Euro-BioImaging ERIC

The community-driven initiative Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy (QUAREP-LiMi) wants to improve reproducibility for light microscopy image data through quality control (QC) management of instruments and images. It aims for a common set of QC guidelines for hardware calibration and image acquisition, management and analysis.

Bioimaging has now entered the era of big data with faster-than-ever development of complex microscopy technologies leading to increasingly complex datasets. This enormous increase in data size and informational complexity within those datasets has brought with it several difficulties in terms of common and harmonized data handling, analysis, and management practices, which are currently hampering the full potential of image data being realized. Here, we outline a wide range of efforts and solutions currently being developed by the microscopy community to address these challenges on the path towards FAIR bioimaging data. We also highlight how different actors in the microscopy ecosystem are working together, creating synergies that develop new approaches, and how research infrastructures, such as Euro-BioImaging, are fostering these interactions to shape the field.

Intermediate filaments (IFs) comprise a large family of versatile cytoskeletal proteins, divided into six subtypes with tissue-specific expression patterns. IFs have a wide repertoire of cellular functions, including providing structural support to cells, as well as active roles in mechanical support and signaling pathways. Consequently, defects in IFs are associated with more than 100 diseases. In this Cell Science at a Glance article, we discuss the established classes of IFs and their general features, their functions beyond structural support, and recent advances in the field. We also highlight their involvement in disease and potential use as clinical markers of pathological conditions. Finally, we provide our view on current knowledge gaps and the future directions of the IF field.

Imaging technologies are used throughout the life and biomedical sciences to understand mechanisms in biology and diagnosis and therapy in animal and human medicine. We present criteria for globally applicable guidelines for open image data tools and resources for the rapidly developing fields of biological and biomedical imaging.

Abstract Persistent cell migration requires focal adhesions to assemble and disassemble locally while maintaining global front-rear alignment. The mechanism that enforces this long-range spatial coherence remains unresolved. Here we identify the intermediate filament protein vimentin as a cell-scale organizer that stabilizes focal adhesion alignment during directed fibroblast migration. Using quantitative live-cell imaging, we show that vimentin-deficient fibroblasts lose directional persistence and a complete collapse of global focal adhesion alignment. Quantitative analysis reveals that vimentin stabilizes focal adhesion alignment by constraining angular fluctuations and preserving the periodic bias of adhesion birth across the adhesion field. Loss of vimentin results in smaller, rapidly turning-over adhesions with disrupted orientation. Trajectory analysis reveals a mechanically anchored adhesion state selectively associated with vimentin recruitment, distinguishing mechanical stabilization from biochemical maturation. Super-resolution and iPALM imaging further show that vimentin integrates within the focal adhesion nanoarchitecture near the force-transduction layer. Together, our findings establish that vimentin intermediate filaments impose spatial coherence on adhesion dynamics, converting locally stochastic adhesion assembly, turnover, and disassembly into globally coordinated adhesions and persistent directional migration.

The COVID-19 pandemic devastated substantial portions of the tourism industry; the cruise industry particularly suffered from negative publicity as the virus spread rapidly on cruise ships. The pandemic is a disaster that the industry has been forced to adapt to. This study illustrates, through a mixed-methods research design, what factors cruiseferry operators considered in their responses to the pandemic, whether the implemented countermeasures increased their customers' sense of security, and what countermeasures customers would agree to follow before boarding a ship. The study thereby provides insights into which countermeasures are likely to decrease customers' perceived health risks and which they are ready to accept or not on cruises during pandemics.

