To begin with, could you briefly introduce yourself?

Hi, I’m Raphaël Braud-Mussi. I’m a research engineer at Institut Cochin in Paris, where I lead the development of OpenCID, a platform developed with an open collaboration model that helps thousands of scientists manage and process their biological data.

I started at the institute in 2023, working on interoperability between OMERO and our in-house image database, and integrating deep learning tools for image segmentation. Before that, I studied mathematics and computer science at Université Paris Cité, then completed a master’s degree in image processing and computer vision at Université de Montpellier.

What’s driven me throughout is a genuine interest in building tools that make researchers’ work more efficient and OpenCID is exactly that kind of project

What are you currently working on?

Right now, the team and I are focused on the next major version of OpenCID. The core of the platform has been entirely rebuilt in Python, which ensures portability across server environments and makes it easier for the broader community to contribute to the codebase.

This new version will also include a redesigned web interface with more fluid and intuitive workflows for researchers. We’re planning to deploy it at Institut Cochin this summer, with a rollout to other institutes starting in September.

My role is to make sure everything runs as expected across environments and to coordinate the deployment with each site. Beyond that release, we already have a roadmap of new features to continue expanding what the platform can do; we’re currently managing over 350 TB of data at Cochin with a data flow exceeding 10 TB per month, so scalability stays a constant priority.

Could you explain what OpenCID is and what need it addresses?

OpenCID started as an internal project at Institut Cochin called CID. The Cochin Image Database is designed to help researchers manage their imaging data. As the user base grew, we expanded the platform to include processing pipelines directly accessible through the web interface, removing the need for researchers to install software locally.

Institut Cochin hosts a large number of core facilities across different disciplines, so once the imaging management layer was stable, we extended OpenCID to handle other types of biomedical data (genomic, proteomic, cytometry…) produced by those facilities as well.

Today, OpenCID is openly available upon request and allows research institutes to manage and process large volumes of biomedical data entirely through a web interface. It’s built to scale, and its open nature makes it easier for the community to adopt and contribute to it.

In practical terms, how does OpenCID work for users?

Three words: simplicity, efficiency, usability

Let me give you a concrete example. You’re a biologist who needs to acquire microscopy images and RNA sequencing data for your project. Traditionally, getting that data from the core facility to your workstation means copying files onto an external hard drive or by using a shared space on your network, a process that eats into your time slot on the acquisition machine and breaks your workflow.

With OpenCID, everything is streamlined. Once your acquisition is done, leave the machine to the next user. Then log into OpenCID, select the machine you used and your data folder directly from the web interface, and import your files into the database in just a few steps, accessible from anywhere, at any time. From there, you can run your processing pipelines (segmentation, deconvolution…) and download your results with a couple of clicks, without ever installing software locally, whether you’re working remotely, attending a congress, or even on the beach.

Who can currently benefit from OpenCID?

OpenCID is currently deployed at Institut Cochin, where it serves users across multiple core facilities, including IMAG’IC for bioimaging. External users who acquire data at the institute can also import and retrieve their own data through the platform, even if they are not based at Cochin. The platform is designed to go well beyond a single institute.

Any research institute interested in deploying OpenCID can reach out to the team at cid.u1016@inserm.fr  to get started. The solution is ready for deployment, and we are genuinely happy to support new sites through the process. For those who want to explore first, we can also provide access to our GitLab repository, where the documentation and the full deployment procedure are available.

What are the main benefits of OpenCID for researchers, engineers and imaging facilities?

For researchers, OpenCID simplifies the management of an entire team’s data and supports a genuine open science workflow. Every dataset can be shared and downloaded based on access rights defined by the team leader, and an automated open science link generator allows any dataset to be connected to a DOI, making data citation and publication straightforward.

Beyond that, OpenCID is designed to help research teams meet the requirements of Data Management Plans, which are now mandatory for most public funding bodies. By centralizing data storage, traceability, and sharing in a single platform, OpenCID makes it significantly easier to demonstrate compliance with FAIR data principles, findable, accessible, interoperable, and reusable, without adding administrative burden to the team. (https://hal.science/hal-04834159v1/file/INSTITUT_COCHIN_ENTITY_DMP_-_CID_V1.pdf)

For engineers, OpenCID brings structure and accessibility to data management. Processing pipelines can run workflows on a workstation connected to the OpenCID system, allowing engineers to launch analyses on a dedicated machine and continue working on other tasks in the meantime. Results are made available directly on the web interface as soon as the workflow completes. And thanks to our fully Python-based codebase, integrating new workflows is straightforward, either by requesting an addition from the team, or by contributing directly if you are comfortable doing so.

