Interdisciplinary access call to Structural biology, Biological imaging and Proteomics facilities
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Category: Announcement
Deadline: February 13th, 2026
The three national infrastructures ProFi, France-BioImaging and FRISBI along with the GIS IBiSA are pleased to announce a fourth call for a funded access to IBiSA-labelled facilities. Our aim is to promote IBiSA facilities networking through transdisciplinary research projects.
Applications should request access to at least two different IBiSA facilities from two disciplines (structural biology, Biological imaging and proteomics, see below a non-exhaustive list). The call is open to any academic laboratory.
Modalities for application are described in the attached document.
Explore the endless possibilities of microscopy through the 2025 FBI digital calendar!
Once again this year, the participants in the France-BioImaging Image Contest have outdone themselves, providing us with stunning microscopy images captured using a variety of techniques. These images also showcase the diversity of models and applications, highlighting the many possibilities offered by microscopy. Take a look at 12 of the 37 images submitted to the France-BioImaging Image Contest 2025!
A big thank you again to all the participants!
You can download the A4 print version (one month per page) 2025 FBI digital calendar here:
As 2025 comes to an end, this year once again proved to be rich in exchanges and collaborations. Through interviews, webinars and events, discover a snapshot of an inspiring year for the France-BioImaging community.
International collaborations
Through various international events and collaborations, France-BioImaging strengthened its presence on the global stage.
Official launch of the IRN BioImage
An International Research Network (IRN) has been launched to strengthen collaboration between France and China in biological optical imaging research. This initiative brings together leading institutions from France-BioImaging and the National Biomedical Imaging Center (NBIC) in China to advance microscopy technologies and methodologies.
The partnership focuses on four main areas: image analysis and data management, probes, super-resolution imaging, and deep-tissue imaging.
All Hands Nodes Meeting
In March, several FBI members attended Euro-BioImaging All Hands Meeting at EMBL in Heidelberg. This event provided an opportunity to meet colleagues from all Euro-BioImaging nodes and discuss imaging technology innovation, data, access, training, and international collaboration.
A session was specifically dedicated to the Euro-BioImaging User Access Experience, featuring an interactive discussion during which Yves Lutz (IGBMC) presented the experience of the France-BioImaging Alsace Node.
10th Global BioImaging Exchange of Experience
In October, FBI participated in the GBI Exchange of Experience 2025, to explore “Imaging in 2035 – Sustaining Infrastructure Ecosystems & Advanced Technologies.” France-BioImaging was represented by Caroline Thiriet and Jean Salamero.
As Mission Officer for Inter-Infrastructure Relationships at FBI and member of the GBI Working Group on Impact, Jean Salamero moderated the session “Micro-to-Macro: Measuring the Hidden Impacts of Imaging Scientists & Networks.”
Normandie & Rhone-Alpes nodes officially joined Euro-BioImaging
Since their integration in June, the Normandie and Rhône-Alpes nodes have significantly expanded the scope and excellence of the French node of Euro-BioImaging.
The Normandie Node brings unique expertise in: * Intravital imaging for vascular diseases, * Microalgal biosciences and marine biology imaging, * Advanced cryo-correlative microscopies and super-resolution imaging.
The Rhône-Alpes Node enhances national capabilities with: *Deep expertise in large-volume 3D EM with integrated image analysis pipelines, * Pioneering technologies in biomechanics and mechanobiology, * Rare capacities in spatial transcriptomics, adaptive optics, and metabolic imaging.
Insightful job shadowing
In October, several members of FBI took part in the opportunities offered by EVOLVE project, enabling valuable exchanges and experiences.
Through the Job Shadowing initiative, Guillaume Gay, Data Engineer for the FBI.data mission welcomed Kenneth Ho from the Francis Crick Institute to discusse shared challenges and solutions in microscopy data management. Caroline Thiriet, Deputy Administrative Director for International Relations and Industry at FBI, hosted Virginia Pierini from the EMBL Imaging Centre to exchange on how France-BioImaging coordinates its distributed national infrastructure.
Finally, Fabrice Cordelière, Head of Training for FBI, took part in the Train-the-Trainer event, mentoring Iva Švecová from the Light Microscopy Facility at the Institute of Experimental Medicine. Eva benefited from Fabrice’s extensive experience in team management, user training, coding practices, and user-driven data backup workflows.
Competitions in the spotlight
Challenge Fuse My Cells
For the second consecutive year, France-BioImaging organized its data and machine-learning competition. The challenge aimed to predict a fused 3D image using only one or two available 3D views, addressing key limitations of current microscopy techniques such as image quality, live-imaging duration, photon budget optimization and image analysis facilitation.
