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Except for the used logos the content of these slides is shared under the terms of Creative Commons Attribution License (CC-BY 4.0)unless the content is marked otherwise. This presentation was created using as source: DOI: 10.5281/zenodo.8070038 NFDI4BIOIMAGE National Research Data Infrastructure for Microscopy and BioImage Analysis Speaker Dr. Riccardo Massei Contributions from Christian Schmidt, Stefanie Weidtkamp-Peters, Josh Moore, Janina Hanne, Katharina Schmitz Find thispresentationon Zenodo: DOI: 10.5281/zenodo.8414319 05.10.2023 https://nfdi4bioimage.de office@nfdi4bioimage.de 1
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NFDI4BIOIMAGE Core mission Enable FAIR bioimage data management for German researchers, across disciplines and embedded in the international framework. www.ufz.de 2
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The bioimaging data challenge Adaptedafter: Ouyangand Zimmer, CurrOpSysBiol, 2017, doi: 10.1016/j.coisb.2017.07.011
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Tackling the challenge Y. Stahl, S. Weidtkamp-Peters, HHU Düsseldorf
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Objectives Figure: Josh Moore
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Community integration
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TA leads
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The participants
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UFZ in the NFDI4BIOIMAGE UFZ is participant in three different task area (TA 1, 3, 4): • Apply and advise on FAIR-IO concepts for HCS data (aka data stewardship) • Provide semi(automated) integrative workflows for transferring analytical HCS into cloud based systems (i.e. OMERO) • Test and provide tools for automated sample tracking and naming to facilitate data linkage and synchronization • Provide workflows to link between laboratory sample management systems and analytical instrumentations and for automatic transfer to an image repository Integration at UFZ in CITEPro (TB CITE) and iCyt platform (TB Ecosystems): • Human cell lines • The zebrafish embryos • Phytoplankton, particulate matter and pollen
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UFZ in the NFDI4BIOIMAGE Copyright © 2021, Springer Nature America, Inc. Source: Sarkans, U., Chiu, W., Collinson, L.et al.REMBI: Recommended MetadataforBiological Images—enablingreuseof microscopydatain biology.Nat Methods18, 1418–1422 (2021). https://doi.org/10.1038/s41592-021-01166-8
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UFZ in the NFDI4BIOIMAGE OMERO upload – Manual workflow OMERO upload – Automatic workflow
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NFDI4BIOIMAGE online
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How to reach us to… Align activities? You or your group work on the same or similar topics? Do you want to align activities and collaborate? → Contact us via email to: stefanie.weidtkamp-peters@hhu.de (cc: office@nfdi4bioimage.de) → What then? Let‘s get in touch to discuss this!
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How to reach us to… Get support? You are in need of bioimaging RDM solutions? → Contact the Consortium at support@nfdi4bioimage.de → What then? Your email goes to the Data Stewards Team. The team is still forming, so some time might be required still. Follow-up actions depend on the nature of the request (from pointing at useful resources to establishing a Community Use Case collaboration)
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How to reach us to… Stay informed? You want to stay informed about the progress, results, and events of the Consortium? → Subscribe to the mailing list at: https://nfdi4bioimage.de/en/get-involved/ → What then? We will send you regular updates.
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NFDI4BIOIMAGE Contact
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FundedbytheDeutsche Forschungsgemeinschaft (DFG, German Research Foundation) undertheNational Research Data Infrasstructure–NFDI 46/1 –501864659 www.ufz.de 17
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