[RDM4Mic2025] Data stewardship for Bio-Image Research Data Management Support and Training in NFDI4BIOIMAGE

Data stewards for Bio-Image RDM Support and Training in NFDI4BIOIMAGE Conni Wetzker, Vanessa Fuchs and Jens Wendt RDM4Mic Meeting Münster 2025, zenodo.org/records/17472821 The content of this slide is shared under the terms of the Creative Commons Attribution License (CC-By 4.0, creativecommons.org/licenses/by/4.0) Data stewardship for Bio-Image Research Data Management Support and Training in NFDI4BIOIMAGE Conni Wetzker, Vanessa Fuchs and Jens Wendt Data stewards, NFDI4BIOIMAGE RDM4Mic Meeting @ Multiscale Imaging Centre, Uni Münster, October 21 2025 1 Data stewards for Bio-Image RDM Support and Training in NFDI4BIOIMAGE Conni Wetzker, Vanessa Fuchs and Jens Wendt RDM4Mic Meeting Münster 2025, zenodo.org/records/17472821 The content of this slide is shared under the terms of the Creative Commons Attribution License (CC-By 4.0, creativecommons.org/licenses/by/4.0) Data and metadata handling in bio-imaging requires research data management •Bioimaging data is multi-dimensional (5D and beyond) and annotated with metadata. •Datasets can easily reach GB and TB in size. •The variety of microscopic techniques, manufacturers and consequently bio-image formats is large. •Handling and analysis of microscopy data of biological samples requires sophisticated (and partially tailored) tools, workflows including trainings for users to support the scientific community. 2 Data stewards for Bio-Image RDM Support and Training in NFDI4BIOIMAGE Conni Wetzker, Vanessa Fuchs and Jens Wendt RDM4Mic Meeting Münster 2025, zenodo.org/records/17472821 The content of this slide is shared under the terms of the Creative Commons Attribution License (CC-By 4.0, creativecommons.org/licenses/by/4.0) NFDI4BIOIMAGE –an NFDI consortium for research data management in bio-imaging and bio-image analysis NFDI is the Nationale Forschungsdateninfrastruktur e.V: It envisions ‘data as a common good for excellent research, organised by the scientific community in Germany’. –nfdi.de TA1: Image (meta)data formats & standardization Leads: Susanne Kunis, Stefanie WeidtkampPeters, Josh Moore TA2: Technical infrastructure & cloud resources Leads: Björn Grüning, Markus Blank-Burian TA3: Multimodal data linking & integration TA3: Multimodal data linking & integration Lead: Jan-Philipp Mallm, Stefan Remy TA4: Bioimage informatics & analysis Leads: Anna Kreshuk, Marc Tilo Figge, Christian Tischer TA5: Training & community integration Leads: Robert Haase, Thomas Zobel TA6: Coordination, governance & networking Leads: Stefanie Weidtkamp-Peters, Elisa May *modified from Moore, J.A. et al. (2024) NFDI4BIOIMAGE - National Research Data Infrastructure for Microscopy and Bioimage Analysis. https://doi.org/10.5281/zenodo.13168692 3 * Data stewards for Bio-Image RDM Support and Training in NFDI4BIOIMAGE Conni Wetzker, Vanessa Fuchs and Jens Wendt RDM4Mic Meeting Münster 2025, zenodo.org/records/17472821 The content of this slide is shared under the terms of the Creative Commons Attribution License (CC-By 4.0, creativecommons.org/licenses/by/4.0) Our task force: the NFDI4BIOIMAGE data stewardship team Düsseldorf Konstanz Leipzig Münster Dresden Greifswald Expertise across •open data & open science •IT infrastructure •various fields of biological, biophysical & biomedical research •light microscopy facility services •bio-image data processing & analysis •bio-image data & metadata formats •open sharing of data in community repositories •teaching & training 4 Data stewards for Bio-Image RDM Support and Training in NFDI4BIOIMAGE Conni Wetzker, Vanessa Fuchs and Jens Wendt RDM4Mic Meeting Münster 2025, zenodo.org/records/17472821 The content of this slide is shared under the terms of the Creative Commons Attribution License (CC-By 4.0, creativecommons.org/licenses/by/4.0) Our task force: the NFDI4BIOIMAGE data stewardship team Düsseldorf Konstanz Leipzig Münster Dresden Greifswald TA6 TA2 TA1 TA5 TA4 TA3 •Support the bio-imaging community in RDM topics via our helpdesk service or direct contact •Guide data handling, metadata annotations, data upload to community repositories (such as BioImage Archive, Image Data Resources and others) •Develop tools and workflows for the community •Connect to experts in the consortium and beyond •Share training materials and offer trainings reach us