For the 2026 edition of the CNRS “Visites Insolites”, four France-BioImaging member research institutes and imaging facilities will open their doors to the general public. The Institut Fresnel, IBDM, the IMAG’IC facility at Institut Cochin, and theImagoSeine facility at Institut Jacques Monod will welcome visitors in October for a series of hands-on activities and demonstrations exploring imaging, light and the hidden world of living systems. Find out more about each event below.
Please note: registration for all four events closes on 20 September 2026.
Institut Fresnel: Photonics is fantastic!
Hervé Rigneault’s MOSAIC R&D team, together with the Photonics facility, will introduce visitors to the fascinating possibilities of manipulating light to reveal what cannot be seen with the naked eye, through interactive experiments and demonstrations.
Institut Jacques Monod: Take a closer look at your plate with flow cytometry
The flow cytometry unit of the ImagoSeine facility will invite visitors to discover the hidden world of living organisms found in our food. Participants will also have the opportunity to visit the facility and discover some of its imaging equipment.
At IBDM, the visit will focus on developmental biology and the earliest stages of life. Through hands-on activities and observations using a stereomicroscope, visitors will explore this otherwise invisible world and discover how scientists study the first steps of development.
Institut Cochin: Biomedical research – a journey into the heart of cells
The IMAG’IC imaging facility will welcome visitors for an exploration deep inside cells using fluorescence imaging. Participants will also be able to build their own mini optical microscope, the Foldscope, which can be used with a smartphone.
And there’s more to come! The following weekend, several laboratories and imaging facilities will also open their doors for the Fête de la Science. Check what is happening near you and take the opportunity to discover even more behind-the-scenes science!
The In Vivo Imaging Unit of the PFIC at Gustave Roussy together with the Revvity team invite you to a half-day session dedicated to in vivo imaging instruments and their preclinical applications.
The event will take place on October 2, 2026, from 12:00 PM to 5:00 PM and will focus on photonic imaging and micro-computed tomography.
The programme will include:
A presentation of in vivo imaging applications
Practical demonstrations on IVIS and Quantum GX3 imaging systems
Planning to attend? To help tailor the presentations and demonstrations to participants’ projects and areas of interest, please complete and return the dedicated form available below, before September 25, 2026.
The Institut Pasteur (France-BioImaging Paris Centre Node) is organizing a seminar in collaboration with Exciting Instruments on September 21, 2026, in Paris. This event will be dedicated to single-molecule fluorescence methods and how they can complement structural biology and biophysics workflows.
Structural biology methods such as cryo-EM and X-ray crystallography provide powerful snapshots of biomolecular systems. This seminar will explore how smFRET and FCS can add a dynamic layer by revealing conformational changes, biomolecular interactions and heterogeneous populations directly in solution.
On the program
1:30 – 1:45 PM Welcome and Introduction – Dr. Patrick England & Dr. Audrey Salles
1:45 – 2:30 PM See your favorite biomolecules in action – Easy-to-use single-molecule fluorescence tools to observe biomolecular dynamics and interactions – Dr. Roman Renger (Exciting Instruments, Sheffield, United-Kingdom)
2:30 – 3:00 PM Peptides at the membrane interface: quantifying binding, understanding translocation – Dr. Alexandre Chenal (Institut Pasteur, Paris, France)
3:00 – 3:30 PM Coffee Break and discussions
3:30 – 4:00 PM Fantastic biomolecules and how to find them – Dr. Steven Quinn (University of York, United-Kingdom)
4:00 – 4:30 PM Q&A and closing remarks
4:30 – 6:00 PM One to one discussions between Exciting instrument scientists and researchers interested in testing single-molecule fluorescence on their biological system
As we have a limited number of seats, we encourage you to secure your place by registering below.
As part of the BIOGEN project, supported by the French National Research Agency (ANR-24-INBS-0005 FBI BIOGEN), some facilities within France-BioImaging are progressively acquiring or upgrading advanced microscopy systems. These investments support a coordinated equipment mutualisation strategy, aligned with key priorities of the infrastructure, including super-resolution imaging and single-molecule tracking.
Among them, the ImagoSeine facility at the Institut Jacques Monod (Paris-Centre node) has recently strengthened its capabilities with the acquisition of a Stellaris TauSTED microscope.
This next-generation confocal system enables:
Imaging deeper in the far-red spectrum thanks to an extended white light laser,
3D super-resolution imaging using STED technology, reaching resolutions down to ~70 nm,
Reduced phototoxicity and photobleaching through TauSTED, leveraging fluorescence lifetime information to improve resolution without increasing laser power, a key advantage for live-cell imaging
Open to both academic and industrial users, this system supports a wide range of samples, from cells and tissues to organoids, embryos and whole organisms. The microscope is already contributing to studies on protein colocalisation in yeast membranes and chromosome dynamics during cell division.
This first example highlights how France-BioImaging is implementing its strategic roadmap by reinforcing access to cutting-edge technologies across its network. More updates will follow as the BIOGEN initiative progresses!
Researchers from the University of Rouen (INSERM UMR1096, EnVI Laboratory), in collaboration with engineers from the Normandy microscopy platform PRIMACEN, both members of France-BioImaging, have identified genetic and cellular remodelling mechanisms of the cardiac lymphatic system in mice with cardiovascular diseases. This work provides new insights into the mechanisms underlying cardiac lymphatic dysfunction(1).
