Publications
Datasets published with the help of NFDI4BIOIMAGE:
How machine learning helped identify drugs that trigger phospholipidosis
Phospholipidosis (PLD) is a cellular side effect caused by many drugs that can interfere with cell-based screening and slow down drug development. Using a large dataset of over 5,000 repurposed drugs tested across different cell lines, the authors developed and validated a machine learning model that predicts which compounds are likely to induce PLD, providing a potential early screening tool for drug discovery.
DOI: 10.6019/S-BIAD2282
12/2025
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How optical clearing and 3D imaging reveal intact primate testicular tissue
This study introduces PT-CLEAR3D, a tissue clearing and 3D imaging technique for intact primate testes, enabling detailed visualization of cellular and tissue structures across humans, marmosets, and macaques. The method allows high-resolution, deep imaging of spermatogonial and somatic cell organization, offering a versatile toolbox for multi-species, multiplexed, and volumetric analysis of testicular tissue.
DOI: 10.6019/S-BIAD1898
05/2025
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Fluorescence lifetime separation of fluorophores in C. elegans embryos and hermaphrodites
This study demonstrates how FLIM phasor analysis can separate fluorescent signals with overlapping spectra in live-cell imaging, using C. elegans as a model system. The authors also introduce the open-source napari-FLIM-phasor-plotter plugin for converting, visualising, and analysing FLIM datasets.
DOI: 10.6019/S-BIAD1967
06/2025
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Using a cell assay to detect viral mono-ADP-ribosylhydrolase activity
This study develops a cell-based assay to monitor macrodomain hydrolase activity in living cells, using PARP15 nuclear foci as a readout. This versatile platform enables screening of macrodomain inhibitors and studying their function, supporting antiviral drug discovery against viruses like Chikungunya and SARS-CoV2.
DOI: 10.6019/S-BIAD1800
04/2025
From meristem to flower: how CLAVATA signalling guides barley inflorescence development
This study reveals that barley inflorescence architecture is controlled by HvCLV1 and HvFCP1, which regulate meristem activity to balance spikelet formation and meristem proliferation. Manipulating this pathway offers a strategy to engineer inflorescence structures by targeting distinct meristem behaviours.
DOI: 10.6019/S-BIAD1673
03/2025
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Root stem cell homeostasis in Arabidopsis involves cell-type-specific transcription factor complexes
This study examines how the transcription factors BRAVO, PLT3, and WOX5 interact to regulate stem cell maintenance and cell division in the Arabidopsis root stem cell niche. Using FRET-FLIM and computational modelling, the authors show that cell-type-specific protein complexes, influenced by prion-like domains in PLT3, contribute to controlling stem cell behaviour.
DOI: 10.6019/S-BIAD1636
03/2025
MULTI-CLARID (Multimodal Category Learning and Resting-state Imaging Data)
This study provides a multimodal fMRI/EEG dataset including 63 EEG channels, physiological signals, and structural MRI scans, alongside additional participant data available on request. The dataset covers a multi-dimensional category learning experiment and was collected at the CNI core facility of the Leibniz Institute for Neurobiology with full ethical approval and informed consent.
Characterising TITAN 5, a tiny GTPase in Arabidopsis
This study characterizes the Arabidopsis small GTPase TTN5, revealing its rapid nucleotide exchange and low GTP hydrolysis activity, suggesting it remains mostly GTP-bound and active in cells. Microscopy shows TTN5 localizes to the plasma membrane and endomembrane compartments, linking its unusual biochemical properties to vesicle trafficking and membrane dynamics.
DOI: 10.6019/S-BIAD1241
07/2024
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Visualising sperm metabolism in fruit flies
Dataset of fluorescence lifetime imaging microscopy raw and processed images of metabolic imaging of NAD(P)H and FAD of Drosophila melanogaster sperm both in vitro and in vivo in intact male and female sperm-storage organs.
DOI: 10.6019/S-BIAD1085
06/2024
Tracking how GABARAP proteins stick to microtubules inside cells
This study uses a GABARAP split-tandem construct to reveal its strong association with microtubules in living cells, independent of lipidation but dependent on N-terminal basic residues and avidity. The findings suggest that enhanced avidity constructs can visualise weak GABARAP interactions, shedding light on its roles in microtubule-related transport and autophagy.
Dataset on BIA: S-BIAD952
05/2024
A safer bovine pericardium proves suitable for heart implants
This study evaluates SULEEI-treated bovine pericardium, a glutaraldehyde-free biomaterial combining decellularization, riboflavin/UVA cross-linking, and electron beam irradiation, as an alternative for bioprosthetic tissue. In a rat model, the material showed comparable immune response and biomechanics to standard patches but with low calcification potential, suggesting promise for cardiovascular and valvular surgery.
