France-BioImaging (FBI), the national research infrastructure in biology and health dedicated to biological imaging, has established an Africa hub aimed at structuring long-term scientific collaborations and supporting the development of bioimaging capacities across the African continent. This initiative builds on several years of exchanges with African partners and is based on training, networking, and collaborative research activities. A new milestone will be reached with the organization of the BEAMS school in Dakar (Senegal) in November 2026, dedicated to the study of biodiversity and ecosystem sustainability.

Structuring Africa-France scientific cooperation in bioimaging

Created in December 2024 at the initiative of Jean Salamero (former Director of France-BioImaging, CNRS Research Director until June 2025), Samira Benadda (head of the Photonic Microscopy Platform at IBENS – ENS/PSL), and Jean-Luc Verdeil (scientific head of the MRI-PHiV imaging facility at CIRAD), the Africa hub of France-BioImaging brings together 12 members from different nodes of the infrastructure. Its objective is to support the emergence of a bioimaging community in Africa while strengthening scientific links between African and French researchers.

This initiative continues discussions initiated in 2021 with the Africa Microscopy Initiative (AMI). A consultation phase conducted in 2022 with African universities and academic partners, in collaboration with French institutions such as CNRS, CIRAD, IRD, and Aix-Marseille University, led to the definition of an open strategy extending beyond francophone regions, in alignment with AMI and the African BioImaging Consortium.

In 2023, these efforts were strengthened with the launch of the Africa-France Joint Initiative for Bioimaging, which supported ten collaborative research projects.

Training, exchanges and co-construction at the core of the initiative

The Africa hub is structured around several complementary priorities: strengthening scientific exchanges, developing training and mobility opportunities for African researchers, supporting the creation of bioimaging schools in Africa, and contributing to international calls for projects.

In 2024-2025, new Africa-France projects were carried out within the Imaging4All program of the Global BioImaging network, supported by the Wellcome Trust and targeting low- and middle-income countries.

Through these actions, France-BioImaging follows a co-construction approach, aiming to build balanced, sustainable partnerships rooted in local realities.

“The impact of the Africa Hub initiatives is twofold: strengthening technological capacities and expertise in biological imaging in Africa, and improving the efficiency of collaborative research in biology, environment and health, addressing challenges faced by our colleagues today and by us tomorrow, such as climate change, biodiversity, biotic and abiotic stress, and emerging diseases.”
– Jean Salamero

A first major action: the BEAMS school in Dakar

Within this framework, France-BioImaging and its partners are organizing the first edition of the thematic school “Bioimaging for the study of biodiversity and ecosystem sustainability in Africa” (BEAMS), which will take place from November 16 to 27, 2026, at Cheikh Anta Diop University (UCAD) in Dakar, Senegal.

This school will combine theoretical lectures, hands-on sessions, and scientific exchanges to address key challenges related to the study of African biodiversity and ecosystems using bioimaging technologies. It aims to contribute to the training of a new generation of scientists and to strengthen collaborations at regional and international levels.

The project has been selected by the Agence Universitaire de la Francophonie within the INTENSCIF program.

The Light My Cells dataset, developed through the first France-BioImaging challenge, has been published in Nature Scientific Data ⁽¹⁾. It represents the first scientific outcome of this initiative which involved 31 contributors across the France-BioImaging network from Montpellier, Toulouse, Marseille, Paris, Rennes, Bordeaux and Strasbourg.

Predicting fluorescence from label-free imaging

Fluorescence microscopy is widely used across life and physical sciences to access specific molecular or structural information within samples. However, it is constrained by phototoxicity, photobleaching, and demanding sample preparation, which can limit its use in long-term observations and high-throughput experiments.

In contrast, transmitted light techniques, such as bright-field, phase contrast, and differential interference contrast, enable non-invasive imaging without labeling, preserving cell integrity over time. However, they do not provide direct molecular specificity.

The Light My Cells challenge builds on existing approaches and stimulates the development of deep learning methods to predict fluorescence signals from transmitted light images, opening new perspectives for label-free and less invasive imaging strategies

A large-scale dataset built across France-BioImaging

The publication introduces an open-access dataset developed within the France-BioImaging infrastructure.

