Recently added (10)#
Didaktisches Konzept zur Einführung ins Forschungsdatenmanagement (FDM) am Beispiel von Elektronischen Laborbüchern (ELNs) und OMERO für Bio-Bild-Verwaltung für Studierende der Lebenswissenschaften#
Cornelia Wetzker, Michael Schlierf
Published 2025-12-10
Licensed CC-BY-4.0
Dieses Dokument beschreibt die Notwendigkeit und einen Entwurf eines didaktischen Lehr-Konzeptes für eine Seminarreihe zum Thema Forschungsdatenmanagement für Studierende der Lebenswissenschaften mit Fokus auf biologischer Mikroskopie. Es beschreibt Lernziele, -inhalte und -methoden, um die Grundlagen des Forschungsdatenmanagements, der Nutzung von elektronischen Laborbüchern und dem Bio-Bild-Verwaltungs-Werkzeug OMERO theoretisch und praktisch zu vermitteln. Damit sollen Wissenschaftlern im Zuge ihres Studiums parallel zu ersten experimentellen Forschungsarbeiten frühzeitig die Grundlagen der guten wissenschaftlichen Praxis vermittelt werden. C.W. wird durch die Deutsche Forschungsgemeinschaft (DFG) gefördert, im Rahmen der Nationalen Forschungsdateninfrastruktur – NFDI 46/1 – 501864659.
Introduction to OME-ZARR, S3 and transformations#
Soltwedel, Johannes Richard
Published 2025-12-09
Licensed CC-BY-4.0
Introductory slides for top-level understanding of ome-zarr, cloud storage (S3) of ome-zarr data and usecases and nature of upcaming RFC5-style transformations.
Life Science Competence Centres: Open by Design#
Romain David, Nektarios Liaskos, Arina Rybina, Christos Arvanitidis, Anne-Sophie Bage, Carvajal-Vallejos, Patricia K., Sudeep Das, De Pascalis, Francesca, Dorothea Dörr, Katrina Exter, Petr Holub, Gurwitz, Kim Tamara, Fabio Liberante, Philippe Lieutaud, Allyson Lister, Joaquin Lopez, Bénédicte Madon, Marzia Massimi, Rafaele Matteoni, Maria Mîrza, Sarah Morgan, Bugra Oezdemir, Maria Panagiotopoulou, Christina Pavloudi, P. Melo, Ana M., Susanna-Assunta Sansone, Harald Schwalbe, Beatriz Serrano-Solano, Sorzano, Carlos Oscar, Emilio Urbinati, Jing Tang, Jonathan Tedds, Gary Saunders, Jonathan Ewbank
Published 2025-12
Licensed CC-BY-4.0
Preprint in submission process to Briefings in Bioinformatics Abstract: European Life Science Research Infrastructures (LS-RIs), one of the five major RI Science Clusters in Europe, were established to provide access to cutting-edge technologies to the scientific community. Individually, and collectively as the LS-RI cluster, they contribute to the development of the European Open Science Cloud (EOSC), under the aegis of the EOSC Federation. They are actively involved in the design and implementation of Competence Centres (CCs). These aim to increase the accessibility of domain-specific knowledge and tools, enhance interoperability, facilitate sharing and harmonisation of procedures, and promote Open Science and FAIR (Findable, Accessible, Interoperable, Reusable) practices. In this paper, we report a landscape mapping of the existing resources that formed the basis for the construction of CCs. We describe the possible design of CCs and their articulation with the LS-RIs. We focus on community-based ideas and recommendations to increase the potential of CCs to address long-standing challenges in sustainability, governance, scalability, and interoperability of Open Science within EOSC and the European Research Area (ERA) more generally.This paper provides a description of the nascent LS CCs, built following a survey of needs and services of existing LS-RI communities. When fully implemented, the LS CCs will serve as dynamic hubs to foster innovation, contribute to the EOSC’s future FAIR web of data, and support ongoing developments of the EOSC Federation. They will act as drivers of collaborative and impactful LS research in Europe and beyond. We explore the underlying challenges, and propose solutions, to ensure that the establishment of CCs will add value to the LS RI community, and to the EOSC, in a sustainable way.