The winners were: 1st place: Marek Wodzinski 2nd place: Shengyan Xu 3rd place: Cyril Meyer
FBI Image Contest 2025
Once again, we were delighted by the diversity of submitted images, showcasing a wide range of microscopy techniques, models and applications. This competition highlights how microscopy images can also take on an artistic and creative dimension, revealing the beauty of the invisible world.
The winners were: 1st place: Nicolas Barois with Gut Flower-Flora 2nd place: Vishwadeep Mane with The Puzzled Awakening 3rd place: Simli Dey with Kaleidoscope
Focus on our community
User Success Stories
In 2025, we highlighted several users who benefited from the FBI User Access Fund in 2024. Through their portraits, you discovered their research journeys and how access to FBI platforms supported their projects.
Throughout 2025, numerous scientific articles were published by FBI members and platform users.
From new protocols to innovative research results, a wide range of topics were covered, including cancer research, virology, plant biology, developmental biology and data analysis.
Digital events
FBI Connect
In November, we launched the first edition of FBI Connect, a new webinar series dedicated to the France-BioImaging community. This initiative aims to highlight cutting-edge techniques developed within FBI facilities and demonstrate how they support research projects.
For this inaugural session, we welcomed Robert Quast (CBS, Montpellier), who presented a novel multicolor single-molecule FRET technique, unique in France and Europe, enabling precise visualization of membrane protein dynamics. The replay is still available on Youtube!
Lots of webinars
Throughout the year, many webinars hosted by FBI members were shared with the community. These events provided opportunities to disseminate expertise, share knowledge and present the latest developments.
Several Working Groups also held online meetings, ensuring continued exchange even when in-person events were not possible.
Conquering new audiences
General public events
This autumn, two FBI microscopy platforms invited the public to dive into the fascinating world of microscopy!
The Montpellier Ressources Imagerie platform presented “Life is Beautiful,” a photography exhibition showcasing microscopy images at several public events. This project was awarded funding through an EVOLVE call.
IMAG’IC, the Institut Cochin imaging platform, participated in the CNRS “Visites Insolites,” offering visitors a rare opportunity to access usually restricted scientific spaces and discover science in unexpected ways.
Looking for industrial partners
Our Business Engineer, Samy Al-Bourgol, represented France-BioImaging at several trade shows targeting the industrial sector.
From environment and health to cosmetics and materials science, he presented the wide range of services and expertise offered by FBI platforms to industrial partners.
We hope you enjoyed this overview of our 2025 activities and discoveries! We look forward to continuing these collaborations and welcoming you again in 2026 for new projects and shared initiatives!
A recent research project led by Margaux Delaporte, Céline Raguénès-Nicol and Michel Samson (collaboration between Irset Institute and H2P2 platform) has introduced a new imaging protocol to explore the immune microenvironment of human hepatocellular carcinoma using multiplex immunofluorescence. Let’s take a closer look!
Understanding tumor heterogeneity through the immune microenvironment
Hepatocellular carcinoma (HCC) is characterized by pronounced intra- and inter-tumor heterogeneity, which represents a major challenge for the development and efficacy of targeted therapies. The immune microenvironment plays a central role in disease pathogenesis and in the response to treatment. Gaining a better understanding of this complexity requires approaches that can identify immune cell populations, their functional states, and their spatial organization within tumor tissue.
A multiplex immunofluorescence strategy based on Cell DIVE
In this study, Delaporte et al.1 present a multiplex immunofluorescence (mIF) protocol based on the Cell DIVE technology, enabling the simultaneous detection of multiple protein markers on a single section of human hepatocellular carcinoma. The aim of this approach is to perform detailed immunophenotyping of the tumor microenvironment while preserving tissue architecture.
Cell DIVE relies on successive cycles of immunofluorescent staining, high-resolution image acquisition, and chemical inactivation of fluorochromes. Images from each cycle are aligned using nuclear DAPI staining as a common reference and assembled to generate a final multiparametric image of the entire tissue section. Image analysis is performed using open-source tools, notably QuPath, for cell segmentation and phenotyping.
Schematic summary of the workflow for tissue processing, antibody preparation, image acquisition, and treatment
A multiparametric view of the tumor immune ecosystem
The protocol is based on a 20-marker panel combining cellular positioning markers, structural markers of normal and pathological liver tissue, vascular markers, and markers identifying major myeloid and lymphoid populations. Markers of lymphocyte activation, exhaustion, and immune checkpoints are also included to explore the functional status of immune cells within the tumor microenvironment.
