Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model

Abstract

While the power of modern microscopy techniques is undeniable, rigorous record-keeping and quality control are required to ensure that imaging data may be properly interpreted (quality), reproduced (reproducibility), and used to extract reliable information and scientific knowledge which can be shared for further analysis (value). In the absence of agreed guidelines, it is inherently difficult for scientists to create comprehensive records of imaging experiments and ensure the quality of resulting image data or for manufacturers to incorporate standardized reporting and performance metrics. To solve this problem, the 4D Nucleome (4DN) Initiative and BioImaging North America (BINA) here propose light Microscopy Metadata specifications that scale with experimental intent and with the complexity of the instrumentation and analytical requirements. They consist of a set of three extensions of the Open Microscopy Environment (OME) Data Model, and because of their tiered nature they clearly specify which provenance and quality control metadata should be recorded for a given experiment. This endeavor is closely aligned with the undertakings of the recently established QUAlity Assessment and REProducibility in Light Microscopy (QUAREP-LiMi; quarep.org) global community initiative. As a result, the ensuing flexible 4DN-BINA-OME (NBO) framework represents a turning point towards increasing data fidelity, improving repeatability and reproducibility, easing future analysis, and facilitating the verifiable comparison of different datasets, experimental setups, and assays. The intention of this proposal is to encourage participation, critiques, and contributions from all imaging community stakeholders, including research and imaging scientists, facility personnel, instrument manufacturers, software developers, standards organizations, scientific publishers, and funders.

Best practices and tools for reporting reproducible fluorescence microscopy methods

“…1), comprehensive checklists (Supplementary Exhibits 1-4) and a customizable checklist-generating tool, MicCheck (Supplementary Exhibit 5). These guidelines are in line with the tier-based system developed in the OME-4DN project for metadata collection to ensure consistency across the microscopy community 6 .…”

“…Imaging scientists are encouraged to stay informed about resources on education, rigor and reproducibility and to contribute to the development of guidelines and standards by many initiatives in the imaging community 6,[48][49][50] . These initiatives (including those in Supplementary Table 1, as well as many others) can help in this task by presenting the resources in conferences, workshops and other educational initiatives they support.…”

“…We recognize that addressing microscopy reproducibility is a complex, multifaceted issue that will require an ongoing and coordinated effort from everyone involved in scientific research. In particular, we recognize the contributions from core facilities and imaging scientists who are uniquely positioned to assist researchers in addressing these challenges by educating and supporting the scientific community 3,5,6,9,17,44,45,[48][49][50][51][52] (Supplementary Table 1). While this Perspective has focused on reporting of microscopy methodology, we emphasize that appropriate method validation and experimental design are critical to ensure the quality of quantitative microscopy data and the continued progress of feasible, rigorous and reproducible image-based science.…”

The BioImage Archive - building a home for life-sciences microscopy data

“…Several options exist to support this process, including automated metadata extraction (“harvesting”) and integration with local data-management solutions such as OMERO 24 . We will also integrate emerging community standards, such as the recently proposed 4DN-BINA extensions to the existing OME metadata model 25 . Where possible we will support importing metadata from external applications, such as tools designed to capture image-acquisition metadata at the time of imaging 26 .…”

The European Bioinformatics Institute (EMBL-EBI) in 2021

“…This process will provide integration with other existing data resources, for example by sharing sample metadata with BioSamples ( 28 ). REMBI will incorporate/support detailed community specifications where they exist, such as the 4DN-BINA-OME standard for light microscopy ( 29 ). The implementation of REMBI into BioImage Archive will improve findability and reuse of image data, to better unlock the potential of the BioImage Archive's collections.…”