It brings together 2,574 acquisition sets (unique fields of view), corresponding to a total of 56,984 two-dimensional microscopy images, derived from 30 independent studies collected across 8 imaging centers within the France-BioImaging infrastructure.

Each acquisition set combines transmitted light images with at least one fluorescence image targeting key subcellular structures, including the nucleus, mitochondria, tubulin, and actin. The diversity of samples, imaging systems, and experimental conditions supports the development of robust and generalizable models.

To ensure interoperability and reuse, all data were standardized using the OME-TIFF format and enriched with REMBI-compliant metadata, following FAIR data principles. A dedicated preprocessing pipeline further ensures consistency, including best-focus selection and harmonized data structure.

First scientific outcome of the Light My Cells challenge

The dataset is publicly available through the BioImage Archive, providing a reliable resource for the scientific community.

This publication represents the first scientific outcome of the Light My Cells challenge, providing a structured and openly accessible dataset designed to support the development and evaluation of deep learning models for fluorescence prediction from transmitted light microscopy.

⁽¹⁾Kauffmann, D., Gay, G., Mateos-Langerak, J. et al. 2D Multimodal Image Collection for Fluorescence Prediction from Transmitted Light Microscopy. Sci Data (2026). https://doi.org/10.1038/s41597-026-07004-w

Registration is now open for the 1st France VolumeEM Scientific Conference, which will take place on September 28-29, 2026 in Bordeaux. This first edition will bring together the community around volume electron microscopy to explore three-dimensional imaging approaches across scales, from cellular to material sciences.

The conference will open with a plenary lecture by Isabelle Bonne (NUS Microscopy Core, Singapore) titled “Volume EM Today: From Cells to Materials”, followed by three thematic sessions:

• Session 1 – 3D Structures across scales, with Elsa Vennat (Paris-Saclay Mechanics Laboratory)
• Session 2 – Complementary Methods, Applications in Science and Industry, with Timm Weitkamp (Synchrotron SOLEIL)
• Session 3 – Life in Context, a Three-Dimensional Story, with Karel Mocaer (EMBL)

Participants are invited to contribute to the scientific programme:

• Submit an oral presentation to share innovative results, ongoing projects or original approaches
• Present your work as a poster during the Monday evening poster session

As additional highlight of the event, workshops will be held on September 29 afternoon (registration required, limited capacity)

Interested? Find the registration link, the submission guidelines and the complete program below!

Understanding how molecules move inside cells is a central question in cell biology, as diffusion underpins essential processes such as signaling, metabolism and intracellular transport. Yet, the cytoplasm is far from a simple fluid: it is a densely packed and highly structured environment filled with organelles, membranes and macromolecular assemblies.

In this study⁽¹⁾, researchers from Institut Jacques Monod and CentraleSupélec combine advanced microscopy techniques with biophysical modelling to investigate how this complex architecture impacts molecular mobility.

By linking quantitative imaging with theoretical approaches, they reveal that intracellular diffusion is strongly shaped by cytoplasmic organization.

Seeing and quantifying cytoplasmic organization

Using confocal microscopy, the researchers examined the spatial organization of the cytoplasm in living cells and identified regions with different levels of accessibility. By using freely diffusing GFP as a probe, they estimated the fraction of accessible volume and showed that the cytoplasm is heterogeneous at the subcellular scale.

These measurements revealed variations in crowding associated with the local distribution of intracellular structures, providing a quantitative description of the physical environment in which diffusion occurs.

Measuring diffusion across scales with FRAP and FCS

Diffusion was quantified by combining Fluorescence Recovery After Photobleaching (FRAP) and Fluorescence Correlation Spectroscopy (FCS), which probe complementary spatial and temporal scales.

The measurements show that GFP diffusion in the cytoplasm is significantly reduced compared to aqueous conditions and varies depending on local crowding. In particular, regions with higher obstacle density exhibit lower diffusion coefficients.

The data further indicate that nanoscale structures are the main contributors to these variations, while larger structures have a more limited and stable effect under the conditions tested.

