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

项目总结(补充项目) 微型计算机断层扫描(µCT)成像核心(µCTIC)是宾夕法尼亚大学医学研究中心的组成部分 肌肉骨骼疾病(PCMD)。自2012年成立以来，PCMD？CTIC已经成长为一个蓬勃发展的 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 由73名在职PCMD教职员工和170多名实习生组成的基地从他们的实验室扩大到 获取超过55,000微米CT扫描，产生超过400 TB的数据。微CT的一项重要最新进展 这项技术是对小动物的活体成像，这使得能够评估活的非动物的变化 随着时间的推移反复侵袭。另一个令人兴奋的进步是高分辨率外设定量 CT(HR-pQCT)，可以评估三维(3D)骨的微结构、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个在体µCT 用于小型啮齿动物和临床研究对象的纵向成像的扫描仪和HR-pQCT扫描仪， 分别进行了分析。因此，单个数据集在大小和复杂性方面都在增长，同时 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开发了一款定制软件 名为计算机断层扫描处理和注册的平台--用于自动化的开源(CTPros) 数据管理、定制图像处理、纵向图像配准和分析，以及两个- 二维(2D)和三维可视化。这是一个开源的带有图形用户的Python软件包 界面(GUI)与Mac、Linux和Windows操作系统兼容。与其他可用的 作为商业和开源软件，CTPros是唯一一个专门设计并已经 用于基于纵向µCT图像的肌肉骨骼组织的定量分析。尽管 CTPros软件具有强大的学术研究功能，目前的CTPros版本还很欠缺 软件文档和记录系统，并且仅支持有限的数据格式。通过…的支持 这一补充，我们的目的是确保CTPros派生测量的严谨性，完善软件 文档和日志记录系统，以改进用户反馈，并将CTPros打包为独立和 具有容器化运行时的可执行程序包，以提高系统间兼容性。此外，通过释放 测试版为了获得用户对文档、功能和可用性的反馈，我们的目标是将这些 反馈给一般研究社区的CTPros正式发布。

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.