Data from: Airway segmentation and centerline extraction from thoracic CT – comparison of a new method to state of the art commercialized methods

Introduction: Our motivation is increased bronchoscopic diagnostic yield and optimized preparation, for navigated bronchoscopy. In navigated bronchoscopy, virtual 3D airway visualization is often used to guide a bronchoscopic tool to peripheral lesions, synchronized with the real time video bronchoscopy. Visualization during navigated bronchoscopy, the segmentation time and methods, differs. Time consumption and logistics are two essential aspects that need to be optimized when integrating such technologies in the interventional room. We compared three different approaches to obtain airway centerlines and surface. Method: CT lung dataset of 17 patients were processed in Mimics (Materialize, Leuven, Belgium), which provides a Basic module and a Pulmonology module (beta version) (MPM), OsiriX (Pixmeo, Geneva, Switzerland) and our Tube Segmentation Framework (TSF) method. Both MPM and TSF were evaluated with reference segmentation. Automatic and manual settings allowed us to segment the airways and obtain 3D models as well as the centrelines in all datasets. We compared the different procedures by user interactions such as number of clicks needed to process the data and quantitative measures concerning the quality of the segmentation and centrelines such as total length of the branches, number of branches, number of generations, and volume of the 3D model. Results: The TSF method was the most automatic, while the Mimics Pulmonology Module (MPM) and the Mimics Basic Module (MBM) resulted in the highest number of branches. MPM is the software which demands the least number of clicks to process the data. We found that the freely available OsiriX was less accurate compared to the other methods regarding segmentation results. However, the TSF method provided results fastest regarding number of clicks. The MPM was able to find the highest number of branches and generations. On the other hand, the TSF is fully automatic and it provides the user with both segmentation of the airways and the centerlines. Reference segmentation comparison averages and standard deviations for MPM and TSF correspond to literature. Conclusion: The TSF is able to segment the airways and extract the centerlines in one single step. The number of branches found is lower for the TSF method than in Mimics. OsiriX demands the highest number of clicks to process the data, the segmentation is often sparse and extracting the centerline requires the use of another software system. Two of the software systems performed satisfactory with respect to be used in preprocessing CT images for navigated bronchoscopy, i.e. the TSF method and the MPM. According to reference segmentation both TSF and MPM are comparable with other segmentation methods. The level of automaticity and the resulting high number of branches plus the fact that both centerline and the surface of the airways were extracted, are requirements we considered particularly important. The in house method has the advantage of being an integrated part of a navigation platform for bronchoscopy, whilst the other methods can be considered preprocessing tools to a navigation system.

引言：本研究旨在提升导航支气管镜（navigated bronchoscopy）的支气管镜诊断阳性率并优化术前准备流程。在导航支气管镜操作中，常借助虚拟三维气道可视化技术，并与实时视频支气管镜同步，引导支气管镜工具抵达外周病变部位。导航支气管镜术中的可视化流程、分割时长与分割方法存在差异。将此类技术整合至介入手术室时，操作耗时与流程逻辑是两大亟需优化的核心要素。本研究对比了三种获取气道中心线与气道表面的方案。

方法：本研究对17例患者的肺部CT数据集分别采用三种方式处理：一是Mimics软件（Materialize，比利时鲁汶），其包含基础模块与肺病学测试版模块（MPM）；二是OsiriX软件（Pixmeo，瑞士日内瓦）；三是本研究的管状分割框架（Tube Segmentation Framework, TSF）方法。对MPM与TSF均以参考分割作为评估基准。通过自动与手动两种设置，可完成所有数据集的气道分割，获取三维模型与中心线。我们从两类维度对比不同处理流程：一是用户交互操作参数，如数据处理所需的点击次数；二是分割结果与中心线质量的量化指标，包括分支总长度、分支数量、分级数以及三维模型体积。

结果：TSF方法的自动化程度最高，而Mimics肺病学模块（MPM）与Mimics基础模块（Mimics Basic Module, MBM）的分支检出数量最多。MPM是数据处理所需点击次数最少的软件。研究发现，免费获取的OsiriX在分割结果的准确性上逊于其他方法。但TSF方法在点击次数维度上耗时最短。MPM可检出最多的分支与分级数。另一方面，TSF为全自动方法，可同时完成气道分割与中心线提取。MPM与TSF的参考分割对比平均值及标准差与现有文献结果相符。

结论：TSF方法可通过单一步骤完成气道分割与中心线提取。其检出的分支数量少于Mimics软件。OsiriX的数据处理所需点击次数最多，分割结果常较为稀疏，且中心线提取需借助其他软件系统。其中两款软件在用于导航支气管镜的CT图像预处理时表现令人满意，即TSF方法与MPM。经参考分割验证，TSF与MPM的性能可媲美其他分割方法。自动化程度高、分支检出数量多，以及可同时提取气道中心线与气道表面，是本研究认为尤为重要的三项要求。自研方法的优势在于可作为支气管镜导航平台的集成模块，而其余两款软件仅可作为导航系统的预处理工具。