Strain Analysis Software for Open Science

开放科学应变分析软件

• 批准号: 10406113
• 负责人: Guy M Genin
• 金额: $ 21.01万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2025-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10406113
• 关键词: 3-Dimensional; Adoption; Age; Algorithms; Area; Bone Regeneration; Bone Tissue; Clinical Research; Cloud Computing; Code; Collaborations; Communities; Computer software; Computers; Connective Tissue; Data; Data Set; Development; Diagnosis; Diagnostic; Disease; Elderly; Ensure; Failure; Friction; Health; Hernia; Image; Image Analysis; Injury; Knowledge; Laboratories; Laboratory Research; Lead; Ligaments; Literature; Magnetic Resonance Imaging; Mechanics; Medical Imaging; Meniscus structure of joint; Mesentery; Methods; Modeling; Muscle; Musculoskeletal; Myocardium; Noise; Operative Surgical Procedures; Orthopedics; Outcome; Pain; Pathologic; Patients; Peritoneal; Pia Mater; Plant Roots; Population; Rehabilitation therapy; Research; Research Personnel; Resources; Risk; Rotator Cuff; Running; Signal Transduction; Software Engineering; Standardization; Stress; Surface; System; Techniques; Technology; Tendon structure; Time; Tissues; Translating; Translational Research; Ultrasonography; Validation; Work; articular cartilage; base; bone; clinically relevant; cloud based; computational platform; computing resources; data modeling; digital imaging; disability; image warping; imaging modality; improved; mechanical properties; microscopic imaging; movie; musculoskeletal injury; older patient; open data; open source; parallel computer; parallelization; parent grant; repaired; rotator cuff tear; soft tissue; software development; tool; two-dimensional; user friendly software

PROJECT SUMMARY The parent grant focuses on interfaces between tissues either transfer load (requiring toughness) or provide a smooth surface (requiring low friction). Fibrous interfaces are very effective at transferring load between tissues, e.g., at connective tissue-bone interfaces (“entheses”), peritoneal-mesentery interfaces, interfaces between layers of the vasculature, and the pia mater. These interfaces require toughness to resist high stresses associated with material mismatches. Surgical repair can lead to smooth interfaces becoming fibrous, (e.g., following hernia surgery) or to tough interfaces becoming weak (e.g., following tendon- and ligament-to- bone repair). In older patients with large rotator cuff repairs, for example, where the desired attachment is not reformed, up to 94% of surgical repairs fail. These challenges arise in part because the features that endow fibrous interfaces with toughness are not known. The parent grant there for aims to develop a comprehensive modeling and experimental approach for studying the factors underlying the transition from tough to weak in a fibrous interface. The supplement proposes to take software that we have developed in the course of this work and make it cloud-ready and broadly available. This software enables quantitative analysis of deformation in microscopy and medical imaging. Although commercial software for this is widespread, these packages employ regularization techniques to ensure a smooth solution, and are therefore often unable to accurately identify local tissue deformations or predict soft tissue tears. We will enable research into the relation between strain fields, injury, and rehabilitation by executing two aims. (1) We will develop open-source, user-friendly software as a plugin to ImageJ for the strain-tracking algorithm in two dimensions (2D), stereo view (2.5D), and three dimensions (3D). Best practices will be used for open source software development, and modules will be created to facilitate the development of a user community. (2) We will develop a working, static code implementation on GitHub that can be run on Amazon AWS using data in the cloud. This will help overcome the second obstacle to widespread adoption of strain mapping techniques in musculoskeletal research, namely that the 3D datasets that must be acquired require substantial computational resources to analyze. The work will enable collaboration between the PIs of the parent grant and an expert on open source software development for clinical and research translation, and enhance the impact of a tool with strong potential.

项目摘要 母基金的重点是组织之间的界面，要么转移负荷（需要韧性），要么提供一个 光滑表面（要求低摩擦）。纤维界面在将负载在 组织，例如，在结缔组织-骨界面（“附着点”）、腹膜-肠系膜界面、界面 在血管系统和软脑膜之间。这些界面需要韧性来抵抗高温。 与材料不匹配相关的应力。手术修复可能导致光滑的界面变成纤维状， (e.g.,在疝手术之后）或坚韧的界面变得脆弱（例如，在肌腱和韧带 骨修复）。例如，在进行大型肩袖修复的老年患者中， 经过改革，高达94%的手术修复失败。这些挑战之所以出现，部分原因是 具有韧性的纤维界面是未知的。那里的父母补助金旨在制定一个全面的 模拟和实验方法，研究从坚韧到软弱的转变， 纤维界面 该补充建议采取我们在这项工作的过程中开发的软件， 云就绪且广泛可用。该软件可以对显微镜中的变形进行定量分析 和医学成像。虽然商业软件是广泛的，这些软件包采用 正则化技术，以确保顺利的解决方案，因此往往无法准确地识别 局部组织变形或预测软组织撕裂。我们将能够研究应变与 领域，伤害和康复，通过执行两个目标。(1)我们将开发开源的、用户友好的软件 作为ImageJ的插件，用于二维（2D）、立体视图（2.5D）和三维（3D）中的应变跟踪算法。 尺寸（3D）。最佳实践将用于开源软件开发，模块将 它是为了促进用户社区的发展而创建的。(2)我们将开发一个工作的静态代码 GitHub上的实现，可以使用云中的数据在Amazon AWS上运行。这将有助于克服 在肌肉骨骼研究中广泛采用应变绘图技术的第二个障碍，即 必须获取的3D数据集需要大量的计算资源来分析。工作 将使父母补助金的PI和开源软件专家之间的合作成为可能 为临床和研究翻译开发，并增强具有强大潜力的工具的影响。