Dataset on BIA: S-BIAD954
04/2024
Finding a tiny RNA that controls Klebsiella cell division
Original image data and associated analysis pipelines for the manuscript entitled “The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division“
DOI: 10.6084/m9.figshare.25186484
02/2024
Studying blood vessel damage in zebrafish embryos to predict toxicity
This study presents a label-free, automated video imaging method to detect angiogenesis inhibition in wild-type zebrafish embryos by tracking moving blood cells in intersegmental vessels. The approach is more sensitive than fluorescent reporter strains and enables high-throughput, non-invasive quantification of dose-dependent effects of tyrosine kinase inhibitors.
Metadata Annotation Workflow for OMERO with Tabbles. Dataset on BIA: S-BIAD954
02/2024
How glial cells organise ion channels in fly nerves
This study shows that in Drosophila melanogaster, voltage-gated sodium and potassium channels cluster at an axon initial segment-like region, with Para channel enrichment depending on peripheral glial cells. During development, increased channel clustering coincides with glial remodeling resembling myelin, suggesting fly axons mimic early steps in myelin evolution for efficient signal conduction.
DOI: 10.7554/eLife.85752
06/2023
Peer reviewed articles in scientific journals:
2025
MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis
This article highlights the challenges of sharing high-quality annotated biological images for AI development and proposes guidelines to overcome them. The MIFA (metadata, incentives, formats, accessibility) recommendations aim to improve data reuse and accelerate bioimage analysis tool development.
High-content screening (HCS) workflows for FAIR image data management with OMERO
This study presents semi-automated workflows using Workflow Management Systems and OMERO to manage the complex metadata and image data generated by high-content screening experiments. These workflows improve data consistency, reproducibility, and efficiency, while paving the way for future integration of machine learning in automated image analysis.
Towards transparency and knowledge exchange in AI-assisted data analysis code generation
2024
Making the most of bioimaging data through interdisciplinary interactions
This Perspective discusses the challenges and opportunities of interdisciplinary collaboration in bioimaging, emphasising how diverse expertise across acquisition and analysis can drive discovery. It advocates for open data sharing to foster a collaborative culture and accelerate innovation in the bioimaging field.
Setting up an institutional OMERO environment for bioimage data: Perspectives from both facility staff and users
This article describes the implementation of the OMERO system for managing complex bioimaging data at TU Dresden’s Core Facility Cellular Imaging. It highlights challenges like standardising naming conventions, curating metadata, and integrating workflows, offering practical guidance for adopting FAIR-compliant research data management in imaging facilities.
Photonic data analysis in 2050
This article highlights the growing complexity of photonic data analysis, which combines imaging, spectroscopy, and machine learning, and requires flexible, data-driven computational approaches. It emphasises the need for interdisciplinary collaboration, standardized infrastructures, and advanced methods to handle limited or variable datasets while integrating novel photonic techniques into routine applications.
SpatialData: an open and universal data framework for spatial omics
This study introduces SpatialData, a framework for managing and analysing large, multimodal spatial omics datasets with unified, memory-efficient representations and coordinate alignment. The framework enables spatial annotations, cross-modal integration, and flexible analysis, demonstrated using multimodal breast cancer data.
Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data
This article outlines key requirements for sharing high-quality bioimage data globally, focusing on managing metadata and contextual information to ensure reproducibility and scientific interpretability. It provides recommendations to standardize imaging quality control and democratize access to tools, enabling broader reuse and integration of imaging data across the life sciences.
The global RNA–RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division
This study maps the RNA interactions of the chaperone Hfq in Klebsiella pneumoniae and identifies the small regulatory RNA DinR, processed from dinI mRNA. DinR represses ftsZ translation during the SOS response, linking Hfq-mediated RNA regulation to DNA damage-induced inhibition of cell division.
2023
Zarr: A Cloud-Optimized Storage for Interactive Access of Large Arrays, Vol. 1
For decades, the sharing of large N-dimensional datasets has posed issues across multiple domains. Interactively accessing terabyte-scale data has previously required significant server resources to properly prepare cropped or down-sampled representations on the fly. Now, a cloud-native chunked format easing this burden has been adopted in the bioimaging domain for standardization. The format – Zarr – is potentially of interest for other consortia and sections of NFDI.
The global RNA–RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division
This study identifies Hfq-associated RNAs in Klebsiella pneumoniae and reveals a species-specific sRNA, DinR, that inhibits cell division by repressing FtsZ translation during DNA damage. DinR acts posttranscriptionally to complement SOS-response mechanisms and promotes bacterial filamentation.
2022
Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey
This survey assesses bioimaging research data management (RDM) practices in Germany, revealing strong community support for FAIR principles but highlighting technical, legal, and knowledge barriers to implementation. Respondents emphasise the need for metadata guidelines, annotation tools, and data management platforms like OMERO to improve data handling and sharing.
2021
NFDI4BIOIMAGE - An Initiative for a National Research Data Infrastructure for Microscopy Data
This article outlines plans for a German consortium within the NFDI to establish FAIR-compliant management of microscopy data, addressing challenges from diverse instruments, large data volumes, and heterogeneous file formats. Building on national and international collaborations, the initiative aims to provide sustainable RDM practices, metadata standards, training, and infrastructure to support quantitative, high-throughput bioimaging research.