For imaging facilities, OpenCID provides a centralized and reliable solution to handle the constant flow of data produced by acquisition machines, with no need for users to manage everything manually.

Ultimately, every one of these benefits points to the same goal: reducing friction at every step of the research workflow, so that scientists and engineers can focus on what actually matters; science

Could OpenCID be deployed across other imaging facilities?

As mentioned earlier, this is precisely our current priority. OpenCID is already being deployed beyond Institut Cochin, we are actively working with sites such as INRAE Montpellier and Institut Max Planck in Cologne, and more are in discussion.

The community-driven nature of the platform is a key enabler here: it lowers the barrier to adoption and allows each site to adapt the solution to their specific environment. Our affiliation with France-BioImaging also gives us a strong network to reach imaging facilities across the country and beyond.

Building a community around OpenCID is not just a goal, it is part of the project’s long-term vision.

What feedback have you received since OpenCID has been implemented?

It has been three years of sustained development rethinking the entire CID project from the ground up. Now that version 2.0 is ready and continuously updated, the feedback from users has been very encouraging.

A big part of that trust comes from how we handle support. The team commits to addressing any issue within 24 hours, whether we identify a bug proactively or a user reports one directly. That responsiveness has built a real relationship with our user base.

User feedback is also a direct input into our roadmap. We actively seek opinions on the platform, and many of the features we have built or are planning came directly from conversations with researchers and engineers in the field.

What are the next steps for OpenCID?

The next steps for OpenCID are threefold: reinforcing the team, completing the current deployment rollout, and delivering several new features that are already in progress.

On the technical side, we are currently in the testing phase for Zarr format support, which will be a significant step forward for open science interoperability. We are also developing an online 3D object viewer, which will allow researchers to visualize volumetric data directly from the web interface without any local software. Both features are on track to be released soon.

The project is at a stage where it needs additional engineers to sustain both maintenance and new development in parallel, and that is precisely what we are actively working to address.

FBI.data recently launched BioImage Cloud. In the future, do you see possible synergies between OpenCID and BioImage Cloud?

OpenCID and BioImage Cloud have been developed with different but complementary goals. BioImage Cloud  focuses on streamlining the transfer of imaging datasets from acquisition to national cloud storage, while OpenCID provides a broader platform for data management, processing, and sharing, regardless of data type or format.

Given that both projects are part of the France-BioImaging ecosystem and share the same underlying objectives, making research data FAIR, accessible, and manageable, I genuinely see potential for synergy. One concrete avenue would be to explore how OpenCID’s data management layer could interface with FBI.data transfer infrastructure, effectively combining the strengths of both solutions. A proof of concept in that direction would be worth considering.

More broadly, I think the community benefits from having multiple approaches being explored in parallel. The most important thing is that researchers end up with tools that actually work for them.

In spring 2026, the IGBMC imaging facility, ICI, located in Illkirch, acquired two new light-sheet microscopes thanks to France-BioImaging and the BIOGEN project, supported by the French National Research Agency (ANR-24-INBS-0005 FBI BIOGEN).

One of the strategic priorities of BIOGEN is to strengthen the national offer in multiscale light-sheet microscopy for the scientific community. By addressing major imaging bottlenecks such as sensitivity, acquisition speed and phototoxicity, light-sheet microscopy opens up new possibilities for the observation of live and delicate biological samples.

At the ICI facility, two complementary systems have been acquired, each designed to address specific imaging needs.

• The lattice light-sheet 7 microscope enables the observation of fast dynamic processes over long periods of time, with very low phototoxicity and photobleaching compared to confocal microscopy. It is particularly well suited for fast volumetric imaging of live samples, without requiring specific sample preparation.
• The lattice SIM microscope, installed on a dedicated system, provides live super-resolution imaging, offering an excellent balance between acquisition speed and resolution gain.

Together, these two instruments significantly reinforce IGBMC’s technological offer by covering a broad range of biological questions, from fast cellular dynamics to super-resolved imaging of subcellular structures.

Light-sheet microscopy is particularly relevant for live and fragile samples, such as living cells, small organoids or early-stage embryos. The systems available at IGBMC are compatible with several common experimental formats, including dishes, multi-chamber slides and multi-well plates, making them easy to integrate into existing workflows.

These technologies are especially suited for projects focusing on intracellular dynamics, cell division, calcium signalling, developmental biology and, more broadly, quantitative cell biology requiring fast and minimally invasive imaging.