From imaging to predictive models of the cytoplasm

By integrating experimental measurements with theoretical modelling, the study shows that the cytoplasm can be described as a porous medium. In this framework, nanoscale obstacles occupy a large fraction of the available space and largely determine the effective diffusion of macromolecules.

The model reproduces the experimental observations and provides a way to relate structural parameters to diffusion coefficients. It also enables predictions for other conditions, suggesting potential applications for studying intracellular transport of biomolecules, including small therapeutic compounds.

All microscopy experiments were conducted at the ImagoSeine facility (France-BioImaging Paris-Centre node).

(1) Destrian O, Moisan N, Mège RM, Ladoux B, Goyeau B, Chabanon M. Cytoplasmic crowding acts as a porous medium reducing macromolecule diffusion. Proc Natl Acad Sci U S A. 2026 Jan 27;123(4):e2519599123. doi: 10.1073/pnas.2519599123. Epub 2026 Jan 23. PMID: 41576074

Nous avons rencontré Wiame et Samira, qui nous ont fait le plaisir de répondre à nos questions pour mieux comprendre les enjeux et bénéfices de cet échange.

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

Pouvez-vous brièvement vous présenter ?

[Wiame] Je suis ingénieure en biotechnologie et doctorante au Centre de Recherche en Biotechnologie (CRBt) et à l’Ecole Nationale Supérieure en Biotechnologie en Algérie. En parallèle de mon doctorat, je suis impliquée dans la mise en place et le développement d’une plateforme de bioingénierie dédiée aux technologies émergentes, notamment en microfabrication pour le développement de systèmes lab-on-chip, en bio-impression 3D et en bioimagerie avancée. Je suis également cofondatrice de la startup MIMIC-AL, dont l’objectif est de développer et diffuser ces technologies.

[Samira] Ingénieure de recherche et responsable de la plateforme de microscopie photonique de l’IBENS, j’évolue dans cet univers depuis près de 20 ans. Cette solide expérience m’a permis de développer une expertise technique que j’ai toujours eu à cœur de partager avec la communauté scientifique. J’ai fait de la transmission de savoir le cœur de mon métier. Pour moi, l’expertise technique n’a de valeur que si elle est partagée. Aujourd’hui, en tant que co-coordinatrice du pôle Afrique de France-BioImaging, je mets ce savoir-faire au service de collaborations internationales comme le programme Imaging 4 All. Pour moi, la microscopie est avant tout un outil de transmission et d’ouverture, permettant de bâtir des ponts scientifiques durables et équitables.

Wiame, sur quel projet de recherche travaillez-vous actuellement ?

[Wiame] Dans le cadre de mon doctorat, je travaille sur le développement de biopuces (lab-on-chip) pour étudier l’édition génétique en conditions contrôlées. Ces dispositifs me permettent d’analyser le comportement cellulaire à l’aide de systèmes microfluidiques et de modèles 3D comme les sphéroïdes. Ce projet vise à mieux comprendre la dynamique cellulaire et à évaluer l’efficacité de ces systèmes dans des environnements proches du physiologique.

En parallèle, sur le plan professionnel, je contribue à la structuration et au développement de la plateforme de bioingénierie, avec un focus sur le développement de systèmes lab-on-chip pour des applications biotechnologiques ainsi que l’intégration et l’optimisation des technologies d’imagerie.

Comment avez-vous vécu le programme Imaging 4 All – Access Track ?

[Wiame] C’était une expérience très enrichissante, autant sur le plan technique que scientifique. J’ai pu accéder à des systèmes d’imagerie avancée, tester différentes approches et échanger avec des experts. Cela m’a aussi permis de prendre du recul sur nos pratiques et d’identifier des axes d’amélioration pour notre plateforme.

Samira, pourquoi est-il important pour vous d’accueillir des bénéficiaires de ce programme ?

[Samira] Dès le lancement d’Imaging 4 All, j’ai souhaité m’y engager car c’est une opportunité unique de transformer l’équité Nord-Sud en action concrète. Pour moi, réduire le fossé technologique signifie offrir à nos collaborateurs africains un accès réel à des technologies d’imagerie les plus avancées.