This approach enables the generation of a multiparametric, single-cell-resolution spatial map of the immune microenvironment in HCC from a single histological section. It allows the spatial distribution of immune cells and their relationships with tumor and vascular structures to be investigated, while remaining compatible with human samples commonly available in translational and clinical research. The authors also indicate that the methodology can be applied to the study of liver immune infiltration in other pathological contexts and adapted to tissues beyond the liver.
Example of final mIF image of human hepatocellular carcinoma whole slide. For visualization purposes, only 5 markers are displayed: WGA (yellow), CD4 (orange), CD20 (green), CD31 (red), CD68 (blue) and DAPI (gray). Scale bar represents 2 mm.
Technical constraints and practical considerations
The main limitation of this protocol is the requirement for access to a Cell DIVE imaging system, which is essential for multiplex image acquisition. The repetition of staining cycles may also pose challenges for fragile tissues, as tissue detachment can compromise image alignment. In addition, the cell segmentation approaches used are primarily optimized for nuclei and may be less suitable for cells with complex or non-rounded morphologies.
Expanding the applications of multiplex spatial imaging
Overall, this protocol highlights the potential of multiplex imaging technologies to overcome the limitations of conventional histology. By combining immunophenotyping with spatial information at single-cell resolution, it provides a powerful framework for studying the immune microenvironment of hepatocellular carcinoma and contributes to a deeper understanding of tumor heterogeneity in human tissues.
1 Delaporte M, Guillout M, Bellaud P, Sébillot A, Turlin B, Pécot T, Samson M, Raguénès-Nicol C. Protocol for studying the immune microenvironment of human hepatocellular carcinoma by Cell DIVE multiplex immunofluorescence imaging. STAR Protoc. 2025 Sep 19;6(3):103946. doi: 10.1016/j.xpro.2025.103946. Epub 2025 Jul 11. PMID: 40652508; PMCID: PMC12274908.
Read their scientific article and access to the detailed protocol here.
The replay of the 1st edition of FBI Connect is now available on YouTube! During this session, we welcomed Robert Quast from the CBS in Montpellier. Robert is a biochemistry researcher specializing in the characterization of membrane protein dynamics.
In this neuroscience-focused webinar, he presented his latest project and introduced a unique multicolor single-molecule FRET technique available in France to study G protein-coupled receptor dynamics. He also illustrated its application through a concrete neuroscience project aimed at better understanding the mechanisms of metabotropic glutamate receptor activation and regulation.
To watch or rewatch the webinar, click on the image below!
We were honored to represent France-BioImaging in Beijing during the Third Sino-French Joint Meeting on BioImaging, held from November 4 to 6, as part of the 30th anniversary celebrations of the CNRS China Office.
This landmark event gathered nearly 100 scholars, researchers and industry representatives, including a delegation of 10 French experts and over 20 leading Chinese specialists led by CAS academician Cheng Heping. The meeting was co-hosted by the Biophysical Society of China (BSC), the CNRS International Research Network for BioImaging (IRN BioImage), the CAS Institute of Biophysics, the Beijing Laboratory of Biomedical Imaging, and the CNRS China Office.
Fostering scientific cooperation through technological innovation
Under the theme “Innovation in Biomedical Imaging Technologies and Facility Development”, the forum featured:
plenary talks and scientific workshops,
technical sessions on advanced multimodal imaging,
facility visits of the National Biomedical Imaging Center (NBIC), showcasing China’s research infrastructure dedicated to biomedical imaging.
We explored major advances in MINFLUX, SIM, STORM imaging, correlative light and electron microscopy, miniature two-photon microscopy, in vivo neuronal activity recording, tissue clearing and data visualization, while also exchanging experience on the construction and operation of imaging centers.
Specialized training sessions combining theory and hands-on practice enabled Chinese participants to translate innovation into real research capabilities, ashared priority for the IRN BioImage community.
Strengthening strategic partnerships
Within the broader CNRS strategy in China, this mission reaffirmed the central role of the IRN BioImage as a structuring instrument for long-term scientific cooperation. By uniting leading research infrastructures, training initiatives, and technological development efforts in bioimaging, the IRN is not only advancing joint research but also building a shared vision for future large-scale scientific partnerships. As part of France-BioImaging, we see this network as a strategic driver, enabling France and China to jointly shape the next generation of biomedical imaging innovations, facilities and expertise.