Operational since March 2026, these two systems are now part of the technological offer of the IGBMC imaging facility and the France-BioImaging Alsace node. They strengthen access to advanced light-sheet microscopy within the national network and open new opportunities for projects requiring fast, high-resolution and minimally invasive live imaging.

Researchers interested in using these microscopes, or in developing collaborative projects within the France-BioImaging network, are invited to contact the IGBMC imaging facility at: ici@igbmc.fr

Three new invited speakers have been announced for SFBS 2026, further enriching the scientific programme dedicated to super-resolution microscopy for biological imaging.

Good news: the deadline for early bird registration and abstract submission has been extended to June 30, 2026! Apply here before June 30, 2026

Giuseppe Vicidomini

In 2016, Dr Vicidomini established the Molecular Microscopy and Spectroscopy (MMS) laboratory at IIT and launched an independent research programme based on single-photon avalanche diode (SPAD) array detectors. This work led to the establishment of photon-resolved microscopy, a new imaging paradigm that assigns spatial and temporal information to individual photons, enabling advances in super-resolution imaging, fluorescence lifetime microscopy, spectroscopy, and single-molecule analysis.

His research has generated multiple patents, technology licensing agreements, and the spin-off company Genoa Instruments, of which he is co-founder and scientific advisor. Established to commercialise photon-resolved microscopy technologies, Genoa Instruments is accelerating its adoption within the life-science community. In parallel, SPAD array detector concepts and methodologies developed in his laboratory have been incorporated into commercial microscopy platforms from Nikon, Abberior, and PicoQuant.

Dr Vicidomini was Principal Investigator of the ERC Consolidator Grant BrightEyes, which established the foundations of photon-resolved microscopy and enabled the development of a new generation of non-invasive imaging and spectroscopy tools for studying biomolecular processes in living systems. He currently leads the ERC Proof-of-Concept project BrightMind, which integrates photon-resolved microscopy with artificial intelligence and smart microscopy concepts to create adaptive imaging systems for autonomous data acquisition and information extraction.

Xiaoshuai Huang

Since establishing his independent laboratory, he has systematically addressed the critical bottlenecks of live-cell volumetric imaging, specifically speed, axial resolution, reconstruction fidelity, and multimodal contrast. Under his leadership, the laboratory has developed flagship platforms such as 3D-MP-SIM and 4Pi-SIM, with landmark findings published as leading or co-corresponding author in premier journals including Nature Photonics, Nature Methods, and Nature Cell Biology.

Anne-Sophie Hafner

Recently, her lab identified a novel promising pathway that likely contributes to Alzheimer’s disease onset. In 2022, she received an ERC Starting Grant from the European Research Council for her project MemCode, to investigate the mechanisms of long-term memory storage in the brain, and in 2026 an ERC proof of concept for her project OligoBlockers, to generate a new innovative therapy to stop Alzheimer’s disease progression at early stages.

Don’t miss this opportunity to meet these experts during SFBS 2026! Join us in Bordeaux from October 19 to 21, 2026!

Would you like to share your work at SFBS 2026? Good news: the abstract submission deadline has been extended! Apply before June 30, 2026 for a chance to give a talk or present a poster.

The RTmfm working group “SMILE”, dedicated to smart microscopy, is organizing its first national meeting in Aussois from November 15 to 20, 2026.

This event is open to engineers, PhD students and researchers interested in learning how to use smart microscopy.

Over six days of hands-on sessions and scientific exchanges, participants will gain an overview of smart microscopy, including introductions to different types of coding.

Take a look at the full programme below

Event details

Venue: AUSSOIS , Centre CNRS Paul Langevin

Deadline to register: July 31st, 2026

Maximal participants: 30

Dans cet échange, découvrez le projet de Rodrigue, comment s’est déroulée cette collaboration et ses ambitions futures!

English-speaking readers, the interview can be found in English at the end of the article.

Rodrigue, Marine et Magalie, pouvez-vous nous partager votre parcours?

Rodrigue Kantati (R.K): Je suis un enseignant-chercheur togolais depuis 5 ans au département de Physiologie animale de la Faculté des Sciences de l’Université de Lomé (Togo).

J’ai effectué un doctorat en Pharmacologie des Substances Naturelles, spécialité neuropharmacologie avec une thèse portant sur l’évaluation des propriétés neuroprotectrices de trois espèces de la flore togolaise, et co-dirigée entre les universités de Rouen Normandie (France) et de Lomé.

