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Training material by the I3D:bio team

FAIR bioimage data management and analysis with OMERO (Workshop material)

In collaboration with the NFDI4BIOIMAGE consortium, the I3D:bio team co-organized two workshops on bioimage data handling and analysis with OMERO.

One two-day workshop was held online on April 29th&30th, 2024, entitled FAIR data handling for microscopy: Structured metadata annotation in OMERO

Additionally, an on-premise workshop was offered at the German Cancer Research Center in Heidelberg on May 13th, 2024, entitled Bioimage data management and analysis with OMERO

The workshop material and associated github repositories are avaialable for reuse as open educational resources on Zenodo.

If you are interested in hosting an OMERO workshop together with member of the I3D:bio team and the NFDI4BIOIMAGE consortium, please reach out via the contact page.

I3D:bio’s OMERO training material: Re-usable, adjustable, multi-purpose slides for local user training

The open-source software OME Remote Objects (OMERO) is a data management software that allows storing, organizing, and annotating bioimaging/microscopy data. OMERO has become one of the best-known systems for bioimage data management in the bioimaging community. The Information Infrastructure for BioImage Data (I3D:bio) project facilitates the uptake of OMERO into research data management (RDM) practices at universities and research institutions in Germany. Since the adoption of OMERO into researchers’ daily routines requires intensive training, a broad portfolio of training resources for OMERO is an asset. On top of using the OMERO guides curated by the Open Microscopy Environment Consortium (OME) team, imaging core facility staff at institutions where OMERO is used often prepare additional material tailored to be applicable for their own OMERO instances. Based on experience gathered in the Research Data Management for Microscopy group (RDM4mic) in Germany, and in the use cases in the I3D:bio project, we created a set of reusable, adjustable, openly available slide decks to serve as the basis for tailored training lectures, video tutorials, and self-guided instruction manuals directed at beginners in using OMERO. The material is published as an open educational resource complementing the existing resources for OMERO contributed by the community.

  • Material / slides:
    • Creative Commons Attribution 4.0 (https://creativecommons.org/licensesby/4.0/)
    • Cite as: 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
  • Videos:
    • Creative Commons Attribution 4.0 (https://creativecommons.org/licensesby/4.0/)
    • Cite as: I3D:bio’s OMERO Training Videos 2023, https://www.youtube.com/playlist?list=PL2k-L-zWPoR7SHjG1HhDIwLZj0MB_stlU, based on: 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.832358

OMERO.figure for reproducible figures with OMERO (Workshop Video)

This ~ 1 h workshop recording provides an introduction to how the image data management platform OMERO can be leveraged to create publication-ready figures in a managed, reproducible manner.
The workshop was offered by Tom Boissonnet (HHU Düsseldorf) during the Halfway to I2K Conference 2023.

  • Video:
    • Creative Commons Attribution license.
    • Cite as: Boissonnet, Tom: OMERO.figure for reproducible figures within the data management platform OMERO. Workshop at I2K Conference 2023, Oct. 17th 2023. Available on YouTube: https://www.youtube.com/watch?v=Mty7_382kMM 

Metadata and data structuring in bioimaging explained (poster and video)

This resource provides an overview of important technical terms and concepts for data and metadata structuring in bioimaging. It also contains information about linked data concepts, ontologies, semantic web technology, resource description framework, ISA, and practical metadata annotation tools.

This poster was discussed with participants at the I3D:bio Kick-Off meeting in May 2022.

  • Poster:
    • Creative Commons Attribution 4.0 (https://creativecommons.org/licensesby/4.0/)
    • Cite as: 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
  • Video:
    • Creative Commons Attribution 4.0 (https://creativecommons.org/licensesby/4.0/)
    • Cite as: 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

External (online) resources

Online Training on RDM in general (list)

Here we provide a collection of online training materials for generic RDM topics.

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Online training bioimaging-specific RDM (list)

Find here a list of online training resources about RDM for bioimaging and bioimage analysis.

Read More