Piloting a web-based neuropathology image resource for the ADRC community

为 ADRC 社区试点基于网络的神经病理学图像资源

• 批准号: 10594297
• 负责人: David Andrew Gutman
• 金额: $ 35.12万
• 依托单位: EMORY UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-07-15 至 2025-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10594297
• 关键词: Address; Adoption; Affect; Algorithms; Alzheimer' s Disease; Alzheimer' s disease related dementia; Archives; Autopsy; Benchmarking; Brain; Clinical Data; Clinical Research; Collaborations; Collection; Communities; Computer software; Custom; Data; Data Set; Dementia; Development; Diagnosis; Disease; Documentation; Engineering; Ensure; Ethnic Origin; Evaluation; Foundations; Functional disorder; Funding; Goals; Grant; Growth; Histology; Image; Image Analysis; Individual; Informatics; Infrastructure; Institution; Logistics; Magnetic Resonance Imaging; Malignant Neoplasms; Metadata; Modeling; Names; Neurodegenerative Disorders; Online Systems; Parents; Pathology; Patients; Persons; Pilot Projects; Pythons; Race; Recruitment Activity; Registries; Research; Research Activity; Resources; Running; Science; Secure; Senile Plaques; Side; Site; Slide; Staging; Stains; Techniques; Testing; Tissues; United States National Institutes of Health; Universities; Work; anticancer research; brain tissue; cancer imaging; cell type; cloud based; cohort; community center; computing resources; data curation; data dictionary; data ingestion; data modeling; data repository; data sharing; data standards; digital; digital pathology; file format; genomic data; gigabyte; imaging system; improved; innovation; interest; neuropathology; new technology; pathology imaging; sharing platform; task analysis; tool; whole slide imaging; working group

The goal of the parent Emory Goizueta Disease Research Center (ADRC) is to provide support and facilitate the growth of clinicians and the clinical and research research activities for Alzheimer's disease and related disorders (ADRD). Central to this goal is the ability to freely distribute and share relevant data generated through these efforts. The National Alzheimer's Coordinating Center (NACC) facilitates these efforts, helping to harmonize clinical data from across individual ADRC sites. Neuropathologic evaluation of brain tissue is central to the diagnosis and staging of these diseases, but the histology data is not widely shared within this community. The increasing availability of whole slide imaging systems now makes data sharing feasible, although this is currently challenging. The lack of standard file formats, inconsistent naming schemas, image de-identification, and the enormous size of these images are ongoing challenges. We have developed the Digital Slide Archive (DSA) platform at Emory, which has been funded through a U24 and U01 grants from the NCI/NIH and has primarily been optimized for Cancer related image analysis workflows. Over the past year, as a proof of principle, we have collected image sets from six ADRC sites using the DSA platform. As described in this notice of special interest, numerous challenges remain to transform and harmonize heterogenous imaging data sets before they can be made AI/ML ready. In this proposal, we propose enhancing the DSA platform to support federating large neuropath imaging data sets. This will include developing a standardized data dictionary to describe slide level metadata, and tooling to facilitate data cleanup. We will also benchmark and optimize our analysis suite (HistomicsTK) on NP slide sides on local and cloud-based computational resources, and prepare tutorials demonstrating how our tools can be used for ADRD related image analysis tasks. These aims paired with the complementary and synergistic expertise of our informatics, pathology, and engineering will aid in development of robust, scalable, reliable, and sharable platforms to provide a foundation for innovative transformative science addressing a critical unmet need in neurodegenerative disease research.

母公司埃默里·戈伊苏埃塔疾病研究中心(ADRC)的目标是提供 支持和促进临床医生的成长以及临床和研究活动 阿尔茨海默病及相关疾病(ADRD)。这个目标的核心是能够自由地 分发和共享通过这些努力产生的相关数据。全国阿尔茨海默氏症 协调中心(NACC)促进了这些工作，帮助协调来自 在各个ADRC站点上。脑组织的神经病理评估是 这些疾病的诊断和分期，但组织学数据在这方面并没有广泛共享 社区。整个幻灯片成像系统的可用性不断提高，现在使得数据共享 这是可行的，尽管目前这是具有挑战性的。缺乏标准的文件格式，不一致 命名方案、图像识别以及这些图像的巨大尺寸正在进行中 挑战。我们已经在埃默里开发了数字幻灯片档案(DSA)平台，它已经 由NCI/NIH的U24和U01赠款资助，并已初步优化 用于癌症相关图像分析工作流。在过去的一年里，作为原则的证明，我们 使用DSA平台从六个ADRC站点收集图像集。如本通知所述 特别感兴趣的是，在转换和协调异质成像方面仍然存在许多挑战 数据集在它们可以被AI/ML准备好之前。 在本提案中，我们建议增强DSA平台以支持大型联合 神经路径成像数据集。这将包括开发标准化数据字典以 描述幻灯片级别的元数据，以及便于数据清理的工具。我们还将制定基准和 在本地和基于云的NP幻灯片上优化我们的分析套件(历史记录TK) 计算资源，并准备教程演示如何将我们的工具用于 ADRD相关图像分析任务。这些目标与互补和协同作用相匹配 我们的信息学、病理学和工程学的专业知识将有助于开发强大的、 可扩展、可靠且可共享的平台，为创新转型奠定基础 解决神经退行性疾病研究中未得到满足的关键需求的科学。