Looking ahead: Bordeaux 2026
The meeting concluded with the announcement that the Fourth Sino-French Joint Meeting on BioImaging will take place in Bordeaux, France, in October 2026, a milestone we are proud to help deliver.
For France-BioImaging, this mission was a powerful opportunity to deepen our shared research ambitions, strengthen our international network, and accelerate innovation in multimodal bioimaging.
A big thank you to the organizing teams, our Chinese partners, and all CNRS and France-BioImaging colleagues who contributed to these rich exchanges and to the strengthening of our cooperation.
Last month, Samira Benadda, Head of the core imaging facility at IBENS (France-BioImaging Paris Centre node) was invited to the 4th Annual ABIC Meeting, held in Cairo and bringing together the African community specialized in biological imaging. Samira co-coordinates the Africa division of France-BioImaging with Jean-Luc Verdeil, Researcher at CIRAD. The event highlighted the Africa-France initiative, supported by France-BioImaging, which is committed to promoting and strengthening access to imaging technologies through expertise sharing, training, and the development of sustainable collaborations.
Working closely with ABIC, Samira presented the activities and achievements of the Africa division, including the grants obtained by Global BioImaging which have enabled the hosting of African researchers within the France-BioImaging nodes, facilitating access to imaging technologies for both research projects and professional training. The meeting also provided a major opportunity to discover and better understand imaging infrastructures in Africa, their needs, their organization, and the prospects for collaboration. Exchanges with local platforms emphasized the importance of supporting capacity building and fostering broader access to advanced imaging technologies.
This participation has thus contributed to strengthening existing partnerships and encouraging the emergence of new collaborations.
France-BioImaging and all the French community aims to develop and promote innovative imaging technologies and methods. But microscopy images can also take an artistic, creative look and make the invisible world beautiful, allowing people to see the visual appeal of the life sciences.
We enjoyed the diversity of the images submitted with many different microscopy techniques, models and applications represented. A big thank you to all the participants!
The National Coordination Team and the Executive Board are proud to announce the winners of the FBI Image Contest 2025:
1st Place: Nicolas Barois, BioImaging Center Lille (BICeL)
Gut Flower-Flora
Cross-sectional view of a thin slice of mouse gut. By cutting a thin slice of the gut, the inner went out. Normally I cut the gut in small tubes, which are cut in two longitudinal pieces. I kept this piece because I was curious to see it with the SEM. Scanning Electron Microscopy
2nd Place: Vishwadeep Mane, Plant Reproduction and Development Laboratory (RPD, ENS Lyon)
The Puzzled Awakening
Cotyledons, the first leaves of a plant, break free from the seed to launch life after germination. Emerging as a pair, they unfold into a nearly perfect, circular lamina that captures light for photosynthesis. At the microscopic scale, their surface reveals a mosaic of interlocking puzzle-shaped cells, dotted with stomata. These intricate cell shapes are nature’s solution to balancing internal pressure, relieving mechanical stress, while guiding growth into a robust and harmonious form. Between the cotyledons rises the first genuine leaf, a quiet promise of the plant’s future. Cotyledons mark the awakening of life, and in their puzzled cells, we see both resilience and beauty. Confocal Laser Scanning Microscopy
A recent study published in The Journal of Neuroscience highlights the successful collaboration between the Normandie and Bordeaux nodes of France-BioImaging. Researchers from UMR INSERM 1245 (Rouen), in partnership with the Rouen University Hospital, UMR INSERM 1237 (Caen), the Institut des Neurosciences des Saints-Pères (Paris), the PRIMACEN imaging platform (Rouen) and the Bordeaux Imaging Center (BIC), investigated the role of the endothelial NMDA receptor in the positioning and differentiation of cortical oligodendrocytes.
Using a conditional gene knockout model, the team demonstrated that the absence of this endothelial receptorleads to impaired myelination during development. These defects include reduced myelin sheath thickness and an increased number of axonal mitochondria, as observed by transmission electron microscopy (TEM) performed at the BIC. For TEM, the project received support from France-BioImaging through the Euro-BioImaging user access portal.
Importantly, these structural alterations were associated with long-lasting motor deficits in adult mice. The findings provide new insights into how disruptions in oligodendrocyte-vascular interactions contribute to white matter lesions associated with prematurity, which in severe cases can lead to cerebral palsy.
