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 interpretationof 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 ]   .
The application of microscopy in biomedical research has come a long way since Antonie van Leeuwenhoek discovered URLanisms. Countless innovations have positioned light microscopy as a cornerstone of modern biology and a method of choice for connecting omics datasets to their biological and clinical correlates. Still, regardless of how convincing published imaging data looks, it does not always convey meaningful information about the conditions in which it was acquired, processed, and analyzed. Adequate record-keeping , reporting, and quality control are therefore essential to ensure experimental rigor and data fidelity, allow experiments to be reproducibly repeated, and promote the proper evaluation, interpretation, comparison, and re-use. To this end, microscopy images should be accompanied by complete descriptions detailing experimental procedures, biological samples, microscope hardware specifications, image acquisition parameters, and image analysis procedures, as well as metrics accounting for instrument performance and calibration. However, universal, community-accepted Microscopy Metadata standards and reporting specifications that would result in Findable Accessible Interoperable and Reproducible (FAIR) microscopy data have not yet been established. To understand this shortcoming and to propose a way forward, here we provide an overview of the nature of microscopy metadata and its importance for fostering data quality, reproducibility, scientific rigor, and sharing value in light microscopy. The proposal for tiered Microscopy Metadata Specifications that extend the OME Data Model put forth by the 4D Nucleome Initiative and by Bioimaging North America 1-3] as well as a suite of three complementary and interoperable tools are being developed to facilitate the process of image data documentation and are presented in related manuscripts 4-6 .
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High-resolution digital microscopy provides powerful tools for probing the real-time dynamics of subcellular structures, and adequate
The application of microscopy in biomedical research has come a long way since Antonie van Leeuwenhoek discovered URLanisms. Countless innovations have positioned light microscopy as a cornerstone of modern biology and a method of choice for connecting omics datasets to their biological and clinical correlates. Still, regardless of how convincing published imaging data looks, it does not always convey meaningful information about the conditions in which it was acquired, processed, and analyzed. Adequate
R
is necessary to evaluate results, share data, and
, reporting, and quality control are therefore essential to ensure experimental rigor and data fidelity,
R
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 interpretationof 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
reproducibly repeated, and promote the proper evaluation, interpretation, comparison, and re-use. To this end, microscopy images should be accompanied by complete descriptions detailing experimental procedures, biological samples, microscope hardware specifications, image acquisition parameters, and image analysis procedures, as well as metrics accounting for instrument performance and calibration. However, universal, community-accepted Microscopy Metadata standards and reporting specifications that would result in Findable Accessible Interoperable and Reproducible (FAIR) microscopy data have not yet been established. To understand this shortcoming and to propose a way forward, here we provide an overview of the nature of microscopy metadata and its importance for fostering data quality, reproducibility, scientific rigor, and sharing value in light
R
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
for tiered Microscopy Metadata Specifications that extend the OME Data Model put forth by the 4D Nucleome Initiative and by Bioimaging North America
A
1-3
A
as well as a suite of three complementary and interoperable tools are being developed to facilitate the process of image data documentation and are presented in related manuscripts
A
4-6