En plus des cours magistraux dispensés aux élèves de Licence et de Master de l’Université, je mène des travaux de recherche au sein de l’unité SRU Physiopathologies-Substances Bioactives et Innocuité (PSBI). Je m’intéresse à la validation scientifique des plantes médicinales locales, celles dotées de propriétés neuroprotectrices, capables de faire face à des pathologies neurodégénératives telles que la maladie d’Alzheimer, la maladie de Parkinson, ou encore la mort neuronale consécutive à des situations d’ischémies cérébrales.

Je travaille actuellement sur l’étude des propriétés neuroprotectrices de Sterculia setigera, une plante médicinale de la flore togolaise.

Marine Pernes (M.P): Je suis diplômée depuis 2025 d’un Master sur les Biotechnologies et bioproduits pour la Santé, après avoir obtenu une Licence en Biochimie. Je travaille actuellement en tant qu’Assistante Ingénieure Inserm en expérimentation et instrumentation biologique à PRIMACEN depuis février 2026, plus précisément au niveau de la préparation des échantillons avant microscopie.

Magalie Bénard (M.B): Je suis docteure en Biologie Cellulaire et spécialiste des Neurosciences, recrutée à l’Inserm en 2005 sur la plateforme d’imagerie de Rouen pour m’occuper de la partie photonique. Actuellement, je suis Ingénieure de Recherche Inserm et responsable de la plate-forme d’imagerie HeRacLeS-PRIMACEN. Je m’occupe plus particulièrement de la préparation des échantillons et des équipements de microscopie photonique pour le vivant.

Rodrigue, comment avez-vous vécu le programme Imaging 4 All – Access Track?

R.K: Des moments mémorables : chaque journée passée sur la plateforme PRIMACEN a été une journée de découverte et d’apprentissage, dans une atmosphère conviviale et stimulante!

Magalie et Marine, pourquoi est-il important pour vous d’accueillir des bénéficiaires du programme Imaging 4 All?

M.B et M.P: L’accueil de (futurs) collaborateurs du programme Imaging 4 All est très important pour nous afin de permettre aux bénéficiaires un accès aux équipements et aux technologies avancées et diversifiées peu accessibles dans leur environnement de travail actuel (pays africain). L’échange d’expertise est très enrichissant et il est toujours très intéressant de pouvoir partager nos connaissances et nos savoir-faire autour de projets comme celui de Rodrigue.

Rodrigue, pourquoi avoir choisi la plateforme PRIMACEN?

R.K: Je ne saurai vous dire si c’est moi qui ai choisi PRIMACEN ou si c’est PRIMACEN qui m’a choisi (Rires). La ville de Rouen en général, et ce depuis l’époque de ma mobilité doctorale Erasmus (2015-2016), m’a toujours porté chance. Je me sens très bien à Rouen, une sorte de connexion entre moi et cette ville extraordinaire. Enfin, je crois que je m’y suis toujours senti à l’aise parce que des gens formidables m’y ont toujours bien accueilli et bien encadré. Je voudrais donc dire merci au Dr David Vaudry (HDR, Inserm), ancien directeur de PRIMACEN et co-directeur de ma thèse de doctorat, et à toute la nouvelle équipe, notamment au Dr Magalie Bénard (ma collaboratrice sur le programme Imaging 4 All), à Mlle Marine Pernes son assistante, et à l’actuel directeur Dr Ludovic Galas.

Sans cette collaboration, je n’aurais pas pu poursuivre mes travaux de recherche!

L’Université de Lomé ne dispose pas encore du plateau technique pour cultiver des neurones et réaliser de l’imagerie sur les cultures neuronales.

Magalie et Marine, comment la plateforme a-t-elle bénéficié de cette collaboration?

M.B et M.P: Cette collaboration nous a permis d’avancer de manière significative sur un projet entre nos deux structures avec l’aide financière d’Imaging 4 All de Global Imaging. Mais elle fut aussi l’occasion de partager d’agréables moments et de travailler en commun pendant un mois avec un collaborateur que je connais depuis sa thèse réalisée à Rouen. Pour finir, cette collaboration fut aussi pour nous l’occasion d’intégrer Marine, tout juste arrivée sur la plateforme, à un projet complet, de la culture des cellules, leurs différenciations et leurs traitements à l’acquisition et l’analyse des images.

Rodrigue, Magalie et Marine, en quoi cette collaboration a-t-elle enrichi vos approches scientifiques?

