相对离散和使用频率足够高的任务，以便用户可以 在一个程序中完成工作流程的主要部分。例如，我们开发了一种分段 名为Seg3D的应用程序，包含对组织鉴定通常所需的所有步骤的支持 解剖体积数据集中的区域，例如来自MRI、CT或共焦显微镜的区域。细分是必不可少的 在许多设置中执行步骤，甚至可能代表特定类型分析的几乎整个工作流程。 我们已经实现的这种基于工作流的程序的其他示例包括map3d(用于渲染和分析 多时间信号的基于表面的测量或模拟)、BioMesh3D(用于构建多边形网格 来自分段的卷)、ImageVis3D(用于超大体积数据集的交互式可视化)和ShapeWorks (用于曲面的统计形状分析)。每个程序现在都是我们软件套件中的一部分，可以免费获得 供下载，并由文档、邮件列表以及定期维护和更新提供支持。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The initial focus of the CIBC software group was on the Biomedical Problem Solving Environment, BioPSE. This environment provides a rich a diverse set of modules and capabilities designed to make the design and implementation of modeling, simulation and visualization very flexible and powerful. The idea behind this environment is to provide an infrastructure that liberates the scientist from the user-intensive, mundane tasks associated with most existing software tools. By commanding a modular, extensible, interactive set of software tools, scientists are free to apply their expertise to the science at hand. Traditional Methods Traditional methods for investigating biomedical applications often use multiple, non-integrated computer programs. For example, a scientist using a computer simulation to examine the effect of electrode patch placement on transcardiac current density in defibrillation would require geometric modeling, numerical simulation, and scientific visualization tools to complete the task. One program might be used to define the thoracic surfaces from medical images, another to create a discrete mesh of the volume contained within the surfaces. Another application would be necessary to run a finite element simulation of the electric current distribution from the electrodes through the thoracic volume. Each program is such a scenario is often independent and perhaps comes from a different source and is written in a different language. It will almost certainly have different user interface layout and structure. Such separations and differences form a barrier to integration and rapid development and evaluation of simulations. BioPSE is one approach to integrating the steps of a simulation and thus simplifying both the development and execution of the model. Such simplification, in turn, facilitates the rapid iterations necessary to evaluate the model and the results it generates and explore the behavior of the underlying system. Workflow based program organization Over the past years the CIBC has extended the approach to software environments to developing smaller applications that, while integrated through common formats and interfaces, are actually standalone programs. Initially, we built such applications as instances of BioPSE with a customized interface but found the data flow paradigm intrinsic to BioPSE to be somewhat limiting. As a result, we now organize these applications to share code and algorithms with BioPSE (and the underlying SCIRun architecture) but combine them into workflows that match the assumed use of these programs. We have selected tasks that are relatively discrete and used frequently enough so that users can complete a major piece of the workflow within one program. For example, we have developed a segmentation application called Seg3D that contains support for all the steps typically required to carry out the identification of tissues regions in anatomical volumetric data sets, e.g., from MRI, CT, or confocal microscopy. Segmentation is an essential step in many settings and may even represent almost the entire workflow for particular types of analysis. Other examples of such workflow based programs that we have implemented include map3d (for rendering and analysis of surface based measurements or simulations of multiple time signals), BioMesh3D (for constructing polygonal meshes from segmented volumes), ImageVis3D (for interactive visualization of very large volume data sets), and ShapeWorks (for the statistical shape analysis of surfaces). Each of the programs is now a piece in our software suite, freely available for download and supported with documentation, mailing lists, and regular maintenance and updates.