OMERO and Research Data Management Workshop at the Georg-Speyer-Haus in Frankfurt#
Jens Wendt, Michele Bortolomeazzi
Published 2025-12-11
Licensed CC-BY-4.0
OMERO and Research Data Management Workshop at the Georg-Speyer-Haus in Frankfurt 09-10/12/2025. Colllection of slides and materials for the OMERO and Research Data Management Workshop at the Georg-Speyer-Haus in Frankfurt. funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI 46/1 – 501864659 Program Dec 9th 2025 – Day 1 (Everyone) 10.00 a.m.: Introduction and Welcome 10.15 a.m.: FAIR data management and OMERO introduction 11.15 a.m.: Data organization in OMERO using Tags 12.00 a.m.: Lunch Break 01.00 p.m.: Metadata annotation in OMERO using Key-Value Pairs 02.00 p.m.: OMERO and image analysis -access through GUI-based plugins -access through the API Macros and python scripts for data analysis and interrogation AI-models at a glance (e.g., segmentation) 03.30 p.m.: Break 04.00 p.m.: OMERO.figure 04.45 p.m.: A glance at data sharing in public repositories 05.15 p.m.: Time for questions and individual case discussions ~ 05.30 /05.45 p.m.: End of Day 1 Dec. 10th 2025 - Day 2 (IT staff and project management) 09:00 a.m. ~ 10:00 a.m.: OMERO practical Short break
OMERO technical setup: ~ 10:45 a.m. ~ 12:00 a.m.: OMERO and storage ~ 12:00 a.m. ~ 12.30 a.m.: OMERO and HPC 12.30 a.m.: Lunch Break 1.00 p.m. ~ 1.30 p.m.: User Groups, User handling, pilot user phases to set up OMERO
Sample image data and annotations associated to Presynaptic Actin Nanostructures: A Reproducibility Case Study#
Rensu Theart, Florian Levet, Hernandez-Herrera, Christophe Leterrier, de la Ballina, Laura R
Published 2025-12-02
Licensed CC-BY-4.0
Raw, processed and annotated images associated with the manuscript “Presynaptic Actin Nanostructures: A Reproducibility Case Study”. This work is part of an initiative of the Global BioImage Analysts’ Society (GloBIAS) to assess reproducibility of published bioimage analysis workflows. We present our attempt to reproduce Figure 7 of the article Presynapses contain distinct actin nanostructures. J Cell Biol 2 October 2023; 222 (10): e202208110. doi: https://doi.org/10.1083/jcb.202208110. Original images and annotations were kindly provided by their authors.
Test files for Nikon NEF distorted image #4389#
Dayer, Andrew J
Published 2025-12-12
Licensed CC-BY-4.0
[Workshop] Image Data Management in the Biological Sciences and Agriculture Research#
Lucia Vedder, Paul Peschel, Michele Bortolomeazzi, Christian Schmidt, Katrin Schröder
Published 2025-12-02
Licensed CC-BY-4.0
Veranstaltungsformat: Präsenz- und Online-Veranstaltung Veranstaltungsort:
Hybrid event at University of Kassel (FB 10)
Veranstalter:
Universitätsbibliothek Forschungsdaten-Service NFDI4BIOIMAGE FAIRagro RTG Multiscale Clocks
Zielgruppen:
Promovierende/Doktorand:innen Absolvent:innen Wissenschaftliche Mitarbeitende Gruppenleitungen Postdoktorand:innen/Postdocs Mitarbeitende der Universität Kassel
Workshop: Image Data Management in the Biological Sciences and Agriculture Research Do you work with image data and want to optimize your data management workflows? This workshop provides an overview of the key challenges associated with managing image data and presents available support services. You will learn about useful tools for image data management and how Bioimaging Research Data Management (RDM) can be integrated into your everyday practice. This workshop will not only provide knowledge in imaging data management but also create an opportunity to get to know each other, network, and exchange ideas. For the best learning outcome, we recommend in-person attendance. Content Module 1: General Introduction to Imaging Research Data Management 1.00 pm - 1.50 pm: for all audiences, incl. non-bioimaging stakeholders Module 2: NFDI4BIOIMAGE: Tools and Software for Bioimage Data Management FAIRagro: Observation data: From ground robots to UAVs 2.10 pm - 3.00 pm: for researchers at all career levels and tool providers Module 3: NFDI4BIOIMAGE: Bioimaging RDM in the everyday-practice FAIRagro: Satellite and grid data: the view from above 3.10 pm - 4.00 pm: for researchers at all career levels It is possible to attend individual modules, and your choices can be made during the registration process.
de.NBI hackathon 2025 - Project 7 introduction and report presentations#
Tom Boissonnet, Riccardo Massei
Published 2025-12-08
Licensed CC-BY-4.0
This record contains the presentations given at the 4th BioHackathon Germany (1–5 Dec 2025, Walsrode) by de.NBI / ELIXIR-DE, introducing the project on “Integrating Data Science Capabilities within the OMERO Data Management Ecosystem” and summarizing its results. We acknowledge funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI 46/1 – 501864659.
multi-channel-image#
Ellen Geibelt
Published 2025-11-26
Licensed CC-BY-4.0
a multi-channel-image with a BF and 5 fluorescence channels acquired with a 20x objective and Axioscan.Z1 (Zeiss slide scanner)
https://zenodo.org/records/17725097
https://doi.org/10.5281/zenodo.17725097