R.K: Cette collaboration nous a permis d’approfondir les données existantes sur les propriétés neuroprotecteurs de Sterculia setigera, notamment en abordant au niveau cellulaire les mécanismes de la neuroprotection : la neuritogenèse et la dynamique mitochondriales, à l’aide de trackers et sondes spécifiques, et de l’imagerie en time-lapse et en très haute résolution.

M.B et M.P: D’un point de vue scientifique, ce projet nous a permis de découvrir l’effet significativement protecteur d’un extrait de Sterculia setigera, issu d’un arbre d’Afrique. Nous avons pu visualiser par microscopie confocale avancée et mesurer cette action sur des neurones préalablement cultivés, et plus spécifiquement au niveau de la forme et de la dynamique des mitochondries.

Rodrigue, Magalie et Marine, prévoyez-vous de poursuivre cette collaboration?

R.K: Oui! C’est vital pour moi, car comme mentionné plus haut, le plateau technique local de l’Université de Lomé ne me permet pas d’avancées majeures en pharmacologie. Seules des collaborations de ce niveau peuvent me permettre d’exister en tant que chercheur en neurosciences, et de continuer par améliorer et affiner mes compétences en restant au contact de mes pairs en France, et au contact également des nouvelles technologies.

À terme, ceci permettra d’une part de renforcer les échanges avec PRIMACEN, et d’autre part de faire émerger véritablement l’enseignement et surtout la recherche en Neurosciences-Neurobiologie à l’Université de Lomé.

M.B et M.P: Oui! Nous restons en contact avec Rodrigue pour les étapes de valorisation des résultats qui ont été très concluants et nous travaillons sur l’élaboration d’une publication de ces résultats. Ce fut un réel plaisir de travailler avec Rodrigue et nous espérons avoir l’occasion de l’accueillir à nouveau dans un futur proche.

The Sino-French BioImaging Symposium 2026 is coming to Bordeaux from October 19 to 21, 2026, for three days dedicated to Super-Resolution Microscopy for Biological Imaging.

Organized in the framework of the CNRS International Research Network – BioImage, SFBS 2026 will bring together leading international scientists to explore the latest advances in super-resolution microscopy, advanced optical imaging and quantitative biology.

The programme is gradually being unveiled, with exciting scientific sessions, invited talks and key topics that will shape this international symposium. Take a look!

Good news! The deadline for abstract submission and early bird registration has been extended to June 30, 2026.

Find more information, submit your abstract and register now!

Could you introduce yourself?

I am a physicist by training. After my PhD (in 2006) I joined a cell biology lab to work on a microscope prototype. I also started developing image analysis and modelling software within the same lab.

I then worked for some time as an independent consultant, before joining the CENTURI multi engineer platform in Marseille, and France-BioImaging two years later in 2022.

I tried early on to deploy OMERO in my lab (in 2009, I did not succeed), I am convinced good data management is both a good practice and a huge time saver for research teams in the long run.

At France BioImaging, I am a research software engineer in the FBI.data team. As the senior engineer in the team, I overview software design and the exchanges with our national and international partners.

You are strongly involved in FBI.data project, what are the main goals of this team?

The main focus of the project is the development and deployment of the BioImage Cloud solution.

The goal is to provide the French research community with tools and standards to ease microscopy data management, federate computation and storage resources and help the adoption of FAIR (Findable, Accessible, Interoperable and Reusable) practices.

What are the origins of BioImaging Cloud? How did this idea first emerge?

The project developed as part of the ANR “equipex” project Mudis4LS. The overall objective of this project, a collaboration between the French Bioinformatics Institute (IFB) and FBI, is to advance the French Government Open Science roadmap.

In practice, for bioimages, the stated goals imply a lot of technical and human constraints:

• we have to manage data with huge disparities in shape and size, that are produced in facilities siloed inside a local network, with often restricted availability of IT staff.
• furthermore, FAIR data culture is still developing in the field, so we also need to offer easy to use tools, as a way to favor the change of mindset toward an open science / FAIR culture.

So we started by stating these constraints explicitly, and developed the tool that would satisfy them.

In simple terms, how does BioImage Cloud work?

BioImage Cloud works at two levels. The lower one is the network layer between a facility and a mesocentre, the regional datacenter hosting the service. BioImage Cloud relies on setting up a ‘tunnel’ out of the facility’s private network toward the mesocenter. The strength of the solution is that this is done securely and reduces the IT work load involved with data transport. Of course users need not concern themselves with this layer, but it’s actually quite important that it is there.

