Recently added (10)#
AI4Science Training @ UFZ Magdeburg#
Höck, Lina Lisa, Robert Haase
Published 2026-03-27
Licensed CC-BY-4.0
This slide deck accompanies the AI4Science for scientists at UFZ Magdeburg: https://scads.github.io/ai4science-ufz-madgeburg-2026/intro.html It outlines the topics:
Introduction to Artificial Intelligence, AI systems, and language models
Application areas and limitations of AI in text generation
AI-assisted literature research
Prompt engineering
Prompting with large context
Knowledge distillation
Text Analysis / Information Retrieval
Embeddings and retrieval-augmented generation
Data analysis
Data and code generation
Bias
Privacy-compliant use
Copyright
EU AI Act
GerBI community meeting 2026: Developing towards the ideal FAIR research data management environment#
Soltwedel, Johannes Richard, Tom Boissonnet, Stefanie Weidtkamp-Peters
Published 2026-03-17
Licensed CC-BY-4.0
The German BioImaging research software engineering (RSE) unit is active in a wide collection of projects. Here we sketch out how we envision these to function together towards a better research data management environment for our community of researchers, microscopists and bio-image analysts.
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).
How Generative Artificial Intelligence impacts Bio-Image Data Science#
Robert Haase
Published 2026-02-22
Licensed CC-BY-4.0
In this slide deck we dive into generative artificial intelligence in particular used for code generation and see how it impacts Bio-Image Data Science. We learn about benchmarking large language models for data analysis code generation, and how to use them practically in our work.
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
Transforming ome-zarr: What’s (going to be) new in 0.6#
Soltwedel, Johannes Richard
Published 2026-03-31
Licensed CC-BY-4.0
Summary of new features and use cases of transformation metadata in the upcoming ome-zarr 0.6 metadata standard
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.
[2026 GerBI Community Meeting] NFDI4BIOIMAGE and its Help Desk for Community Support in Bioimage Research Data Management#
Cornelia Wetzker, Müller, Maximilian E., Fuchs, Vanessa Aphaia Fiona
Published 2026-03-19
Licensed CC-BY-4.0
The poster presents the consortium NFDI4BIOIMAGE with its objectives, key achievements until February 2026 and the support offered by its data stewardship team and help desk service. We recommend strategies to make bioimage data FAIRer along the individual stages of the research data life cycle. Version 2 additionally comprises the poster in svg format for more flexible reuse.
The consortium NFDI4BIOIMAGE is funded by DFG grant number NFDI 46/1, project number 501864659.
[Chemnitzer Linux Tage 2026] Open Source VDI: SPICE / QEMU with Video stream support#
von Suchodoletz, Dirk, Rafael Gieschke, Michael Scherle
Published 2026-03-28
Licensed CC-BY-4.0
The poster was presented at the Chemnitzer Linux Tage 2026. Additionally, the state of developments in Open Source VDI (OSVDI) was further presented in a talk by Rafael Gieschke, Michael Scherle and Dirk von Suchodoletz. The solution developed in WP2 of NFDI4BIOIMAGE provides a complete remote desktop representation via virtualization or cloud environments, accessible over a network connection. The goal is to implement a typical imaging workstation available remotely using a fully open and freely available software stack. OSVDI aims to complete a free and open IT toolkit in the spirit of digital sovereignty. The talk therefore particularly addresses co-developers as well as IT decision-makers and infrastructure administrators, with the goal of promoting the project beyond NFDI4BIOIMAGE and ensuring its long-term sustainability. Link to the recording of the talk (in German): https://media.ccc.de/v/clt26-417-open-source-vdi-hw-beschleunigter-remote-access-zu-libvirt Link to the slides of the talk (in German): https://chemnitzer.linux-tage.de/2026/media/programm/folien/417.pdf The project is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure - NFDI 46/1 - 501864659.
https://zenodo.org/records/19469051
https://doi.org/10.5281/zenodo.19469051