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Minimum Information guidelines for fluorescence microscopy: increasing the value, quality, and fidelity of image data
arXiv - CS - Databases Pub Date : 2019-10-24 , DOI: arxiv-1910.11370
Maximiliaan Huisman, Mathias Hammer, Alex Rigano, Farzin Farzam, Renu Gopinathan, Carlas Smith, David Grunwald, and Caterina Strambio-De-Castillia

High-resolution digital microscopy provides powerful tools for probing the real-time dynamics of subcellular structures, and adequate record-keeping is necessary to evaluate results, share data, and allow experiments to be repeated. In addition to advances in microscopic techniques, post-acquisition procedures such as image-data processing and analysis are often required for the reproducible and quantitative interpretation of images. While these techniques increase the usefulness of microscopy data, the limits to which quantitative results may be interpreted are often poorly quantified and documented. Keeping notes on microscopy experiments and calibration procedures should be relatively unchallenging, as the microscope is a machine whose performance should be easy to assess. Nevertheless, to this date, no widely adopted data provenance and quality control metadata guidelines to be recorded or published with imaging data exist. Metadata automatically recorded by microscopes from different companies vary widely and pose a substantial challenge for microscope users to create a good faith record of their work. Similarly, the complexity and aim of experiments using microscopes vary, leading to different reporting and quality control requirements from the simple description of a sample to the need to document the complexities of sub-diffraction resolution imaging in living cells and beyond. To solve this problem, the 4DN Imaging Standards Working Group has put forth a tiered system of microscopy calibration and metadata standards for images obtained through fluorescence microscopy. The proposal is an extension of the OME data model and aims at increasing data fidelity, ease future analysis, and facilitate objective comparison of different datasets, experimental setups, and essays.

中文翻译:

荧光显微镜最低信息指南:提高图像数据的价值、质量和保真度

高分辨率数字显微镜为探测亚细胞结构的实时动态提供了强大的工具,并且需要足够的记录来评估结果、共享数据和允许重复实验。除了显微技术的进步外,图像数据的可重复和定量解释通常还需要诸如图像数据处理和分析之类的采集后程序。虽然这些技术增加了显微镜数据的有用性,但可以解释定量结果的限制通常很难量化和记录。记录显微镜实验和校准程序应该相对没有挑战性,因为显微镜是一台性能应该易于评估的机器。尽管如此,时至今日,不存在与成像数据一起记录或发布的广泛采用的数据来源和质量控制元数据指南。由来自不同公司的显微镜自动记录的元数据差异很大,这对显微镜用户创建其工作的善意记录提出了重大挑战。同样,使用显微镜进行实验的复杂性和目的各不相同,导致报告和质量控制要求不同,从简单的样品描述到需要记录活细胞及其他亚衍射分辨率成像的复杂性。为了解决这个问题,4DN成像标准工作组针对荧光显微镜获得的图像提出了显微镜校准和元数据标准的分层系统。
更新日期:2020-05-18
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