Mais au-delà de l’aspect technique, cet accueil est essentiel car il crée une réciprocité précieuse : en partageant notre expertise en microscopie, nous recevons en retour des perspectives scientifiques nouvelles et des problématiques de recherche différentes. C’est ce dialogue d’égal à égal qui fait la force de notre pôle Afrique au sein de France-BioImaging.

Pourquoi avoir choisi une plateforme France-BioImaging ?

[Wiame] France-BioImaging regroupe des plateformes reconnues pour leur expertise en imagerie avancée et leur accompagnement scientifique. C’était une opportunité idéale pour accéder à des technologies que nous n’avons pas encore sur notre site, tout en bénéficiant d’un encadrement technique solide, et pour intégrer notre plateforme dans un réseau international actif, en lien direct avec nos besoins en microscopie.

Comment la plateforme a-t-elle bénéficié de cette collaboration ?

Wiame, en quoi ce séjour a-t-il fait avancer votre projet ?

[Wiame] Ce séjour m’a permis de tester certaines approches sur des échantillons en lien avec mon travail, notamment en microscopie avancée et en expansion microscopy. J’ai également acquis des bases solides en métrologie et en évaluation des performances des microscopes, ce qui est essentiel pour garantir la qualité des données. Ces acquis sont directement utiles, à la fois pour mon projet de thèse et pour le développement de notre plateforme.

En quoi cette collaboration a-t-elle enrichi vos approches scientifiques ?

[Wiame] Cette collaboration m’a surtout permis de confronter nos approches à celles d’une plateforme plus spécialisée et d’avoir des retours concrets sur certaines pratiques. Les échanges avec les équipes m’ont aidée à mieux comprendre les limites de certaines technologies et à identifier des points à améliorer dans notre plateforme.

[Samira] Cette rencontre a été un véritable enrichissement scientifique pour nous. Cette collaboration nous a permis d’explorer la thématique des biopuces, un domaine jusqu’alors inédit sur notre site. L’adaptation de nos équipements à ces supports miniaturisés a non seulement diversifié notre champ d’expertise technique, mais a également stimulé l’évolution de nos protocoles d’acquisition. Au-delà de l’échange humain, cette rencontre a enrichi notre offre scientifique en intégrant de nouvelles méthodologies qui pourraient être bénéfiques à nos utilisateurs.

Comment Global BioImaging favorise-t-il des collaborations équilibrées ?

[Samira] Global BioImaging favorise des collaborations équilibrées en transformant la relation technique en un véritable partenariat de pairs. Si la plateforme offre l’accès aux technologies de pointe avancées, le chercheur visiteur enrichit en retour le site d’accueil par des thématiques novatrices. Notre expérience avec le programme Imaging 4 All l’illustre parfaitement : l’introduction de la thématique des biopuces, inédite sur notre site, a stimulé l’évolution de notre offre. Ce programme assure une reconnaissance scientifique mutuelle et transforme une mobilité ponctuelle en une collaboration de recherche durable et équitable.

Comment envisagez-vous la suite de cette collaboration ?

[Samira] La suite de cette collaboration s’annonce ambitieuse grâce à notre sélection au PiTCH Program de l’AMI (Africa Microscopy Initiative). Ce programme nous permet de passer d’un échange technique ponctuel à un véritable partenariat pédagogique durable. Notre objectif est de co-construire un module de formation structuré en bioimagerie. En devenant acteurs au sein du réseau AMI, nous ne nous contentons plus de partager une technologie, nous souhaitons mettre en place ensemble un pôle de compétences local autonome afin de faire profiter durablement à l’ensemble de la communauté de chercheurs en Afrique.

Samira, en tant que cofondatrice du pôle Afrique de FBI, comment ce type de collaboration contribue-t-il aux missions du pôle ?

[Samira] Ce projet est le cœur même de notre mission : créer des ponts concrets et durables. Cette collaboration prouve que nos plateformes ne sont pas seulement des lieux de haute technologie, mais des hubs de coopération internationale. En passant de l’accueil Imaging 4All à la formation de mentors PiTCH de l’AMI par exemple, nous transformons une expertise locale en un levier d’autonomie pour nos partenaires africains. C’est ainsi que nous contribuons, pas à pas, à bâtir une communauté scientifique plus équitable.