with questions and feedback via [email protected] or forum.image.sc 5 Data stewards for Bio-Image RDM Support and Training in NFDI4BIOIMAGE Conni Wetzker, Vanessa Fuchs and Jens Wendt RDM4Mic Meeting Münster 2025, zenodo.org/records/17472821 The content of this slide is shared under the terms of the Creative Commons Attribution License (CC-By 4.0, creativecommons.org/licenses/by/4.0) Seek for help? •Tell us about your problem or question •We distribute your request among us DaSts •You will receive an answer within 1-2 working days 1) We point you to the solution 2) We need to talk and a) Solve it together b) Develop a solution together –become a community use case •Alternative way: contact us via image.sc by using the tag #NFDI4BIOIMAGE 6 https://nfdi4bioimage.de/help-desk/ Data stewards for Bio-Image RDM Support and Training in NFDI4BIOIMAGE Conni Wetzker, Vanessa Fuchs and Jens Wendt RDM4Mic Meeting Münster 2025, zenodo.org/records/17472821 The content of this slide is shared under the terms of the Creative Commons Attribution License (CC-By 4.0, creativecommons.org/licenses/by/4.0) Facts about the NFDI4BIOIMAGE Helpdesk •operational since 03-2024 •38 requests so far •7 ongoing, 8 closed, 23 finished Topics covered so far: •DMPs and RDM for grant applications •Data organization and management •OMERO •Set-up & general usage •connection to ELNs •usage “for” image analysis (Galaxy, QuPath...) •Metadata annotation •Data publication •… your individual request Data stewards for Bio-Image RDM Support and Training in NFDI4BIOIMAGE Conni Wetzker, Vanessa Fuchs and Jens Wendt RDM4Mic Meeting Münster 2025, zenodo.org/records/17472821 The content of this slide is shared under the terms of the Creative Commons Attribution License (CC-By 4.0, creativecommons.org/licenses/by/4.0) Example request: Data publication 1) Request received: Publish data, make data FAIR 2) First meeting: consultation a) Understand the data -> recommendation for repository (here: BioImage Archive) a) Work out data structure b) Explain which metadata is needed in which format => homework: organize your data and collect respective metadata 3) Second meeting: check-up a) Check data structure b) Check metadata (in File list) c) Any issues with data upload? d) Check acknowledgement 4) Publication of dataset (e.g. S-BIAD1241) 8 Data stewards for Bio-Image RDM Support and Training in NFDI4BIOIMAGE Conni Wetzker, Vanessa Fuchs and Jens Wendt RDM4Mic Meeting Münster 2025, zenodo.org/records/17472821 The content of this slide is shared under the terms of the Creative Commons Attribution License (CC-By 4.0, creativecommons.org/licenses/by/4.0) •A scientist becomes a CAi user •Contact to CAi •Intro to microscopes by imaging specialists •First mentioning of OMERO •User is introduced to OMERO •After first log-in: Data management team contacts user •1on1 OMERO introduction •offer for a RDM session •User is introduced to RDM •Intro to FAIR1, naming conventions, data organization, data management, metadata annotation and REMBI2 •Customized OMERO-tags •Customized metadata template RDM-Training @CAi OMERO-workflow for our users 1) FAIR –Findable, Accessible, Interoperable, Reusable (doi: 10.1038/sdata.2016.18); 2) REMBI –Recommanded metadata for biological images (doi: 10.1038/s41592-021-01166-8); 3) I3D:bio –Information Infrastructure for BioImage Data (https://gerbi-gmb.de/i3dbio/) Find the workflow on Zenodo: Find the I3D:bio3training material on Zenodo: 9 Data stewards for Bio-Image RDM Support and Training in NFDI4BIOIMAGE Conni Wetzker, Vanessa Fuchs and Jens Wendt RDM4Mic Meeting Münster 2025, zenodo.org/records/17472821 The content of this slide is shared under the terms of the Creative Commons Attribution License (CC-By 4.0, creativecommons.org/licenses/by/4.0) The role of data stewards in ‘bio-image town’ •Connectors and communicators between bio-imaging scientists, imaging facilities, research software engineers and providers of services and networks for research data management (guides of change management) Different language and vocabulary (none or mis-communication) Common language and shared vocabulary 16 Moore, J.A. (2025) [ELMI2023] Finding Ways Through BioImage Town. https://zenodo.org/records/8019855 Cartoons modified from ‘Mind the Gap’ and ‘Common Language’ by Henning Falk, ©2024 NumFOCUS, used under a CC BY 4.0 license. https://zenodo.org/records/14762483