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A: 3D model visualizing oligodendrocyte precursors (green) migrating along cortical vessels (red) in 2-day-old mice. B: Electron microscopy images of the corpus callosum of wild-type (left) and endothelial NMDA receptor knockout mice (right) at 15 postnatal days. Receptor knockout results in reduced myelin sheath thickness (arrowheads) and increased number of axonal mitochondria (arrows). C: Impairments of the myelination process are associated with motor disorders persisting in young adult mice (P45).
This collaboration illustrates how complementary expertise across France-BioImaging nodes can advance the understanding of complex neurodevelopmental mechanisms.
DNA-PAINT is a super-resolution imaging technique that relies on the transient binding of short fluorescent DNA “imager” strands to complementary “docking” strands attached to the target structure. Each binding event produces a localized burst of fluorescence that can be precisely detected and accumulated to reconstruct the image at nanometer resolution.
However, one major limitation remains: imager strands that are not bound continue to diffuse in the sample and emit fluorescence, creating background signal. This prevents researchers from using high imager concentrations and significantly slows down the acquisition process.
To overcome these limitations, a research team led by Yves Mely at the Laboratory of Bioimaging and Pathology (Strasbourg University) in collaboration with a team led by Alain Burger (Nice Institute of Chemistry) developed a new approach that incorporates a dark donor dye into the imager strand. A dark donor is a dye that remains almost non-fluorescent on its own but can transfer its energy to a nearby fluorescent acceptor when the two are brought together. In this system, the modified nucleobase X acts as the dark donor: it stays essentially dark in solution, but when the imager hybridizes with the docking strandlabelled with ATTO 647N, X activates the acceptor’s fluorescence. As the signal appears only during true binding events, this fluorogenic behaviour markedly reduces background noise and enables the use of higher imager concentrations.
Schematic of the DRET-DNA PAINT concept. Oligonucleotides containing the dark donor X as a nucleoside substitute act as imager strands and transiently bind to the docking strands labeled with the acceptor dye ATTO 647N. This leads to DRET from X to ATTO 647N and thus to the turn-on of the acceptor emission
Single-molecule experiments confirm that the system maintains binding kinetics compatible with DNA-PAINT, and that fluorescence increases roughly 50-fold upon duplex formation. The method was then applied to fixed HeLa cells: microtubules were reconstructed in around 30 seconds, with a resolution of ~50 nm and a median localization precision of 18 nm. By comparison, classical DNA-PAINT required 30 minutes to reach a similar result.
When compared to FRET-PAINT, a variant of DNA-PAINT in which fluorescence is generated through energy transfer between a donor and an acceptor dye brought together during hybridization, the dark-donor strategy showed a clear advantage. FRET-PAINT can suffer from signal leakage, as the donor dye may emit light in the acceptor detection channel. In contrast, the dark-donor system produced far less leakage, leading to cleaner images while preserving a similar acquisition speed.
Composite of TIRF projection and super-resolution image reconstruction of microtubules in HeLa cells. a) DRET-PAINT with 100 nM S-Im imager strand and 30 seconds of imaging time. b) FRET-DNA PAINT with 100 nM S-Im imager strand and 30 seconds of imaging time c) DNA-PAINT with 1 nM of imager stand and 30 min of acquisition time. d) DNA-PAINT with 100 nM S-Im imager strand and 30 seconds of imaging time. Scale bar is 5 µm.
The main limitation of this first-generation system lies in the photobleaching of ATTO 647N, which shortens the usable imaging time. The authors suggest possible improvements, including the use of more photostable acceptor dyes or the development of new donor–acceptor pairs with enhanced brightness to support longer and higher-resolution acquisitions.
Overall, this work provides the first proof of concept that dark-donor DNA-PAINT can deliver fast, low-background super-resolution imaging and could become a valuable addition to the growing set of DNA-based nanoscopy tools.
F-BIAS is a professional network that brings together bioimage analysts across France. Hosted within France-BioImaging core facilities, its mission is to support researchers with high-quality expertise in image processing and analysis. Created in 2021, the network provides analysts with a strong community where they can share technical and methodological knowledge, and collaborate on innovative solutions.
F-BIAS also offers a monthly Open Desk in bioimage analysis: short sessions with imaging experts where you can ask any question related to image processing challenges you encounter in your research projects. If you need guidance in bioimage analysis, this is the perfect place to start!
No Open Desk available, or need more time to address your issue? F-BIAS also provides collaborative projectsupport for more complex requests that require customized tools and a significant time commitment from analysts.
Join the network, discuss the challenges you face with your microscopy data, and let our experts help you find the best solutions!
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