The France-BioImaging Annual Meeting 2026 came to a close after two days held on March 12-13 in Rouen. This year’s edition, centered on the theme “Multimodalities for organ and organism imaging”, brought together the community for rich scientific discussions and new perspectives for collaboration.

Through a series of insightful presentations, the event showcased the wide spectrum of imaging approaches developed within France-BioImaging, highlighting both their potential and the challenges ahead. This edition also marked the first participation of industry sponsors (F-DGSi, Inscoper, Leica Microsystems, Nikon, Thermo Fisher Scientific and Zeiss) whom we warmly thank for their valuable support.

Day 1 – Infrastructure, collaboration and emerging synergies

The morning continued with key updates from France-BioImaging, followed by an overview of the Normandie Node. Several strategic topics were then addressed, reflecting the infrastructure’s core priorities:

• strengthening collaborations between academia and industry, notably through partnership models such as the collaboration between PRIMACEN and the start-up Alga Biologics cSMARt project,
• reinforcing education and training, from master’s programs to career development initiatives supported by Euro-BioImaging,
• advancing data management and sharing, with significant progress highlighted within the FBI.data initiative and the BioImage Cloud.

The day concluded with the first scientific session dedicated to plant and invertebrate imaging. Presentations illustrated advanced 3D analysis approaches and electron microscopy applications, followed by a keynote lecture from Marie Walde (EMBRC infrastructure), who shared recent advances and challenges in imaging marine organisms.

Day 2 – Multimodal imaging across biological systems

A keynote lecture by Maxime Gauberti (FLI infrastructure) introduced innovative developments in immuno-MRI, further illustrating the power of multimodal strategies in neuroscience.

The programme then featured an industry-focused session, where partners including Inscoper, Leica Microsystems, Thermo Fisher Scientific, and Zeiss presented advanced imaging solutions and discussed current challenges in multimodal bioimaging .

In the afternoon, scientific sessions explored imaging applications across multiple organ systems. Topics included:

• muscle and cardiovascular imaging, with a focus on pathological conditions,
• lung intravital microscopy revealing immune cell dynamics,
• advanced methodologies for gastrointestinal and liver imaging, including studies on hepatic diseases and infection models.

A dynamic and collaborative community

Over the course of these two days, the Annual Meeting highlighted the diversity and excellence of imaging technologies within the France-BioImaging network, as well as the strong expertise of its platforms and R&D teams.

The event also reinforced the importance of collaboration between nodes, disciplines and industry partners, to address current and future challenges in bioimaging.

A replay of the Annual Meeting will be available soon for those who wish to revisit the sessions.

We would like to warmly thank the local organizing team for their outstanding work, as well as all our sponsors for their support in making this event a success.

The Photonic Microscopy Platform at Imagerie-Gif (France-BioImaging Île-de-France Sud node) is organizing two events to introduce its new imaging system: the Thunder Imager Cell / Spinning Disk Cicero.

A first event, Pizza Tech, will take place on March 27 (12:00–13:30). After a pizza lunch, Leica will present the new setup and its capabilities.

A Demo Week will then be organized from March 31 to April 2, during which researchers, PhD students and engineers will have the opportunity to bring their own samples and test the system.

Participants interested in attending can register by email at: plt-phot@i2bc.paris-saclay.fr

The AgroServ translational/virtual access programme is back with its fifth and final call, offering researchers working on agroecology projects access to more than 140 research services across Europe.

As Euro-BioImaging is a partner of the programme, researchers can benefit from access to advanced microscopy facilities, including the France-BioImaging facility Imagerie-Gif.

New in this call: applicants can now request access to services from a single research infrastructure if this better fits their research needs. Previously, applications had to combine services from multiple infrastructures.

This programme supports research addressing sustainable and resilient agri-food systems, including topics such as plant biology, soil, water and microorganisms. Selected projects benefit from free access to leading European research infrastructures, providing cutting-edge technologies and expertise to support agroecology research.

