An open-source software for microCT-based longitudinal tracking of musculoskeletal tissues

用于基于 microCT 的肌肉骨骼组织纵向跟踪的开源软件

• 批准号: 10609255
• 负责人: LOUIS J SOSLOWSKY
• 金额: $ 24.38万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-07-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10609255
• 关键词: 3-Dimensional; Address; Animals; Bone Density; Clinical; Clinical Research; Collaborations; Communities; Computer software; Custom; Data; Data Analyses; Data Set; Development; Disease; Distal; Documentation; Ensure; Evaluation; Faculty; Feedback; Funding; Geometry; Goals; Image; Image Analysis; Individual; Laboratories; Lead; Linux; Measurement; Modeling; Musculoskeletal; Musculoskeletal Diseases; Operating System; Patients; Pennsylvania; Peripheral; Pythons; Reproducibility; Research; Research Subjects; Resolution; Resources; Rodent; Scanning; Skeleton; Software Tools; System; Technical Degree; Technical Expertise; Technology; Testing; Three-Dimensional Image; Time; Tissues; Training; United States National Institutes of Health; Universities; University resources; Visualization; Work; X-Ray Computed Tomography; base; bone; data exchange; data format; data management; design; empowered; flexibility; graphical user interface; image processing; image reconstruction; image registration; improved; in vivo; in vivo imaging; injury and repair; innovation; insight; instrument; longitudinal analysis; member; microCT; open data; open source; ranpirnase; serial imaging; skeletal; terabyte; three-dimensional visualization; two-dimensional; usability

Project Summary (Supplement Project) The micro computed tomography (µCT) Imaging Core (µCTIC) is an integral part of the Penn Center for Musculoskeletal Disorders (PCMD). Since its inception in 2012, the PCMD µCTIC has grown into a thriving resource for the University of Pennsylvania and the region’s MSK research community, serving a vibrant and growing base of 73 active PCMD faculty members and more than 170 trainees from their laboratories to acquire over 55,000 µCT scans, resulting in over 400 terabytes of data. An important recent advance in µCT technology is in vivo imaging of small animals, which enables evaluation of changes in a living animal non- invasively and repeatedly over time. Another exciting advancement is high-resolution peripheral quantitative CT (HR-pQCT), which can assess three-dimensional (3D) bone microarchitecture, geometry, and bone mineral density in the distal peripheral skeleton of clinical patients. Currently, the µCTIC operates 3 in vivo µCT scanners and an HR-pQCT scanner for longitudinal imaging of small rodents and clinical research subjects, respectively. Consequently, individual datasets have grown in size and complexity, along with a growing demand for specialized image analysis for longitudinal image data registration, post-processing, and visualization from our users. To address these needs, the µCTIC has developed a customized software platform called Computed Tomography Processing & Registration - Open Sourced (CTPros) for automated data management, customized image processing, longitudinal image registration and analysis, and two- dimensional (2D) and 3D visualization. This open-source Python software package with a Graphic User Interface (GUI) is compatible with Mac, Linux, and Windows operating systems. Compared to other available commercial and open-source software, CTPros is the only one that is specifically designed and have been validated for quantitative analysis of musculoskeletal tissues based on longitudinal µCT images. Despite the powerful functions of the CTPros software for academic research, the current version of CTPros is still lacking software documentation and a logging system and only supports limited data formats. Through the support of this supplement, we aim to ensure the rigor of CTPros-derived measurements, refine the software documentation and logging system to improve user feedback, and package CTPros into standalone and executable packages with containerized runtime to improve intersystem compatibility. Moreover, by releasing beta versions to obtain user feedback on documentation, features, and usability, we aim to incorporate these feedbacks into a formal release of CTPros to the general research community.

项目概要（补充项目） 微型计算机断层扫描 (μCT) 成像核心 (μCTIC) 是宾夕法尼亚大学中心的一个组成部分 肌肉骨骼疾病（PCMD）。自 2012 年成立以来，PCMD µCTIC 已发展成为一个蓬勃发展的 宾夕法尼亚大学和该地区 MSK 研究社区的资源，为充满活力和 73 名活跃的 PCMD 教员和 170 多名来自实验室的实习生不断壮大 采集超过 55,000 次 µCT 扫描，产生超过 400 TB 的数据。 µCT 的最新重要进展 技术是小动物的活体成像，可以评估活体动物非活体的变化 随着时间的推移，侵入性地、反复地。另一个令人兴奋的进步是高分辨率外围定量 CT (HR-pQCT)，可以评估三维 (3D) 骨微结构、几何形状和骨矿物质 临床患者远端外周骨骼的密度。目前，µCTIC 运行 3 台体内 µCT 用于小型啮齿动物和临床研究对象纵向成像的扫描仪和 HR-pQCT 扫描仪， 分别。因此，单个数据集的规模和复杂性都在增长，同时数据集的数量也在不断增长。 对纵向图像数据配准、后处理和专业图像分析的需求 来自我们用户的可视化。为了满足这些需求，μCTIC 开发了定制软件 称为计算机断层扫描处理和注册 - 开源 (CTPros) 的自动化平台 数据管理、定制图像处理、纵向图像配准和分析以及两 维度 (2D) 和 3D 可视化。这个带有图形用户的开源Python软件包 界面 (GUI) 与 Mac、Linux 和 Windows 操作系统兼容。与其他可用的相比 CTPros 是一款商业和开源软件，是唯一一款经过专门设计和开发的软件 经验证可用于基于纵向 µCT 图像的肌肉骨骼组织定量分析。尽管 CTPros软件对于学术研究的强大功能，目前版本的CTPros仍然缺乏 软件文档和日志系统，仅支持有限的数据格式。通过支持 在本补充中，我们的目标是确保 CTPros 衍生测量的严谨性，完善软件 文档和日志系统，以改善用户反馈，并将 CTPro 打包成独立的和 具有容器化运行时的可执行包，以提高系统间兼容性。此外，通过释放 beta 版本是为了获取用户对文档、功能和可用性的反馈，我们的目标是将这些内容纳入其中 向一般研究界正式发布 CTPro 的反馈。