Advanced Development of an Open-source Platform for Web-based Integrative Digital Image Analysis in Cancer

基于网络的癌症综合数字图像分析开源平台的高级开发

• 批准号: 9059053
• 负责人: Lee Cooper
• 金额: $ 72.15万
• 依托单位: EMORY UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-05-01 至 2020-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9059053
• 关键词: Accounting; Address; Adoption; Advanced Development; Age; Algorithms; Archives; Area; Cell Count; Cell Nucleus; Cells; Cellular Morphology; Clinical; Clinical Data; Clinical Research; Cloud Computing; Collection; Communities; Computer Simulation; Computer software; Custom; Data; Data Analyses; Data Set; Databases; Development; Diagnosis; Ensure; Explosion; Gender; Gene Expression; Generations; Generic Drugs; Genetic; Genomics; Goals; Health; Histology; Human; Image; Image Analysis; Imagery; Immunohistochemistry; Individual; Informatics; Institution; Label; Language; Link; Malignant Neoplasms; Measurement; Medical Genetics; Metadata; Necrosis; Online Systems; Outcome; Pathology; Patients; Performance; Process; Pythons; Recruitment Activity; Research; Research Infrastructure; Research Personnel; Resources; Rest; Sampling; Scanning; Series; Slide; Software Engineering; Software Tools; Solid Neoplasm; Somatic Cell; Somatic Mutation; System; Technology; Testing; The Cancer Genome Atlas; Tissue Extracts; Tissues; Tumor Biology; Visual; Work; angiogenesis; anticancer research; base; cancer imaging; cloud based; dashboard; data sharing; density; design; digital; digital imaging; experience; genetic information; genomic data; gigabyte; image archival system; imaging biomarker; imaging informatics; improved; interest; microscopic imaging; new technology; novel; open source; quantitative imaging; repository; software systems; success; terabyte; tool; treatment response; tumor

DESCRIPTION (provided by applicant): The increasing availability of high-quality digital scanners has enabled the generation of large collections of histology images, confocal/multichannel images, and accompanying metadata. However there is a dearth of robust open- source solutions to efficiently visualize, process and manage these ever growing imaging collections. Our goal is to open-source, document and further develop integrative technologies leveraging our experience with the Cancer Digital Slide Archive (CDSA), a tool we have developed to facilitate analysis of data provided by the NCI's the Cancer Genome Atlas (TCGA). This tool is NOT and will not be limited to the analysis of TCGA data, however by working backwards from public data already available we can ensure the informatics technologies developed are scaleable and usable by the cancer community. In our proposal, we will first go through a process of software engineering review to improve the ease of installation to facilitate distribution to other research groups. We have partnered with Kitware for this proposal allowing us to use their 15+ years of experience in building and maintain quality open source software. The rest of the proposal will focus on the testing and integration of new features such as the ability to perform image quantification (e.g. cell counting, cell profiling), image markup and labeling, as well as perform basic group level analysis allowing the correlation of imaging features with user defined variables of interest. As an example, a user may classify an individual slide based on the mean density of nuclei and correlate this imaging parameter with patient survival, or with tumor grade.

描述（由申请人提供）：高质量数字扫描仪的可用性不断增加，使得能够生成大量组织学图像、共焦/多通道图像以及随附的元数据。然而，缺乏强大的开源解决方案来有效地可视化、处理和管理这些不断增长的图像集合。我们的目标是利用我们在癌症数字幻灯片存档 (CDSA) 方面的经验，开源、记录并进一步开发综合技术，CDSA 是我们开发的一种工具，旨在促进 NCI 癌症基因组图谱 (TCGA) 提供的数据分析。该工具不是也不会仅限于 TCGA 数据的分析，但是通过从现有的公共数据进行逆推，我们可以确保所开发的信息学技术可扩展并可供癌症界使用。在我们的提案中，我们将首先进行软件工程审查过程，以提高安装的便利性，以便于分发给其他研究小组。我们与 Kitware 合作完成了这项提案，使我们能够利用他们在构建和维护高质量开源软件方面超过 15 年的经验。该提案的其余部分将重点关注新功能的测试和集成，例如执行图像量化（例如细胞计数、细胞分析）、图像标记和标记的能力，以及执行基本组级分析以实现成像关联的能力具有用户定义的感兴趣变量的特征。例如，用户可以根据细胞核的平均密度对单个载玻片进行分类，并将该成像参数与患者存活率或肿瘤等级相关联。