The second level is an ensemble of software tools that provide users with a way to annotate, transport and share their data. In not too much detail, once properly described, the data are copied into the federated storage and imported into OMERO, the standard tool for microscopy data management. From there, they can be shared with collaborators, collaboratively annotated, and (soon) analysed on the mesocenter high performance computing resources.

What are the main benefits for the users?

First and foremost it is easier to access all the microscopy data created in your project, with more entry points, and a standard organization and annotation.

Concretely, this means that a PhD student can readily share their latest experiment results with their advisor, and the latter can access those results from anywhere, including once the thesis is over and the student is gone.

For the experimenter, rich annotations means it is easy to filter through experimental conditions, or write the material and methods section.

It also makes life much easier for bioimage analysts, as relevant metadata (e.g. the scale of the image) is readily available in the system, and API access allows to seamlessly shift from a prototype to batch processing of large datasets.

From a practical point of view, what does a user need to do to use BioImage Cloud?

First you need to belong to a French research institution, to create an account on the platform. To import data in the solution, you need access to a collection server, provided by the microscopy facility you work with.

With that set up, data import works in two steps: you first need to upload the data themselves through FTP on the collection server and second trigger the import in OMERO by uploading a spreadsheet describing the data.

Creating this spreadsheet is the most time intensive part of the process, as we ask our users for a detailed description of the experiment behind the data. Yet, the spreadsheet can be if you repeat the experiment, are slightly altered to account for new experimental conditions. So the process is faster and easier after the first time you or someone on your team use the service.

On which facilities is BioImage Cloud already available?

As of today, 8 servers are deployed in 7 cities. For the south-east part, BioImage Cloud is available in Montpellier for all MRI (CRBM + IGH), Marseille in Luminy, Strasbourg at IGBMC, Lyon at LyMic and for the south-west Nantes (at IRS), Rennes at INRIA and Paris at IBENS.

Two additional sites are under deployment, Grenoble and Toulouse, and 5 more servers will be deployed before the end of 2026.

What are the next steps for BioImage Cloud?

There are many new features down the road. The ones I’m most excited about are:

• the support of the OME-ZARR format, adapted to big data, for example from light sheet or spatial omics experiments;
• the automated submission of published data to BioImage Archive (in collaboration with the IFB madbot team);
• the easy access to high performance computing for bioimage analysts, e.g. for heavy deep learning workflows.

What message would you like to share with imaging facility staff or researchers who may be interested in using BioImage Cloud?

First, that they are very welcome and we are here to help understand their use cases!

We hold open desk sessions every Monday and Wednesday afternoon, so the door is open. A big goal for us this year is to adapt the solution to their usage, so we are eager for feedback.

Second, the tool is new so there are bugs, so I’d ask for their patience! We hope we’ll have more and more users this year that will help consolidate and shape a nice tool.

If you jump in early, you’ll be able to brag in a few years that you were there in the heroic era, to not miss that opportunity!

If you are interested in BioImage Cloud, you can find useful links at the end of our dedicated article, including access to the open desk sessions and the mailing list.

You can also watch the replay of the FBI Connect webinar, where Guillaume Gay presented BioImage Cloud and its main features.

Over the past few years, image analysis has become an essential step in the production and interpretation of microscopy images. As bioimaging experiments generate increasingly large and complex datasets, image analysis now plays a central role in transforming imaging data into meaningful scientific insights.

To support this rapidly growing field, the Network of European BioImage Analysts (NEUBIAS) was founded in 2016. NEUBIAS played a key role in structuring the European bioimage analysis community and in promoting the recognition of the bioimage analyst profession, positioned at the interface between biology, physics, computer science and data science.

Building on this success, an international consortium of researchers, including Florian Levet (Interdisciplinary Institute for Neuroscience, Bordeaux Imaging Center), received funding from the Chan Zuckerberg Initiative in 2023 to extend this effort beyond Europe and establish a sustainable global organisation dedicated to bioimage analysis. This initiative led to the creation of GloBIAS, the Global BioImage Analysts’ Society.

In an article published in Nature Methods⁽¹⁾, the GloBIAS community presents the origins of the society, its missions and the actions implemented to support the development of bioimage analysis worldwide.

Over the years, this European initiative progressively opened up to international partners and inspired other bioimaging communities, including in North America, Latin America, Asia and Oceania. GloBIAS emerged from this momentum, with the ambition to create a sustainable global network for the entire bioimage analysis community.

