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Metadata guides for bioimaging

Here we present practical guidelines and recommendations on metadata annotation for bioimaging.

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OMERO installation

We will work on guidelines for implementing OMERO at based on the experience with OMERO instances at the project partner sites (under development).

Electronic Lab Notebooks

We are working on guideline information to electronic lab notebooks for bioimaging data management (under development).

Data Flow and Storage

We plan to evaluate optimal data flow and storage scenarios for microscopy data management.(under development).

Metrology and Microscopy Quality Control

We aim to establish an added-value database for metrology data (under development).

Instrument PC Supervision in Core Facilities

We are working on a tool to help maintaining the instrument PCs in an imaging core facility (under development).

OMERO = OME Remote Objects, a software product by the Open Microscopy Environment Consortium: https://www.openmicroscopy.org

Publications from or with contribution from the I3D:bio project

  • Jannasch, A., Tulok, S., Okafornta, C. W., Kugel, T., Bortolomeazzi, M., Boissonnet, T., Schmidt, C., Vogelsang, A., Dittfeld, C., Tugtekin, S.-M., Matschke, K., Paliulis, L., Thomas, C., Lindemann, D., Fabig, G., & Müller-Reichert, T. (2024). Setting up an institutional OMERO environment for bioimage data: Perspectives from both facility staff and users. Journal of Microscopy, 1–15. https://doi.org/10.1111/jmi.13360

  • Schmidt, C., Boissonnet, T., Dohle, J., Bernhardt, K., Ferrando-May, E., Wernet, T., Nitschke, R., Kunis, S., & Weidtkamp-Peters, S. (2024). A practical guide to bioimaging research data management in core facilities. Journal of Microscopy, 294, 350–371. https://doi.org/10.1111/jmi.13317
  • Anett Jannasch, Cindy Welzel, Jessica Pablik, Elizabeth von Hauff, Roberta Galli, Jan Rix, Antje Schauer, Claudia Dittfeld, Sems-Malte Tugtekin; In vivo application of a glutaraldehyde-free, UVA/riboflavin cross-linked bovine pericardium confirms suitability for cardiovascular substitutes. APL Mater. 1 January 2024; 12 (1): 011104. https://doi.org/10.1063/5.0182672
    (The data of this research article is publicly available in the TU Dresden’s OMERO instance, which was set up with support from I3D:bio. The metadata annotation in compliance with the REMBI checklist was support by I3D:bio and NFDI4BIOIMAGE)
  • Schmidt, C., Bortolomeazzi, M., Boissonnet, T., Dohle, J., Wernet, T., Hanne, J., Nitschke, R., Kunis, S., Bernhardt, K., Weidtkamp-Peters, S., & Ferrando-May, E. (2023). Bringing FAIR Bioimage Data Management into Practice: the Information Infrastructure for BioImage Data (I3D:bio) Project – bottom-up Community Support for Microscopy Data Sharing and Preservation. In V. Heuveline, N. Bisheh, & P. . Kling (Hrsg.), E-Science-Tage 2023: Empower Your Research – Preserve Your Data (S. 289-294). heiBOOKS. https://doi.org/10.11588/heibooks.1288.c18090
  • Schmidt, C., Bortolomeazzi, M., Boissonnet, T., Fortmann-Grote, C., Dohle, J., Zentis, P., Kandpal, N., Kunis, S., Zobel, T., Weidtkamp-Peters, S., & Ferrando-May, E. (2023). I3D:bio’s OMERO training material: Re-usable, adjustable, multi-purpose slides for local user training. Zenodo. https://doi.org/10.5281/zenodo.8323588 (training material and videos)
  • Kunis, Susanne, & Dohle, Julia. (2022). Structuring of Data and Metadata in Bioimaging: Concepts and technical Solutions in the Context of Linked Data. Zenodo. https://doi.org/10.5281/zenodo.7018750 (poster)
  • Kunis, Susanne. (2022, August 24). Structuring of Data and Metadata in Bioimaging: Concepts and technical Solutions in the Context of Linked Data. Zenodo. https://doi.org/10.5281/zenodo.7018929 (video)
  • Schmidt C, Hanne J, Moore J et al. Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey [version 2; peer review: 2 approved]. F1000Research 2022, 11:638 https://doi.org/10.12688/f1000research.121714.2

Conference Contributions

  • Kunis S., J. Lacoste, C. Strambio-De-Castillia, S. Weidtkamp-Peters: Data Management for Bioimaging Data and Metadata Annotation Tools. Conference Workshop, European Light Microscopy Initiative (ELMI) Meeting 2023, June 6th – 9th, Noordwijkerhout, NL
  • Boissonnet T., J. Dohle, C. Schmidt, C. Strambio-De-Castillia, T. Wernet: Hands-on metadata annotation for bioimaging using a REMBI-based annotation template. Conference Workshop, European Light Microscopy Initiative (ELMI) Meeting 2023, June 6th – 9th, Noordwijkerhout, NL
  • Schmidt C et al.: Bringing FAIR bioimage data management into practice: the Information Infrastructure for BioImage Data (I3D:bio) project – bottom-up community support for microscopy data sharing and preservation. Conference Poster, E-Science Tage 2023, March 1-3, Heidelberg, Germany
  • Boissonnet T et al.: Bioimage analysis for Research Data Management, Conference Poster, Crick Bioimage Analysis Symposium 2022, November 21-22, London, UK
  • Schmidt C: Bringing FAIR data management into practice for the bioimaging community, Conference Talk, Max Planck BioImaging Core Unit Network Assembly, October 6th, 2022, Potsdam, Germany

Other types of public contributions: