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

ITK-SNAP 3D 图像分割软件的持续开发和维护

• 批准号: 8531010
• 负责人: Paul A. Yushkevich
• 金额: $ 46.54万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-19 至 2015-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8531010
• 关键词: Acceleration; Address; Aging; Algorithms; Area; Automation; Back; Biomedical Research; Brain Diseases; Cardiovascular Diseases; Cations; Classification; Color; Communities; Complex; Computer software; Computers; Confocal Microscopy; Data; Data Set; Defect; Dependency; Development; Diffusion; Documentation; Education and Outreach; Educational workshop; Ensure; Environment; Exhibits; Fluorescence Microscopy; Funding; Future; Generations; Goals; Image; Imagery; Imaging technology; Industry; Lesion; Libraries; Magnetic Resonance Imaging; Maintenance; Malignant Neoplasms; Manuals; Maps; Measures; Memory; Modality; Operating System; Paper; Pattern; Performance; Probability; Process; Protocols documentation; Public Health; Publications; Publishing; Quality Control; Reproducibility; Research; Research Personnel; Resolution; Resources; S-nitro-N-acetylpenicillamine; Sampling; Slice; Software Tools; Speed; Structure; Texture; Three-Dimensional Image; Three-Dimensional Imaging; Time; Training; Ultrasonography; Update; Validation; Weight; Work; base; bioimaging; design; flexibility; graphical user interface; image processing; imaging Segmentation; imaging modality; improved; innovation; interest; interoperability; meetings; multimodality; next generation; novel; open source; operation; outreach; success; tool; tumor; usability

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.

该项目旨在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成的 3D 体积的功能 生物医学成像。 ITK-SNAP 是一款免费、开源的软件工具，在业界拥有大量用户 生物医学界（估计有数千人）自 2006 年以来已为 200 多篇出版物做出了贡献， 涵盖广泛的生物医学应用和成像模式。此外，ITK-SNAP 占据 在当今成像研究人员可用的开源工具系列中拥有独特的地位，拥有成熟的用户 界面和功能特别关注图像分割问题。本次活动的总体目标 项目的目的是确保 ITK-SNAP 在面对不断增加的情况下的长期可用性和可行性 成像数据集的复杂性和快速变化的软件环境；并显着扩大 可以从 ITK-SNAP 的自动功能中受益的一类生物医学图像分割问题。 为了实现这些目标，提出了五个具体目标。目标 1 将开发一个新颖的软件框架 多模态和多通道成像数据的半自动分割。这一目标将扩展现有的 主动轮廓分割框架，具有灵活的工具箱，用于用户引导的对象/背景生成 图像体积的概率图。该工具箱将支持纹理分析和图案分类，如 以及用户生成的空间分割先验。目标 2 将通过以下方式提高 ITK-SNAP 的性能 采用显卡加速并将更改内部数据结构以允许该工具使用 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。目标 3 将消除 ITK-SNAP 对老化且支持不良的 FLTK 用户界面软件库的依赖， 改用 QT 库，它拥有强大的社区和行业支持。这一目标也将 对 ITK-SNAP 可用性进行重大改进，包括对项目范例的支持。在目标 4 中， 将开发基于新 ITK-SNAP 功能的分段协议，以解决各种不同的问题 生物医学图像分割问题。然后将根据手动分段验证这些协议 使用公共数据集。成功的标准是实现两倍或更好的分割减少 时间，观察者间或观察者内部的可靠性没有损失。目标 5 是继续支持 ITK-SNAP 通过实现用户请求的功能、纠正软件中的缺陷并提供 完整的文档，包括视频教程以及培训和外展工作。