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.

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.

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 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.

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 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.

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.

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 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

This dataset contains a copy of the spreadsheet used to collect the entries for the Bloch-McConnell Simulation Study. The original spreadsheet can be found here: https://docs.google.com/spreadsheets/d/1JN7VN-f1ktDrJgokb0FlUFwkH0MWYlPA_jSfnQoFOVc More information about the study can be found here: https://github.com/pulseq-cest/BMsim_challenge

This dataset contains a copy of the spreadsheet used to collect the entries for the Bloch-McConnell Simulation Study. The original spreadsheet can be found here: https://docs.google.com/spreadsheets/d/1JN7VN-f1ktDrJgokb0FlUFwkH0MWYlPA_jSfnQoFOVc More information about the study can be found here: https://github.com/pulseq-cest/BMsim_challenge

The raw image and numerical data used to make the figures in the preprint: Filopodia-mediated trans-endocytosis Hanna Grobe1,2,3, Sujan Ghimire1,2,3, Marcela Xiomara Rivera Pineda1,2,3, Marjaana Ojalill1,2,3, Marie-Catherine Laisne2, Anna Nylund2, Monika Vaitkeviciute1,2,3, Helena Vihinen4, Anu Prakash4, Johanna Tammi1,2,3, Pia Boström5, Pauliina Hartiala6,7, Johanna Englund4, Emilia Peuhu1,8,9, Eija Jokitalo4, Guillaume Jacquemet1,2,3,10 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

The foundingGIDE project has brought together imaging research and data infrastructures from across the globe to lay strong foundations towards image data sharing. A key measure of project success is the partners’ commitment towards sustainability of the project outputs based on fruitful collaborations enabled under the foundingGIDE project. This commitment is critical for the imaging and wider scientific community as the project outputs are deemed extremely relevant for building a global image data sharing infrastructure in future. This deliverable details the output of the project that will be maintained by partners beyond the end of the project itself, as well as an outlook towards future growth to extend project activities. The benefits of the foundingGIDE project will hence be felt beyond the project lifetime fueling a future Global Image Data Ecosystem (GIDE).

The foundingGIDE project has brought together imaging research and data infrastructures from across the globe to lay strong foundations towards image data sharing. A key measure of project success is the partners’ commitment towards sustainability of the project outputs based on fruitful collaborations enabled under the foundingGIDE project. This commitment is critical for the imaging and wider scientific community as the project outputs are deemed extremely relevant for building a global image data sharing infrastructure in future. This deliverable details the output of the project that will be maintained by partners beyond the end of the project itself, as well as an outlook towards future growth to extend project activities. The benefits of the foundingGIDE project will hence be felt beyond the project lifetime fueling a future Global Image Data Ecosystem (GIDE).

The raw image and numerical data used to make the figures in the preprint: Filopodia-mediated trans-endocytosis Hanna Grobe1,2,3, Sujan Ghimire1,2,3, Marcela Xiomara Rivera Pineda1,2,3, Marjaana Ojalill1,2,3, Marie-Catherine Laisne2, Anna Nylund2, Monika Vaitkeviciute1,2,3, Helena Vihinen4, Anu Prakash4, Johanna Tammi1,2,3, Pia Boström5, Pauliina Hartiala6,7, Johanna Englund4, Emilia Peuhu1,8,9, Eija Jokitalo4, Guillaume Jacquemet1,2,3,10 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

This deliverable presents the completion of Task 1.4 and Task 1.5, which aimed to improve semantic interoperability and technology-related image data discoverability within the Euro-BioImaging Access Portal (EAP). This version is pending EC approval.