NFDI4BIOIMAGE – An Initiative for a National Research Data Infrastructure for Microscopy Data
This article highlights the need for FAIR-compliant management of bioimaging data in Germany, emphasising challenges from large, complex datasets, heterogeneous file formats, and local storage practices. Leveraging experience from GerBI-GMB, the authors propose a national consortium within the NFDI to standardise data handling, promote sharing, and provide training to support quantitative, AI-driven bioimage research.
Highlighted publications from our community on Zenodo:
2024
Progress on the interoperability between ARC (annotated research context) and the image data management system OMERO
ARC is an ISA-based metadata standard developed in the plant sciences community by the consortium DataPLANT. For image data, we work collaboratively on the interoperability between ARC and the well-established image data management system OME Remote Objects (OMERO). To this end, two hackathons took place in November, and December 2023, resulting in a first extended documentation on advancing OMERO and ARC interoperability.
NFDI4BIOIMAGE - National Research Data Infrastructure for Microscopy and Bioimage Analysis
NFDI4BIOIMAGE aims to standardise and FAIRify bioimaging data across disciplines, enabling sharing, re-use, and integration with other data types like spatial omics. By providing interoperable data objects, analysis tools, cloud-based AI methods, and training, the consortium seeks to unlock the full potential of bioimage data for discoveries in fields from plant biology to cancer research.
Towards Preservation of Life Science Data with NFDI4BIOIMAGE
This talk presents NFDI4BioImage’s efforts to enable FAIR bioimage data management through metadata standards, sustainable cloud infrastructure, and community training. The consortium aims to support long-term preservation, integration, and re-use of life science imaging data across disciplines within Germany and internationally.
Who you gonna call? – Data Stewards to the rescue
The Data Steward Team of the NFDI4BIOIMAGE consortium presents themselves and the services (including the Helpdesk) that we offer.
AI's Dirty Little Secret: Without FAIR Data, It's Just Fancy Math
Poster presented at the European Light Microscopy Initiative meeting in Liverpool (https://www.elmi2024.org/).
RDF as a bridge to domain-platforms like OMERO, or There and back again
This note recounts OMERO’s shift from native RDF storage to SQL for performance reasons and reflects on the renewed recognition of RDF triples as a valuable standard for integrating and exchanging metadata across sources.
[Community Meeting 2024] Supporting and financing RDM projects within GerBI
Overview of GerBI RDM projects: why and how?
The role of Helmholtz Centers in NFDI4BIOIMAGE - A national consortium enhancing FAIR data management for microscopy and bioimage analysis
NFDI4BIOIMAGE develops tools, standards, and best practices to enable FAIR bioimaging data management, addressing challenges in formats, metadata, and open repositories. Through its Data Stewards and collaborations with Helmholtz Centers and initiatives, the consortium supports researchers in implementing FAIR practices and advancing microscopy and image analysis research.
From Paper to Pixels: Navigation through your Research Data - presentations of speakers
This workshop introduced life science researchers to key concepts and practical implementations of research data management, covering topics from data storage and licensing to patient data protection and code management. Special focus was given to electronic lab notebooks (eLabFTW) and the bioimage management platform OMERO, highlighting their benefits, open-source availability, and existing campus use cases, with support from NFDI4BIOIMAGE and DFG-funded projects.
2023
Metadata Annotation Workflow for OMERO with Tabbles
Short presentation given at at PoL BioImage Analysis Symposium Dresden 2023.
Thinking data management on different scales
Presentation given at PoL BioImage Analysis Symposium Dresden 2023.
Zarr: A Cloud-Optimized Storage for Interactive Access of Large Arrays
For decades, the sharing of large N-dimensional datasets has posed issues across multiple domains. Interactively accessing terabyte-scale data has previously required significant server resources to properly prepare cropped or down-sampled representations on the fly. Now, a cloud-native chunked format easing this burden has been adopted in the bioimaging domain for standardization. The format – Zarr – is potentially of interest for other consortia and sections of NFDI.
Conference talk: The Pelagic Imaging Consortium meets Helmholtz Imaging, 5.10.2023, Hamburg
In this talk, the consortium and the contribution to the work programme by the Helmholtz Centre for Environmental Research (UFZ) in Leipzig are outlined.
Combining the BIDS and ARC Directory Structures for Multimodal Research Data Organization
This study compares two standardized research data structures—DataPLANT’s Annotated Research Context (ARC) and the Brain Imaging Data Structure (BIDS) adapted for microscopy—to support FAIR management of multimodal datasets. The authors propose mapping between ARC and BIDS to improve data organization, sharing, and metadata interoperability across research communities.
NFDI4BIOIMAGE: Perspective for a national bioimage standard
Poster presented at Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023).