Center for 3D Structure and Physics of the Genome

基因组 3D 结构和物理中心

• 批准号: 10818049
• 负责人: Job Dekker
• 金额: $ 17.5万
• 依托单位: UNIV OF MASSACHUSETTS MED SCH WORCESTER
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-18 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10818049
• 关键词: Academia; Adopted; Biological; Biological Assay; Calibration; Canada; Categories; Collaborations; Communities; Consensus; Data; Data Set; Detection; Documentation; Ensure; Environment; Funding; Genome; German population; Goals; Human BioMolecular Atlas Program; Image; Imaging Techniques; Individual; Industry; Intuition; Learning; Metadata; Microscope; Microscopy; Modeling; North America; Physics; Process; Production; Publishing; Quality Control; Recommendation; Reporting; Reproducibility; Research Personnel; Scientist; Software Tools; Specific qualifier value; Stains; System; United States National Institutes of Health; Work; bioimaging; data management; data portal; design; empowerment; experimental study; file format; imaging scientist; indexing; interoperability; light microscopy; microscopic imaging; next generation; open source; quality assurance; three dimensional structure; tool; user-friendly; working group

Summary/Abstract For quality, interpretation, reproducibility, and sharing value, microscopy images should be accompanied by detailed descriptions of the conditions that were used to produce them. The NIH-funded 4D Nucleome (4DN) Imaging Standards Working Group (IWG), working in close collaboration with the BioImaging North America (BINA) Quality-Control and Data Management Working Group (QC-DM-WG), has recently published a tiered system of extensions of the existing Open Microscopy Environment (OME) Microscopy Metadata model for microscope hardware specifications, image acquisition setting, and quality-control metrics. The model provides a clear set of OME-model-compatible recommendations guiding scientists in the 4DN community and beyond as to what metadata and calibration results should be provided to ensure the reproducibility of different categories of imaging experiments. Because the tremendous challenges require concerted global action, national organizations such as BINA, Canada BioImaging (CBI/BIC), and German BioImaging have recently joined forces with individual imaging scientists from both academia and industry to establish the QUality Assessment and REProducibility in Light Microscopy (QUAREP-LiMi) initiative as a forum for building broad consensus on quality control, reporting, reproducibility and sharing value for microscopy experiments. Despite these advances, the broader impact of this work crucially depends on how easily biological scientists working at the bench will be able to adopt the proposed specifications and incorporate them into their everyday work regardless of imaging expertise. To meet these goals, in close collaboration with the 4DN Data Coordination and Integration Center (DCIC), we have developed the Micro-Meta App and integrated it in the 4DN-Data Portal. Micro-Meta App is an intuitive, highly interoperable, open-source software tool designed to substantially lower the burden of documentation and quality assurance for light microscopy. Since then, we have made significant progress toward understanding the opportunities and challenges involved with the production of high-quality, well-documented, reproducible, and reusable imaging datasets. In this proposal, we plan to leverage these “lessons learned” and request funds to continue this work and produce the following deliverables: 1. Develop semi-automated processes for capturing 4DN-BINA-OME-QUAREP specified Microscopy Metadata about three key HuBMAP imaging assay types, CO-Detection by IndEXing (CODEX), CellDive and stained microscopy (H&E and PAS) and making available to HuBMAP data generators and users of the HuBMAP data portal. 2. Develop W3C-compatible JSON-LD file formats to be incorporated into the OME-Next Generation File Format (NGFF) and facilitate metadata exchange across different communities.

总结/摘要 为了质量、解释、再现性和共享价值，显微镜图像应附有 详细描述了用于生产它们的条件。4D Nucleome（4DN） 成像标准工作组（IWG），与北美生物成像组织密切合作 （BINA）质量控制和数据管理工作组（QC-DM-WG）最近发布了一份分层的 现有的开放显微镜环境（OME）显微镜元数据模型的扩展系统， 显微镜硬件规格、图像采集设置和质量控制指标。模型 提供了一套清晰的与OME模型兼容的建议，为4DN社区的科学家提供指导 以及应提供哪些元数据和校准结果，以确保 不同类别的成像实验。因为巨大的挑战需要全球协调一致的努力， 行动，国家组织，如BINA，加拿大生物成像（CBI/BIC），和德国生物成像 最近与来自学术界和工业界的个别成像科学家联手， 光学显微镜质量评估和再生（QUAREP-LiMi）倡议作为一个论坛， 在质量控制、报告、再现性和共享显微镜价值方面建立广泛共识 实验 尽管取得了这些进展，但这项工作的更广泛影响关键取决于生物科学家 在工作台工作将能够采用拟议的规格，并将其纳入其 日常工作，无论成像专业知识。为了实现这些目标，我们与4DN密切合作， 数据协调和集成中心（DCIC），我们开发了微型元应用程序，并将其集成到 4DN数据门户Micro-Meta App是一款直观、高度可互操作的开源软件工具， 大大降低了光学显微镜的文档和质量保证负担。 从那时起，我们在了解机遇和挑战方面取得了重大进展 参与高质量、记录良好、可重现和可重复使用的成像数据集的生产。 在本提案中，我们计划利用这些“经验教训”，并请求资金继续开展这项工作， 产生以下可交付成果： 1.开发用于捕获4DN-BINA-OME-QUAREP指定显微镜的半自动化流程 关于三种关键HuBMAP成像分析类型的元数据，通过IndEXing进行CO检测（CODEX）， CellDive和染色显微镜（H&E和PAS），并提供给HuBMAP数据生成器 和HuBMAP数据门户的用户。 2.开发与W3C兼容的JSON-LD文件格式以纳入OME下一代 文件格式（NGFF），并促进不同社区之间的元数据交换。