The three-dimensional (3D) structure of the ductal epithelium and the surrounding extracellular matrix (ECM) are integral aspects of the breast tissue, and they have important roles during mammary gland development, function and malignancy. However, the architecture of the branched mammary epithelial network is poorly recapitulated in the current in vitro models. 3D bioprinting is an emerging approach to improve tissue-mimicry in cell culture. Here, we developed and optimized a protocol for 3D bioprinting of normal and cancerous mammary epithelial cells into a branched Y-shape to study the role of cell positioning in the regulation of cell proliferation and invasion. Non-cancerous cells formed continuous 3D cell networks with several organotypic features, whereas the ductal carcinoma in situ (DCIS) -like cancer cells exhibited aberrant basal polarization and defective formation of the basement membrane (BM). Quantitative analysis over time demonstrated that both normal and cancerous cells proliferate more at the branch tips compared to the trunk region of the 3D-bioprinted cultures, and particularly at the tip further away from the branch point. The location-specific rate of proliferation was independent of TGFβ signaling but invasion of the DCIS-like breast cancer cells was reduced upon the inhibition of TGFβ. Thus, our data demonstrate that the 3D-bioprinted cells can sense their position in the branched network of cells and proliferate at the tips, thus recapitulating this feature of mammary epithelial branching morphogenesis. In all, our results demonstrate the capacity of the developed 3D bioprinting method for quantitative analysis of the relationships between tissue structure and cell behavior in breast morphogenesis and cancer.

Background: that live in biofilms on tooth surface. The ECM protects the bacteria from the flushing and buffering effects of saliva resulting in highly acidic microenvironments inside the biofilm. Materials and methods: strains, as well as acid neutralization inside the mature biofilm. Results were compared with the biofilm composition. Effects of a non-fermentable polyol, xylitol, on acid production and acid neutralization in mature biofilms were evaluated by real-time pH measurements and confocal microscopy. Results: Combination of real-time pH measurements with biofilm accumulation assays revealed growth media dependent differences in the pH decrease and biofilm accumulation, as well as strain differences in acid production and biofilm formation but not in the buffer diffusion through ECM. The presence of xylitol reduced the pH drop during biofilm formation of all strains. In addition, with strain Ingbritt xylitol reduced the amount of ECM in biofilm, which increased the rate of acid neutralization inside the biofilm after buffer exposure. Conclusion: ECM after xylitol exposure may allow acid-neutralizing saliva to reach deeper layer of the biofilms and thus, in part, explain previous clinical observations of reduced plaque acidogenicity after frequent xylitol use.

The ongoing coronavirus disease 2019 (COVID-19) pandemic has negatively affected the cruise and ferry industry as the passenger numbers and revenues have plummeted. Therefore, we developed a holistic approach for mitigating COVID-19 during seaborne transportation in a cost-efficient way by combining behavioural changes, procedural workflows and technical innovations to reset the industry.

Bioimaging has now entered the era of big data with faster than ever development of complex microscopy technologies leading to increasingly complex datasets. This enormous increase in data size and informational complexity within those datasets has brought with it several difficulties in terms of common and harmonized data handling, analysis and management practices, which are currently hampering the full potential of image data being realized. Here we outline a wide range of efforts and solutions currently being developed by the microscopy community to address these challenges on the path towards FAIR bioimage data. We also highlight how different actors in the microscopy ecosystem are working together, creating synergies that develop new approaches, and how research infrastructures, such as Euro-BioImaging, are fostering these interactions to shape the field.

The small GTPase Ras is frequently mutated in cancer and a driver of tumorigenesis. The recent years have shown great progress in drug-targeting Ras and understanding how it operates on the plasma membrane. We now know that Ras is non-randomly organized into proteo-lipid complexes on the membrane, called nanoclusters. Nanoclusters contain only a few Ras proteins and are necessary for the recruitment of downstream effectors, such as Raf. If tagged with fluorescent proteins, the dense packing of Ras in nanoclusters can be analyzed by Förster/ fluorescence resonance energy transfer (FRET). Loss of FRET can therefore report on decreased nanoclustering and any process upstream of it, such as Ras lipid modifications and correct trafficking. Thus, cellular FRET screens employing Ras-derived fluorescence biosensors are potentially powerful tools to discover chemical or genetic modulators of functional Ras membrane organization. Here we implement fluorescence anisotropy-based homo-FRET measurements of Ras-derived constructs labelled with only one fluorescent protein on a confocal microscope and a fluorescence plate reader. We show that homo-FRET of both H-Ras- and K-Ras-derived constructs can sensitively report on Ras-lipidation and -trafficking inhibitors, as well as on genetic perturbations of proteins regulating membrane anchorage. By exploiting the switch I/II-binding Ras-dimerizing compound BI-2852, this assay is also suitable to report on the engagement of the K-Ras switch II pocket by small molecules such as AMG 510. Given that homo-FRET only requires one fluorescent protein tagged Ras construct, this approach has significant advantages to create Ras-nanoclustering FRET-biosensor reporter cell lines, as compared to the more common hetero-FRET approaches.

