FAQ image data services

Euro-BioImaging offers a range of data services. Those include expert image data analysis and workflow development offered at its Nodes, technical tool development to enhance data management and reproducibility as well as support and training for FAIR image data to create a FAIR data ecosystem. Euro-BioImaging also coordinates community efforts to develop standards for image data, metadata, and analysis tools, empowering the scientific community to manage and share imaging data according to international standards.

No, Euro-BioImaging does not provide direct access to already existing image datasets. However we can connect you to external, specialized repositories and guide you to appropriate data resources. For medical datasets we can help connect you with institutions hosting Nodes that may have access to certain medical image datasets. We are not liable for negotiations between parties.

There are several access mechanisms for the full range of data services. To start using the image data analysis service, visit the Euro-BioImaging access portal to explore the available technologies and Nodes that fit your needs. If you are unsure, you can seek advice from our staff by contacting us. Next, submit an access proposal through the portal by creating an account, filling out the application form and providing a description of your project. Your proposal will then undergo scientific and technical review and Node selection (unless you have already liaised with a specific Node). Once approved, the Node will contact you to arrange the necessary details.

Other services, such as FAIR stewardship and technical development consultations, can currently be accessed via the request form on the FAIR data subpage. Openly available resources, such as guideline materials and tools, can be found on the corresponding pages and on the Euro-BioImaging GitHub repository. Details of outcomes from community services can be found on the corresponding page. For information on training opportunities offered by the Nodes and the Hub, see the question below.

Yes, Euro-BioImaging offers a variety of training opportunities in image data and analysis at its Nodes, which are open to anyone and suitable for users at all levels. To explore current and upcoming training offers from Euro-BioImaging Nodes, including workshops and practical courses, please visit the training courses page.

Euro-BioImaging also regularly hosts image data events, such as the annual Euro-BioImaging Image Data Community Days, which feature talks, workshops and interactive sessions to help participants keep up to date with the latest practices in the field.

Euro-BioImaging has further created extensive self-learning resources, including video recordings of past events, downloadable course materials and curated lists of online tutorials and resources. These can be found on the individual event's pages.

Euro-BioImaging’s image analysis service provides expert support for a range of biological and biomedical image data tasks, including denoising, registration, segmentation, tracking, and more. Bioimage analysts develop bespoke workflows and machine learning methods, use specialized software and high-performance computing, and help users produce quantitative, publication-ready results. This service can be accessed together with imaging at a Node or as a standalone option for image data from elsewhere. Analysts also support FAIR data management and tool development to ensure open and interoperable workflows. For detailed, up-to-date information, consult the Euro-BioImaging Access Portal or contact individual Nodes directly.

No! Image analysis support is not limited to data collected at Euro-BioImaging Nodes. You can obtain image analysis support from Euro-BioImaging even if your image data was not acquired at a Euro-BioImaging Node. While some Nodes offer image analysis services only in conjunction with imaging access at their facility, certain Nodes also provide standalone image analysis services for external image data, regardless of where it was generated. For details, consult the Access Portal or contact the relevant Nodes.

The cost of the Euro-BioImaging image analysis service varies depending on the scale and complexity of the analysis and the support required. As Euro-BioImaging is a publicly funded, non-profit infrastructure, the costs are kept minimal to cover operational expenses. Pricing depends on the Node, project complexity, and required expertise. All Nodes have their own costing model where some Nodes charge hourly rates while others may provide fixed project cost estimates after a consultation. For some projects the image analysis services may be free of charge with funding support through grants or dedicated access funds, which can cover travel and service costs. Overall, please feel encouraged to contact the specific Euro-BioImaging Node or the Euro-BioImaging Helpdesk for a tailored quote and information on funding opportunities.

Many—but not all—Euro-BioImaging Nodes offer image analysis services. Some Nodes provide image analysis only alongside imaging access, meaning you get analysis support as part of your imaging project at that Node. Other Nodes also offer standalone image analysis services, where you can submit your image data for analysis irrespective of where the data was acquired. Availability varies by Node depending on their specialization and resources. For exact details on which Nodes provide image analysis and their offerings, consult the Euro-BioImaging Access Portal, ask the Euro-BioImaging Helpdesk or contact the Nodes directly.

Euro-BioImaging Node bioimage analysts use a range of open-source and commercial software tools for image analysis, depending on project needs. Common open-source platforms include Fiji/ImageJ, CellProfiler, Ilastik, QuPath, and Napari. Analysts also create custom scripts and workflows—often in Python or MATLAB—and sometimes use high-performance computing for large datasets. There is also a focus on tools supporting the OME-Zarr format. For more specific information on which tools are used at a particular Node, you may contact the Node or refer to their individual service descriptions.

