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4DN-BINA-OME (NBO) Tiered Microscopy Metadata Specifications - v2.01 - XSD schema

Alessandro Rigano; Caterina Strambio-De-Castillia

This is the XSD Schema representing the latest version (v02.01) of the 4DN-BINA-OME (NBO) tiered system of Microscopy Metadata Specifications extending the OME Data Model.

Note: v2.01 is a minor release that corrects minor errors that were found in v2.00.

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 latest version of the Open Microscopy Environment (OME) Data Model, which was released in 2016. Because of their scalable nature, the 4DN-BINA-OME Microscopy Metadata Specifications clearly specify which provenance and quality control metadata should be recorded for a given experiment. Last but not least, this endeavor is closely aligned with the undertakings of the recently established global community initiative dedicated to Quality Assessment and Reproducibility in Light Microscopy (QUAREP-LiMi; quarep.org). As a result, the ensuing flexible 4DN-BINA-OME (NBO) framework represents a turning point towards achieving community-driven Microscopy Metadata standards that would increase data fidelity, improve repeatability and reproducibility, ease future analysis and facilitate the verifiable comparison of different datasets, experimental setups, and assays. The intention of this proposal is to encourage participation, critiques, and contributions from the entire imaging community and all stakeholders, including research and imaging scientists, facility personnel, instrument manufacturers, software developers, standards organizations, journals, and funding agencies.

Additional support: -- Chan Zuckerberg Initiative grant #2019-198155 (5022) awarded to C.S.D.C. as part of the Imaging Scientist Program.
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  • Huisman, M., Hammer, M., Rigano, A., Farzam, F., Gopinathan, R., Smith, C., Grunwald, D., & Strambio-De-Castillia, C. (2019). Minimum Information guidelines for fluorescence microscopy: increasing the value, quality, and fidelity of image data. In arXiv [q-bio.QM]. arXiv. http://arxiv.org/abs/1910.11370

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