The raw image and numerical data used to make the figures in the preprint: Filopodia-mediated trans-endocytosis Hanna Grobe1,2,3, Marcela Rivera1,2,3*, Sujan Ghimire1,2,3*, Marie-Catherine Laisne2, Anna Nylund2, Monika Vaitkeviciute1,2,3, Helena Vihinen4, Anu Prakash4, Johanna Tammi1,2,3, Marjaana Ojalill1,2,3, Pia Boström5, Pauliina Hartiala6,7, Johanna Englund4, Emilia Peuhu1,8,9, Eija Jokitalo4, Guillaume Jacquemet1,2,3,10 * equal contribution Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, FI Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, FI InFLAMES Research Flagship Centre, University of Turku, Turku, FI Institute of Biotechnology, HiLIFE, University of Helsinki, Finland Department of Pathology, Turku University Hospital, University of Turku, Turku, FI Department of Plastic and General Surgery, Turku University Hospital, Turku, FI Medicity Research Laboratories and InFLAMES Research Flagship Centre, University of Turku, Turku, FI Institute of Biomedicine, University of Turku, Turku, FI Western Finnish Cancer Centre (FICAN West), University of Turku and Turku University Hospital, Turku, FI Foundation for the Finnish Cancer Institute, Tukholmankatu 8, Helsinki, FI

Imaging facilities underpin a growing share of modern life-science research, yet the career conditions and scholarly recognition of the Imaging Scientists in core facilities who design, deliver, and interpret imaging research remain uneven. This mismatch risks loss of expertise, reduced service quality, and weaker long-term sustainability of shared research capabilities. To provide an evidence base for practical change, we synthesise findings from two complementary international community surveys run by Global BioImaging: a “Top 5” survey on career development and job conditions (>290 responses spanning 43 countries) and an authorship/acknowledgement survey examining how publication credit is assigned for imaging-related contributions of core facility staff (>330 responses spanning 43 countries). Across both surveys, respondents consistently link limited recognition to constrained career prospects. The career survey highlights recurring bottlenecks around progression routes, job stability and attractiveness, access to professional development, and the day-to-day consequences of being perceived primarily as service providers rather than scientific partners. The authorship/acknowledgement survey documents substantial variability in credit practices across facilities, disciplines, and regions, with many respondents reporting uncertainty about expectations, difficulty initiating credit discussions, and concerns about bias and power dynamics. Taken together, the results suggest a reinforcing cycle: inconsistent credit reduces visibility and leverage for Imaging Scientists in core facilities, which in turn entrenches fragile career pathways and inhibits retention. We translate these findings into targeted, stakeholder-specific actions. Recommendations focus on defining career paths that match facility roles, aligning evaluation with the full range of facility outputs (including methods, data, software, and training), and ensuring that institutions, funders, publishers, and research teams share responsibility for fair and consistent credit.

