Continued Development and Maintenance of ITK-SNAP 3D Image Segmentation Software

描述(由申请人提供)：本项目寻求继续开发和维护软件应用程序ITK-SNAP，该应用程序提供用户引导的自动分割和手动注释生物医学成像生成的3D体积的功能。ITK-SNAP是一个免费的开源软件工具，在生物医学社区拥有大量用户(估计有数千人)，自2006年以来已发表了200多份出版物，涵盖了广泛的生物医学应用和成像模式。此外，ITK-SNAP在当今成像研究人员可用的开源工具中占有独特的位置，具有专门针对图像分割问题的成熟用户界面和功能。该项目的总体目标是确保ITK-SNAP在面对日益复杂的成像数据集和快速变化的软件环境时的长期可用性和生存能力；并显著扩展可受益于ITK-SNAP的自动功能的生物医学图像分割问题的类别。为实现这些目标提出了五个具体目标。AIM 1将开发一种新的软件框架，用于半自动分割多模式和多通道成像数据。这一目标将用一个灵活的工具箱扩展现有的活动轮廓分割框架，该工具箱用于用户引导从图像体积生成目标/背景概率图。该工具箱将支持纹理分析和模式分类，以及用户生成的空间分割先验。AIM 2将通过采用显卡加速来提高ITK-SNAP的性能，并将改变内部数据结构，使该工具能够处理非常大的图像体积，如高分辨率多层CT或共焦显微镜产生的图像。AIM 3将消除ITK-SNAP对老化和支持较差的FLTK用户界面软件库的依赖，而是过渡到拥有强大社区和行业支持的Qt库。这一目标还将对ITK-SNAP的可用性做出重大改进，包括对项目范例的支持。在目标4中，将开发基于新的ITK-SNAP功能的分割协议，以解决各种生物医学图像分割问题。然后，将使用公共数据集对照手动分割来验证这些协议。成功的标准是在不影响观察者间或观察者内可靠性的情况下，将分割时间减少两倍或更好。目标5是继续支持ITK-SNAP用户社区，实施用户要求的功能，纠正软件中的缺陷，并提供全面的文件，包括视频教程以及培训和外联工作。 公共卫生相关性：ITK-SNAP是一个交互式软件工具，可以简化和自动化数千名生物医学研究人员面临的一项困难任务：如何测量和量化MRI和CT等三维医学图像中的相关结构？ITK-SNAP为数百项已发表的研究做出了贡献，这些研究涵盖了许多研究领域，包括癌症、心血管疾病和大脑疾病等关键公共卫生领域。如果获得资金，该应用程序将确保ITK-SNAP在未来可供研究人员使用，并实施创新，使更多的研究人员能够利用该工具的自动化能力。

DESCRIPTION (provided by applicant): This project seeks to continue developing and maintaining a software application ITK-SNAP, which provides functionality for user-guided automatic segmentation and manual annotation of 3D volumes generated by biomedical imaging. ITK-SNAP is a free, open-source software tool that has a large number of users in the biomedical community (estimated in the thousands) and has contributed to over 200 publications since 2006, spanning a wide range of biomedical applications and imaging modalities. Furthermore, ITK-SNAP occupies a unique place in the spectrum of open-source tools available to today's imaging researcher, with a mature user interface and functionality specifically focused on the problem of image segmentation. The broad goals of this project are to ensure the long-term availability and viability of ITK-SNAP in the face of ever increasing complexity of imaging datasets and rapidly changing software environment; and to significantly expand the class of biomedical image segmentation problems that can benefit from the automatic features of ITK-SNAP. Five specific aims are proposed to achieve these goals. Aim 1 will develop a novel software framework for semi-automatic segmentation of multimodality and multichannel imaging data. This aim will extend the existing active contour segmentation framework with a flexible toolbox for user-guided generation of object/background probability maps from image volumes. The toolbox will support texture analysis and pattern classification, as well as user-generated spatial segmentation priors. Aim 2 will boost the performance of ITK-SNAP by employing graphics card acceleration and will change the internal data structures to allow the tool to work with very large image volumes, like those produced by high-resolution multi-slice CT or confocal microscopy. Aim 3 will remove ITK-SNAP dependencies on an aging and poorly supported FLTK user interface software library, transitioning instead to the QT library, which has strong community and industry support. This aim will also make critical improvements to ITK-SNAP usability, including support for the project paradigm. In Aim 4, segmentation protocols based on new ITK-SNAP functionality will be developed to address a diverse set of biomedical image segmentation problems. These protocols will then be validated against manual segmentation using public datasets. The criterion for success is to achieve a two-fold or better reduction in segmentation time with no penalty in inter-observer or intra-observer reliability. Aim 5 is to continue supporting the ITK-SNAP user community by implementing user-requested features, correcting defects in the software, and providing thorough documentation, including video tutorials, and training and outreach efforts. PUBLIC HEALTH RELEVANCE: ITK-SNAP is an interactive software tool that simplifies and automates a difficult task faced by thousands of biomedical researchers: how to measure and quantify relevant structures in three-dimensional medical images like MRI and CT? ITK-SNAP has contributed to hundreds of published studies spanning many areas of research, including in key public health areas such as cancer, cardiovascular disorders, and brain disorders. If funded, this application will ensure that ITK-SNAP is available to researchers in the future, as well as implement innovations that will allow even more researchers to take advantage of the tool's automation capabilities.