Center for 3D Structure and Physics of the Genome

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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.