Recently added (10)#
“Data Stewardship at NFDI4BIOIMAGE” presentation at Data Stewardship Knowledge Exchange Event @EMBL-Heidelberg#
Jens Wendt
Published 2026-05-18
Licensed CC-BY-4.0
Presentation held at the Data Stewardship Knowledge Exchange Event at EMBL-Heidelberg in May 2026 about the implementation of Data Stewardship at NFDI4BIOIMAGE. We acknowledge funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI 46/1 – 501864659.
Building Research Infrastructure Communities That Last#
Carole Goble
Published 2026-05-01
Licensed CC-BY-4.0
Invited keynote for 19th OME Community Meeting, Düsseldorf, Germany, 28-30 April 2026, https://www.openmicroscopy.org/events/ome-community-meeting-2026.html
From Microscope to Repository: Managing Image Data with OMERO#
Müller, Maximilian E.
Published 2026-05-05
Licensed CC-BY-4.0
This presentation was developed by NFDI4BIOIMAGE and held online as part of the CRC 1551 Data Week on 05. May 2026. It provides a general introduction to research data management (RDM) and public data deposition and highlights their specific relevance in research. Furthermore, it introduces OMERO as a platform for structured data storage, metadata management, and collaborative access and introduces repositories for imaging data. The slides are intended for educational use and may serve as a resource for teaching and training in research data management within the life sciences. We acknowledge funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI 46/1 – 501864659.
GloBIAS mission and working groups figure#
Corbat, Agustin Andres, Walther, Christa G., de la Ballina, Laura R., Condon, Nicholas David, Felder, Alessandro A., Martin Schätz, Bettina Schmerl, Ko Sugawara, Clara Prats, Anna Klemm, Florian Levet, Kota Miura, Paula Sampaio, Christian Tischer, Rocco D’Antuono, Cimini, Beth A., Robert Haase
Published 2026-04-17
Licensed CC-BY-4.0
GloBIAS figure (available in .ai, .pdf and .png formats).
Poster and Lightning Talk for “enriched” OMERO from the OME Community Meeting 2026#
Jens Wendt
Published 2026-05-04
Licensed CC-BY-4.0
This publication contains the Poster and accompanying Lightning Talk about the “enriched” OMERO held at the OME Community Meeting 2026 in Düsseldorf We acknowledge funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI 46/1 – 501864659.
Process management for the institutional deployment of OMERO as an image data RDM platform#
Michele Bortolomeazzi, Christian Schmidt
Published 2026-04-17
Licensed CC-BY-4.0
OMERO has been established as a valuable, community-tested platform to facilitate research data management with bioimaging data. It allows the central, secure storage of original image files, collaborative access and analysis, metadata curation, and figure creation directly from the original data. However, deploying OMERO as a solution for laboratories, departments, or whole institutes requires a coordinated multi-stakeholder process. Consequently, researchers who would like to use OMERO as their RDM solution may be overwhelmed by the effort that an OMERO implementation demands. On the basis of the „Information Infrastructure for BioImage Data“ (I3D:bio) project, and the NFDI4BIOIMAGE consortium, we have developed structured processes and installation management approaches to realize institutional OMERO instances as a resource for all researchers. In this workshop, we share hands-on experience for the initiation and steering the OMERO implementation process. This workshop is directed primarily at research support facility staff and leaders, senior researchers, and project managers in the field of bioimaging-data-driven research fields.
SWAT4HCLS Tutorial: KG Construction with ONTOP#
Carsten Fortmann-Grote, Damien Goutte-Gattat, Lubiana Alves, Tiago, Josh Moore, Olvera Cabrera, Daniel, Andra Waagmeester
Published 2026-04-07
Licensed CC-BY-4.0
Source files and pdf of the tutorial held at SWAT4HCLS 2026
Workflow and Example Dataset for Python-Based Stitching of Confocal Zebrafish Images from VAST BioImager-Based Screening#
Dutta, Suchetana Bias, Sarai Valerio-Cabrera
Published 2026-02-28
Licensed CC-BY-4.0
A Python-based stitching script for individual tiles obtained with an automated imaging platform that combines the Vertebrate Automated Screening Technology (VAST) BioImager system (Union Biometrica), the Large Particle (LP) Sampler (Union Biometrica), and the Zeiss Cell Observer Spinning Disk Confocal Microscopic System (SDCM) (Early et al., 2018). The Lyons Lab (https://www.lyons-lab.com/) designed the system as a screening tool for automated, high-resolution, in vivo imaging of 2–5-day-old zebrafish larvae. Two datasets are available to test the script, along with the final stitched files for comparison.
[FDM-Werkstatt 2026] [talk] NFDI - Nationale Forschungsdaten Infrastruktur -2 Lifescience consortia - NFDI4BIOIMAGE + DATAPlant#
Fuchs, Vanessa Aphaia Fiona
Published 2026-03-31
Licensed CC-BY-4.0
This publication contains the slides from the presentation “NFDI - Nationale Forschungsdaten Infrastruktur - 2 Lifescience consortia - NFDI4BIOIMAGE + DATAPlant” held on the 24th of March 2026 during the FDM Werkstatt 2026 in Düsseldorf.
[Workshop] Imaging data management with OMERO - Hands-on - by Vanessa Fuchs | NFDI4BIOIMAGE#
Fuchs, Vanessa Aphaia Fiona
Published 2026-04-01
Licensed CC-BY-4.0
In this workshop the participants get an introduction to OMERO and its core concepts (projects, datasets, images, metadata, permissions). Additionally they perform a few hands-on tasks: OMERO functionalities, data annotation using a REMBI table, and OMERO.figure. This workshop was part of the FDM-Werkstatt 2026 in Düsseldorf.
https://zenodo.org/records/19366801
https://doi.org/10.5281/zenodo.19366801