GloBIAS aims to become a true “global hub for bioimage analysis” by bringing together a wide range of profiles, including bioimage analysts, developers, bioinformaticians, research software engineers, biologists, physicists, educators and scientists from various disciplines.

To address the needs of this international community, GloBIAS focuses on several key missions: fostering knowledge exchange, encouraging collaboration, promoting training, organising events, and collectively addressing emerging challenges in the field.

To better identify the needs and expectations of the community, GloBIAS conducted an international survey among bioimage analysts. The results helped structure several concrete actions, including the creation of new working groups dedicated to training and education, high-performance computing and cloud computing, annual events and publications. The society also organises monthly seminars and international workshops to encourage knowledge sharing and skills development within the community.

Through these actions, GloBIAS aims to democratise access to bioimage analysis resources, strengthen the recognition of the bioimage analyst profession and create an international platform for exchange, helping the community develop shared solutions to scientific, technical and professional challenges.

To learn more and join the network, visit the GloBIAS website.

(1) Corbat, A.A., Walther, C.G., de la Ballina, L.R, Condon, N.D., Felder, A.A., Schätz, M., Schmerl, B., Sugawara, K., Prats, C., Klemm, A., Miura, K., Sampaio, P., Tischer, C., Levet, F*., D’Antuono, R.*, Cimini, B.A.*, Haase, R*. GloBIAS: strengthening the foundations of bioimage analysis. Nat Methods (2026). https://doi.org/10.1038/s41592-026-03060-7

*co-corresponding authors

The France-BioImaging Preclinical Microscopy Working Group is pleased to organise its 4th webinar, which will take place on 18 June 2026, from 2:00 pm to 4:00 pm.

This webinar will feature two presentations dedicated to intravital imaging and animal welfare, followed by an open discussion.

Programme

2:00 pm – Welcome and introductory remarks

2:05 pm – Intravital microscopy physiology and pathology: from whole organs to cell, sub-cellular structures and single molecules – Roberto Weigert (Center for Cancer Research)

2:55 pm – Animal welfare in oncology: preventing and taking action. Application to intravital imaging –
Karine Ser-Le Roux (Institut Gustave Roussy)

3:45 pm – Open discussion

Here’s the connection link to join the webinar: Webinar Preclinical Microscopy Working Group | Microsoft Teams | Meetup-Join

The SFBS 2026 Scientific Symposium, hosted in Bordeaux from October 19 to 21, 2026, will be dedicated to super-resolution and advanced microscopy. On this occasion, renowned international experts will share their latest research and exchange with attendees on their vision of the field.

We are also pleased to reveal three new invited speakers in the programme: Ricardo Henriques, Francesca Pennacchietti and Wei Ji! Discover their background and current research work in this article.

If you are also interested in presenting your work at SFBS 2026, the abstract submission deadline has been extended! Apply here before June 15, 2026 for a chance to give a talk or present a poster.

Ricardo Henriques

He established his first independent group at UCL in 2013, opened a satellite laboratory at the Francis Crick Institute in 2017, was promoted to Full Professor at UCL in 2019, and moved the group to Portugal in 2020, first at the Instituto Gulbenkian de Ciência and then to ITQB NOVA in 2024.

The lab works at the interface of live-cell super-resolution microscopy, AI-driven bioimage analysis, and host-pathogen biology, organised around one recurring question: how do you see more of a living system while disturbing it less? Methods that emerged from that question (QuickPALM, SRRF, eSRRF, NanoPyx, ZeroCostDL4Mic, DL4MicEverywhere) are used in thousands of labs and helped make deep-learning microscopy accessible to biologists with no computational background.

His current programme builds adaptive nanoscopy for long-term imaging of viral and bacterial infections, paired with shared infrastructure that keeps the resulting AI tools open and reusable. He co-founded FocalPlane and AGRAFr.

Francesca Pennacchietti

Her work explores how the unique photophysical properties of these proteins can be harnessed not only to achieve nanoscale resolution but also to advance bioimaging toward spectral multiplexing, minimally invasive imaging, and biosensing.

By bridging the fields of super-resolution microscopy and photoreceptor biology, she aims to enable real-time visualization and control of cellular processes with unprecedented spatial and temporal resolution.

Wei Ji

He has pioneered a series of interferometric single-molecule localization microscopy (SMLM) methods, including ROSE, ROSE-Z, and ROSE-3D. These techniques localize fluorescent molecules using intensity information from multiple excitation patterns of an interference fringe, achieving higher precision than conventional centroid fitting under the same photon budget. He has also developed cryogenic correlated light, ion, and electron microscopy (cryo-CLIEM), a method that enables the preparation of cryo-lamellae guided by three-dimensional confocal imaging.