Advanced imaging core facilities are critical pillars of modern life sciences research, providing access to complex technologies, specialized expertise, and training. At the heart of these facilities are Imaging Scientists, whose work spans technology development, operations, training, data stewardship, and community coordination. Despite their central role, Imaging Scientists have rarely been the focus of coordinated funding at scale. Here, we evaluate the Chan Zuckerberg Initiative Imaging Scientist program—to our knowledge, one of the first large-scale efforts to support this workforce—through an anonymous survey and selected case profiles across diverse institutional, technical, and geographic contexts. Survey responses highlight the program’s value in enabling structurally underfunded activities such as technology integration, scalable training, leadership, and community building. By abstracting across cases, we identify recurring impact themes, showing how support for Imaging Scientists strengthens core facility foundations, accelerates adoption of new technologies, and fosters national and international networks. These findings illustrate that investing in Imaging Scientists generates measurable scientific, institutional, and community-level returns, complementing technology-focused funding and maximizing the impact of research investments.

This Deliverable 3.3 is a report on the Digital Life Sciences Open Call and two Internal Calls organised by EOSC-Life WP3. The organisation of these Calls followed the successful integration and support of 8 Demonstrator projects which provided the first concrete use cases in the initial phase of EOSC-Life. The three Calls overall supported 11 scientific user projects, selected to facilitate integration of concrete use-cases across Life Sciences domains into the European Open Science Cloud (EOSC) framework. Through the Calls, the practical goal was to facilitate co-creation of an open, digital collaborative space for life science research by developing FAIR tools, workflows, resources, infrastructures, and guidelines together with the EOSC-Life RIs experts and communities. We report in this Deliverable the following achievements: Organisation of the EOSC-Life Open and Internal Calls; Integrating and training the EOSC-Life WP3 Open Call and Internal Call project teams in EOSC-Life; Activities for connecting project teams with EOSC-Life and LS-RI communities and dissemination of projects outcomes to broader communities; Work done in the individual projects, their results, and impact of developed resources; Recommendations from the EOSC-Life WP3 project teams and the EOSC-Life community for future Open Calls.

The second foundingGIDE Community Event was held on October 17-18, 2025, in Brisbane, Australia. The event brought together researchers, infrastructure providers, and community members to explore the latest developments and challenges in imaging interoperability. Over 1.5 days, participants shared insights, discussed challenges, and collaborated on practical solutions for advancing the imaging data ecosystem.

Modern microscopy enables us to measure structural and dynamical properties of many biological processes and is therefore an indispensable research tool. However, the amount and complexity of the produced imaging data is steadily increasing. Thus, handling the data as well as reproducibly and automatically extracting accurate scientific information requires dedicated “bioimage analysis” expertise. To facilitate the dissemination of this ubiquitously required expertise we developed an open-access bioimage analysis training resource. The resource is designed to help trainers to design and run courses on bioimage analysis for life scientists. The material is modular where each module covers one concise topic and provides corresponding activities. The activities can be executed using various popular software packages (e.g. ImageJ, Python). The material is hosted on a public software repository allowing the bioimaging community to readily contribute new training modules or improve existing modules. Within the last three years, the material has been used by several trainers in numerous courses and continuously improved.

File formats incompatibility has become a major obstacle in biological imaging, complicating downstream processes such as image processing and analysis. One way to address this challenge is to convert the acquired image data into standard image file formats. Here we introduce BatchConvert, a command line tool for parallelised conversion of image collections into OME-TIFF or OME-Zarr using the workflow management system Nextflow. BatchConvert offers functionalities such as remote input-output support, optional execution on Slurm clusters and pattern-based filtering of input files. Conversion can be coupled to image concatenation, allowing selected images to be merged along specified dimensions. Support for remote locations includes an option to submit the output data to S3-compatible object stores or public archives such as BioImage Archive. Overall, BatchConvert is a flexible tool for researchers who are routinely managing and analysing large multidimensional image data that is either locally or remotely stored.

Horizon Europe funded AI4Life project Deliverable D1.2 Strategy for dissemination of information within the consortium.

The second foundingGIDE Community Event was held on October 17-18, 2025, in Brisbane, Australia. The event brought together researchers, infrastructure providers, and community members to explore the latest developments and challenges in imaging interoperability. Over 1.5 days, participants shared insights, discussed challenges, and collaborated on practical solutions for advancing the imaging data ecosystem.