To access the Euro-BioImaging image analysis service, visit the Euro-BioImaging Access Portal and create an account/ log in. You then submit a short proposal describing your project and analysis needs. Next, you select the technology or Node you are interested in or request advice if you are unsure which Node fits your requirements. Your proposal will then undergo scientific and technical review and Node selection (unless you have already liaised with a specific Node). Once approved, the Node will contact you to arrange the necessary details. If you need guidance, you can contact the Helpdesk or contact individual Nodes directly for specific questions about available services.

Euro-BioImaging provides a variety of training opportunities on image analysis at its Nodes, suitable for beginners as well as advanced users. These courses cover theoretical and practical aspects of image processing, analysis workflows, and the use of imaging technologies. Training formats include in-person, virtual, and hybrid sessions, generally taught in English and open to researchers, students, and facility staff. To explore current and upcoming training offers from Euro-BioImaging Nodes, including workshops and practical courses, please visit the training courses page.

FAIR data stewardship means taking good care of your imaging data throughout your research so it’s easy to find, access, use, and share—both now and in the future. It starts with planning how to manage your data, continues with organizing and describing it properly, and includes safely storing it for long-term use and publication.

Euro-BioImaging supports you at every step by providing practical tools, training, and personalized guidance from expert data stewards. We help you implement FAIR principles smoothly, whether you’re just starting your project or preparing your data for publication and reuse. Our resources and one-on-one support make it easier to meet funder requirements, increase your data’s impact, and contribute to open and collaborative science.

FAIR data means your data is managed and organized according to four key principles designed to maximize its value, usability, and impact:

• Findable: Your data and its metadata are easy to locate by both humans and computers. This requires assigning persistent identifiers (like DOIs) and providing rich, standardized metadata so that your data can be reliably discovered and cited.
• Accessible: Your data can be retrieved using standard protocols, with clear information about how to access it. Importantly, even if your data is restricted due to privacy or confidentiality, the metadata describing it should remain openly available.
• Interoperable: Your data is stored in open, widely accepted formats and described using common standards and controlled vocabularies. This ensures it can be integrated, exchanged, and used together with other datasets and tools across different systems.
• Reusable: Your data is well-documented with clear provenance and licensing information, enabling others to understand, verify, and reuse it effectively in new research contexts.

Implementing FAIR principles in your research increases the visibility and citation of your work, enhances reproducibility and reliability, enables easier data sharing and reuse, fosters new collaborations, and helps you meet funder and institutional requirements—ultimately maximizing the impact and long-term value of your data.

Thanks to the generous support of the EVOLVE project (co-funded by the European Union), Euro-BioImaging’s data stewardship service is currently offered free of charge. We understand that managing and sharing research data can be challenging, especially when resources are limited, and we’re truly grateful to EVOLVE for enabling us to provide this valuable support at no cost to you. While this free access may not be guaranteed indefinitely, please be assured that we remain deeply committed to making as many resources, training materials, and guidance as possible freely available online. Our goal is to empower researchers to adopt FAIR data practices with confidence and ease, regardless of project size or funding. We appreciate your understanding and look forward to continuing to support your data stewardship journey.

Yes, you can receive data stewardship support from Euro-BioImaging even if you are not yet a registered user and your data was not acquired through Euro-BioImaging access. Euro-BioImaging offers resources, training, and one-on-one guidance to help anyone in the imaging community make their data FAIR at all stages, from project planning to data deposition and reuse. While expert support is available, please note that capacity is limited and priority is given to Euro-BioImaging users.

To start FAIRifying your data, plan how to organize and describe it with clear metadata and persistent identifiers, and choose a trusted repository for sharing and long-term preservation. Euro-BioImaging offers practical resources, training, and personalized support from expert data stewards to guide you through every step. Contact Euro-BioImaging early—whether you’re just beginning your project or ready to share your data—to get tailored advice and access to workshops, tools, and community events that make FAIR data management easier and more effective.

You can make your data FAIR even after your project is completed—it’s never truly too late to improve your data's FAIRness However, starting early in your project makes the process smoother and more effective, as good planning and documentation from the beginning help ensure your data meets FAIR principles more easily. If you’re revisiting data post-project, focus on adding clear metadata, choosing appropriate repositories, and providing thorough documentation to maximize its value and reuse potential.