Dr. Ji has published numerous papers in high-impact journals such as Nature Methods, and his work has been recognized as one of the Top Ten Advances in Life Sciences in China. He is the recipient of several prestigious awards, including the National Science Fund for Distinguished Young Scholars, the CAS Young Scientist Award, the Xplorer Prize, and the China Youth Science and Technology Award.

Don’t miss this opportunity to meet these experts during SFBS 2026! Join us in Bordeaux from October 19 to 21, 2026!

Would you like to share your work at SFBS 2026? Good news: the abstract submission deadline has been extended! Apply before June 15, 2026 for a chance to give a talk or present a poster.

The Bordeaux Imaging Center, a France-BioImaging facility, has secured new structural funding to strengthen its biological imaging capabilities. Supported by the Nouvelle-Aquitaine Region and the European Union through FEDER (European Regional Development Fund), two major projects led by the Interdisciplinary Institute for Neuroscience and the Bordeaux Imaging Center have been selected: MINFLUX and IMPACT.

With nearly €3 million in FEDER funding, complemented by investments secured through France 2030 and the State-Region Plan Contract (CPER), almost €5 million will contribute to the development of imaging technologies for the Bordeaux scientific community.

MINFLUX and IMPACT: two structuring projects for biological imaging

The MINFLUX project will enable the installation of the first MINFLUX microscope in France and south-western Europe. Installed at the Bordeaux Imaging Center, this equipment represents a major advance for observing individual molecules with nanometric precision.

The IMPACT project will equip the BIC with new multiphoton imaging tools to explore molecular interactions within thick living tissues with enhanced depth and precision. These technologies will open up new perspectives in a wide range of fields, from neuroscience and cell biology to microbiology, plant biology and oncology.

Strengthening imaging capabilities in Bordeaux

These investments are part of a broader effort to develop optical and electron imaging technologies in Bordeaux. This reinforcement will also include the acquisition of a Cryo-FIB-SEM, a unique instrument in the Bordeaux region, made possible via France-BioImaging BIOGEN project within the framework of France 2030 investment plan.

Together, these instruments will help provide the scientific community with access to advanced imaging technologies capable of observing living systems at different scales, from tissues to molecular structures.

By consolidating its technological capabilities, Bordeaux confirms its position among Europe’s leading hubs for biological imaging, serving research, innovation and scientific collaborations.

As a national research infrastructure, France-BioImaging supports the development and access to advanced biological imaging technologies across France. Through its facilities, including the Bordeaux Imaging Center, the infrastructure contributes to strengthening the technological environment available to the life sciences community and to supporting scientific excellence at national and European levels.

The ANERIS consortium gathered in Barcelona for its final in-person meeting, marking an important milestone after four years of collaborative work dedicated to developing and validating innovative technologies for marine ecosystem monitoring.

Representing CNRS and France-BioImaging, Caroline Thiriet, Perrine Paul-Gilloteaux and Fabrice Cordelières contributed to discussions on technology validation, dissemination and community engagement. Through its participation in ANERIS, France-BioImaging has helped bring expertise from the bioimaging community into a new application domain: operational marine biodiversity monitoring.

A highlight of the meeting was the presentation of Case Study 1, which showcased the scientific results and technological advances achieved through the project. As part of this session, Perrine Paul-Gilloteaux presented one of the advanced data products developed within the case study, illustrating how advanced imaging systems, image restoration methods and AI-powered analysis pipelines can be combined to generate continuous biodiversity observations in marine observatories. Together with the deployment of multiple sensing technologies, these developments demonstrate the technological maturity reached within ANERIS and the potential of the framework for operational marine biodiversity monitoring tools supporting environmental sciences.

ANERIS also highlighted the importance of collaboration between European Research Infrastructures. The participation of France-BioImaging alongside Euro-BioImaging has helped strengthen exchanges between imaging experts, marine observatories and environmental research communities, fostering the transfer of technologies, expertise and best practices across disciplines.

As the project enters its final phase, our focus now turns toward dissemination and uptake. Together with ANERIS partners, we are preparing a dedicated workshop later this year to introduce the Operational Marine Biology (OMB) products developed during the project to a broad audience, including researchers, infrastructure staff, environmental stakeholders and potential end users.

A great example of how research infrastructures contribute not only to technology development, but also to training, knowledge transfer and the long-term impact of scientific innovation.