Laboratory for Percutaneous Surgery, School of Computing, 557 Goodwin Hall, Queen's University, K7L 2N8, Kingston, Ontario, Canada.
Laboratory for Percutaneous Surgery, School of Computing, 557 Goodwin Hall, Queen's University, K7L 2N8, Kingston, Ontario, Canada.
Comput Methods Programs Biomed. 2019 Apr;171:19-26. doi: 10.1016/j.cmpb.2019.02.011. Epub 2019 Feb 21.
Segmentation is a ubiquitous operation in medical image computing. Various data representations can describe segmentation results, such as labelmap volumes or surface models. Conversions between them are often required, which typically include complex data processing steps. We identified four challenges related to managing multiple representations: conversion method selection, data provenance, data consistency, and coherence of in-memory objects.
A complex data container preserves identity and provenance of the contained representations and ensures data coherence. Conversions are executed automatically on-demand. A graph containing the implemented conversion algorithms determines each execution, ensuring consistency between various representations. The design and implementation of a software library are proposed, in order to provide a readily usable software tool to manage segmentation data in multiple data representations. A low-level core library called PolySeg implemented in the Visualization Toolkit (VTK) manages the data objects and conversions. It is used by a high-level application layer, which has been implemented in the medical image visualization and analysis platform 3D Slicer. The application layer provides advanced visualization, transformation, interoperability, and other functions.
The core conversion algorithms comprising the graph were validated. Several applications were implemented based on the library, demonstrating advantages in terms of usability and ease of software development in each case. The Segment Editor application provides fast, comprehensive, and easy-to-use manual and semi-automatic segmentation workflows. Clinical applications for gel dosimetry, external beam planning, and MRI-ultrasound image fusion in brachytherapy were rapidly prototyped resulting robust applications that are already in use in clinical research. The conversion algorithms were found to be accurate and reliable using these applications.
A generic software library has been designed and developed for automatic management of multiple data formats in segmentation tasks. It enhances both user and developer experience, enabling fast and convenient manual workflows and quicker and more robust software prototyping. The software's BSD-style open-source license allows complete freedom of use of the library.
分割是医学图像计算中的常见操作。各种数据表示形式都可以描述分割结果，例如标签图卷或表面模型。通常需要在它们之间进行转换，这通常包括复杂的数据处理步骤。我们确定了与管理多种表示形式相关的四个挑战：转换方法选择、数据来源、数据一致性和内存对象的连贯性。
一个复杂的数据容器保留了所包含表示形式的标识和来源，并确保了数据的一致性。转换是按需自动执行的。一个包含已实现转换算法的图确定了每个执行，从而确保了各种表示形式之间的一致性。提出了一个软件库的设计和实现，以便提供一个易于使用的软件工具来管理多种数据表示形式的分割数据。一个名为 PolySeg 的低级核心库在可视化工具包 (VTK) 中实现，用于管理数据对象和转换。它被高级应用程序层使用，该层已在医学图像可视化和分析平台 3D Slicer 中实现。应用程序层提供了高级的可视化、转换、互操作性和其他功能。
验证了构成图的核心转换算法。根据该库实现了几个应用程序，每个应用程序都展示了在可用性和软件开发方面的优势。Segment Editor 应用程序提供了快速、全面且易于使用的手动和半自动分割工作流程。快速原型制作了凝胶剂量学、外部束计划和磁共振成像-超声图像融合在近距离放射治疗中的临床应用程序，从而产生了已经在临床研究中使用的强大应用程序。在这些应用程序中发现转换算法是准确和可靠的。
设计和开发了一个通用的软件库，用于自动管理分割任务中的多种数据格式。它增强了用户和开发人员的体验，使手动工作流程快速方便，并加快了软件原型制作过程。该软件的 BSD 风格的开源许可证允许完全自由地使用该库。