Absolutely—your data can be FAIR without being fully open. FAIR means your data is Findable, Accessible, Interoperable, and Reusable, but it doesn’t require unrestricted public access. If your data contains sensitive or confidential information, you can still make it FAIR by providing clear metadata, specifying access conditions, and using controlled access repositories. This way, others can discover your data and understand how to request access or learn about its existence, while you maintain necessary privacy and security protections. Strive to make data 'as open as possible' but it can be 'as closed as necessary'. Contact us to discuss the best process for your specific data.

To make your data available, you should use a repository that fits your data type and meets FAIR standards. Euro-BioImaging provides detailed guidance to help you choose the right repository, including an overview of recommended repositories for different kinds of image data and a decision tree that guides you step-by-step based on your dataset’s characteristics. Options for bioimaging data include, but are not limited to, the BioImage Archive, IDR, EMPIAR, PIDAR and more.

Yes, you can start learning about FAIR data practices right away by attending workshops. We offer a range of training opportunities which cover the fundamentals of FAIR data principles and research data management. Many of these are open to researchers, students and staff of all backgrounds. You can also access our self-paced training materials and resources, such as event recordings, interactive modules and guides, which you can start at any time and complete at your own pace.

Euro-BioImaging provides a broad range of technical tools and services beyond image analysis software. This includes open-source solutions and workflows that support FAIR (Findable, Accessible, Interoperable, and Reusable) image data management and sharing. For example, Euro-BioImaging supports modern file formats like OME-Zarr for scalable, cloud-friendly bioimage data storage. XNAT-PIC is a community-driven platform for imaging data management and sharing, which Euro-BioImaging helps integrate and support. Technical assistance also covers image annotation, metadata handling, and workflow development to facilitate quality check, robust and reproducible analysis. Training and expert consultation on these tools and FAIR data practices are offered at the Nodes and through online resources.

Yes, Euro-BioImaging develops technical tools for both biological and biomedical imaging. For example, Euro-BioImaging supports preclinical imaging data by helping users annotate and upload datasets to the XNAT platform, tailored to the specific needs of preclinical studies. Tools like XNAT-PIC assist with formats and workflows, ensuring FAIR-compliant, well-organized data. Expert help is available to streamline dataset preparation, annotation, and sharing for reproducible preclinical imaging research.

Yes! You can absolutely use our tools for any image data. We believe that everyone should have access to image analysis and management tools so we openly share all our developments. Even better, most of them are even open source.

All our developed tools are open-source so you cannot only freely use them for your research but also actively shape their development.

No, you are not required to take special training for using the tools. If you have some experience with the command line and programming, as well as with the topics our tools cover, you will be able to use them independently, as we provide extensive documentation with them. However, we also provide regular dedicated training opportunities as well as self-learning resources, such as recordings and written-out tutorials.

Yes, Euro-BioImaging and its Nodes maintain, update, and support our portfolio of technical tools to ensure high performance and compatibility.

Yes, absolutely. We are happy to help you with the tool selection and can also provide assistance with application of the tools.

Community data initiatives or community data services at Euro-BioImaging refer to coordinated efforts focused on developing standards, training materials, tools, and support for managing and analyzing bioimage data with FAIR principles in mind. This ecosystem approach helps researchers generate, share, and analyse high-value biological and biomedical image data effectively

Euro-BioImaging acts as a central coordination point that consolidates various community initiatives related to image data, metadata, and software tools. Euro-BioImaging also facilitates collaboration with European projects and provides resources to produce high-quality, reusable image data sets across the entire data lifecycle, from project planning to deposition and reuse.

Some recent examples of image data projects are:

EUCAIM (2023-2026): Providing access to cancer image data platform for research and enabling AI developments.

AI4Life (2022-2025): Developing AI tools and standards for advanced bioimage analysis.

foundingGIDE (2024-2026): Harmonizing ontologies and metadata standards to enable interoperable, FAIR image data sharing worldwide.

EVOLVE (2024-2028): Strengthening Euro-BioImaging’s infrastructure and community collaboration including one work package solely focused on expanding image data services.

CANDLE (2025-2028): Scaling-up and improving existing (inter)national health data infrastructures - Supporting the European Health Data Space (EHDS) implementation.

You can access the tools, training materials and workflows developed by community efforts via Euro-BioImaging’s website and partner platforms. Most of them are open access and free for everyone to use.

All community initiatives are dependent on active participation, so we would like to encourage you to contribute to the discussions, whether online through forums and meetings or at in-person events. We warmly encourage anyone interested in finding out more to follow the projects on social media and subscribe to their newsletters. Those interested in actively shaping the project's outcomes are also encouraged to participate in community events and workshops.