Deadline for applications: June 8, 2026

More information about the call and the application procedure is available here:
https://agroserv.eu/calls-and-applications/application-procedure

Short-term synaptic plasticity (STP), the rapid modulation of synaptic efficiency during closely spaced neuronal activity, has long been considered primarily presynaptic in origin. In a study published in Neuron⁽¹⁾, Daniel Choquet’s team (IINS, Neurocampus Bordeaux) demonstrates, using several advanced microscopy approaches implemented at the Bordeaux Imaging Center (France-BioImaging Bordeaux node), that postsynaptic AMPA receptor mobility plays a decisive role in this regulation.

Visualizing receptor dynamics in real time

To investigate this mechanism, researchers used primarily lattice light-sheet (LLS) microscopy, a high spatiotemporal resolution system enabling the characterization of AMPA receptor mobility at individual synapses. This approach revealed that AMPA receptors are not static but undergo lateral diffusion within the postsynaptic membrane.

By combining LLS with Fluorescence Recovery After Photobleaching (FRAP) experiments, AMPA receptor mobile fraction can be quantified. The team also used targeted 1P and 2P photo-manipulation, to demonstrate the link between potentiation or depression and receptor mobility. When AMPA receptors are immobilized, synaptic depression increases.

Super-resolution STORM microscopy was also employed to examine the static nano-organization of AMPA receptor subunits. The results show that their nanoscale organization is not altered when immobilizing AMPA by crosslinking agent. Only the mobility is affected as revealed with LLS single particle tracking.

From single synapses to neuronal networks

Finally, two-photon microscopy enabled the study of the impact of AMPA receptor mobility at the network level. The findings indicate that receptor dynamics influence collective neuronal activity and contribute to maintaining appropriate synaptic gain.

These findings establish AMPA receptor mobility as a functional component of short-term plasticity. By directly visualizing and manipulating receptor dynamics, advanced microscopy demonstrates that postsynaptic receptor motion actively shapes synaptic strength regulation.

(1) Agata Nowacka, Angela M. Getz, Hanna L. Zieger, Maxime Malivert, Diogo Bessa-Neto, Elisabete Augusto, Christelle Breillat, Sophie Daburon, Cécile Lemoigne, Sébastien Marais, Mathieu Ducros, Alexandre Favereaux, Andrew C. Penn, Richard Naud, Matthieu Sainlos, Daniel Choquet, Synapse-specific and plasticity-regulated AMPA receptor mobility tunes synaptic integration, Neuron, 2026, ISSN 0896-6273, https://doi.org/10.1016/j.neuron.2025.12.004.

Throughout the day, discussions revolved around real-life workflows in correlative microscopies, advanced light-sheet imaging, and plant imaging under physiological constraints. Correlation was approached broadly, encompassing not only light and electron microscopy, but also multi-modal strategies combining different contrast mechanisms, spatial scales and preparation conditions. Rather than focusing on individual systems, the exchanges centered on how these complementary modalities are orchestrated in practice to answer complex biological questions.

One particularly illustrative discussion concerned live imaging of plant root systems. Unlike many biological samples, plant roots are highly sensitive to gravity and grow continuously during observation. Conventional horizontal microscope configurations can therefore introduce non-physiological constraints, potentially altering the very processes under investigation. This raises the need for vertical imaging solutions capable of maintaining biological relevance during long-term experiments, while preserving resolution, stability and usability. Such cases exemplify how instrumentation must adapt to biological reality -not the other way around- if it is to fully serve the end user.

Across all topics, a common theme emerged: beyond technical performance, researchers require integrated, reliable and user-friendly solutions that fit within complex research infrastructure ecosystems. By confronting field practices with industrial perspectives, the visit fostered a shared understanding of operational constraints, technological opportunities and long-term expectations.

This EVOLVE exchange reinforced the role of Euro-BioImaging and its national nodes, including France-BioImaging and the BIC, as catalysts for structured dialogue between research infrastructures and industry. By anchoring innovation in real user environments and evolving scientific needs, the initiative contributes to shaping sustainable, co-designed technological developments that ultimately benefit the research community.