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

项目摘要（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 资源为宾夕法尼亚大学和该地区的MSK研究社区，服务于一个充满活力和 73名活跃的PCMD教职员工和170多名实习生从他们的实验室， 采集超过55，000 µCT扫描，产生超过400 TB的数据。µCT的最新重要进展 技术是小动物的体内成像，其使得能够评估活体动物的变化， 侵入性地反复进行另一个令人兴奋的进步是高分辨率的外围定量 CT（HR-pQCT），可评估三维（3D）骨微结构、几何结构和骨矿物质 密度在远端外周骨骼的临床患者。目前，µCTIC运行3个体内µCT 扫描仪和HR-pQCT扫描仪，用于小型啮齿动物和临床研究对象的纵向成像， 分别因此，各个数据集的大小和复杂性都在增长，沿着增长的 纵向图像数据配准、后处理的专业图像分析需求，以及 我们的用户的可视化。为了满足这些需求，µCTIC开发了一个定制软件， 一个名为计算机断层扫描处理和配准-开放源代码（CTPros）的平台， 数据管理、定制图像处理、纵向图像配准和分析，以及两个- 三维（2D）和3D可视化。这个开源的Python软件包与图形用户 界面（GUI）与Mac、Linux和Windows操作系统兼容。与其他可用 商业和开源软件，CTPros是唯一一个专门设计，并已 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软件用于学术研究的强大功能，当前版本的CTPros还存在不足 软件文档和日志系统，仅支持有限的数据格式。通过支持 本补充，我们的目标是确保严格的CTPros衍生测量，完善软件 文档和日志系统，以改善用户反馈，并将CTPros打包成独立的， 可执行包与容器化的运行时，以提高系统间的兼容性。此外，通过释放 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 将反馈转化为CTPros的正式版本，提供给一般研究社区。

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.