PRIMACEN, a platform at the heart of the project
As part of a research project dedicated to cardiovascular diseases, the PRIMACEN microscopy platform played a central role in the study of cardiac lymphatic vessel remodelling. The platform was selected for its expertise in microscopy applied to complex biological tissues and for its ability to support advanced imaging strategies.
Seeing to understand: the key contribution of light microscopy
While molecular approaches, including transcriptomics, revealed disease-associated genetic changes, microscopy was essential to visualise and validate these findings at the cellular and tissue levels. Light microscopy enabled direct observation of cardiac lymphatic structures and their organisation.
3D imaging to uncover cardiac lymphatic remodelling
Using advanced microscopy techniques, including light-sheet microscopy and deep confocal imaging, researchers accessed a three-dimensional view of the cardiac lymphatic network, not achievable with conventional histological sections. This approach demonstrated, for the first time, the presence of valves within cardiac lymphatic capillaries and loss of these structures in mice with cardiovascular disease.
Figure 4: Modification of cardiac LEC [Lymphatic endothelial cells] subpopulations post-TAC in BALB/c. (D) Examples of cardiac lymphatic valves in healthy versus post-TAC mice (Lyve1 [lymphatic marker], gray; Podocalyxin [blood capillaries marker], red; yellow arrows: lymphatic valves in capillaries, white arrowheads: valved precollectors. Scale bar, 200 µm. (E) Quantification of lymphatic capillary valves (n = 5 mice/group) in sham (white circles) and TAC (black circles), and assessment of average lymphatic intervalve distances. ##P < 0.0079 Mann–Whitney U test. Data shown as mean ± s.e.m.(Heron, C., Lemarcis, T., Laguerre, O. et al. Molecular determinants of cardiac lymphatic dysfunction in a chronic pressure-overload model. EMBO Mol Med 18, 325–355 (2026). https://doi.org/10.1038/s44321-025-00345-w)
Towards a better understanding of cardiac lymphatic dysfunction
These results highlight a link between lymphatic valve loss and impaired cardiac lymphatic drainage. By combining tailored 3D imaging and complementary transcriptomic analyses, the Rouen branch of France-BioImaging node contributed to the identification of new markers of cardiac lymphatic remodelling, opening new avenues for research into cardiovascular diseases.
Schematic view of the cardiac lymphatic dysfunction mechanism. (Heron, C., Lemarcis, T., Laguerre, O. et al. Molecular determinants of cardiac lymphatic dysfunction in a chronic pressure-overload model. EMBO Mol Med 18, 325–355 (2026). https://doi.org/10.1038/s44321-025-00345-w)
(1) Heron, C., Lemarcis, T., Laguerre, O. et al. Molecular determinants of cardiac lymphatic dysfunction in a chronic pressure-overload model. EMBO Mol Med 18, 325–355 (2026). https://doi.org/10.1038/s44321-025-00345-w
Registrations for SPRINT 2026 are open! This five-day intensive training course dedicated to photonic microscopy will take place from March 16 to 20, 2026 in Paris.
SPRINT 2026 is designed to train researchers and engineers in the practical mastery of advanced imaging techniques, with a particular focus on acquisition speed and resolution.
The program combines theory and intensive practical sessions on cutting-edge equipment, covering:
Widefield,
Confocal Microscopy,
Dynamic Imaging,
Light-sheet,
Super Resolution (STED),
Holotomography,
Expansion Microscopy,
Image Analysis.
General information
Practical information
Location: Gustave Roussy, Plateforme d’Imagerie et Cytometrie PFIC, Pavillon de Recherche nr2, 20 Rue du Dr. Pinel 94800 Villejuif
Participation Fee: €250 per person. This amount covers pedagogical costs, consumables, lunches, and coffee breaks for the five days.
Registration details
Target Audience: Researchers, engineers, post-docs, and phD students with a foundational knowledge of microscopy.
Capacity: Strictly limited to 10 participants to ensure optimal supervision and maximum hands-on time with the equipment.
How to Apply: A selection process will be applied due to the limited number of places.
Application Deadline: January 31, 2026
To submit your application: Simply send your letter of motivation to the following address: tudor.manoliu@gustaveroussy.fr
The Rhône-Alpes node, co-led by Xavier Jaurand and Olivier Destaing, unites the imaging communities of Lyon and Grenoble. With platforms such as ISDV and LyMIC, and several R&D teams, the node covers a broad range of applications from metabolic imaging to spatial transcriptomics. Recent years have seen major scientific publications and significant technical upgrades. Looking ahead, the node aims to expand training, foster joint technology developments, and will proudly host the infrastructure Annual Meeting in 2027, while deepening collaborations within Euro-BioImaging.
Could you introduce yourself and your role within the Rhône-Alpes node?
The Rhône-Alpes node brings together the large imaging communities of Lyon and Grenoble. I’m Xavier Jaurand and I’m co-leading the node with Olivier Destaing. This way of co-sharing responsibility is at the heart of our project in order to have synergy of both science-technology and Grenoble-Lyon communities. This organization has been transposed at the different levels of our node, through duo of peoples from Lyon and Grenoble invested in the multiple working group of FBI.
[Xavier Jaurand]: I’m the technical director of the “Centre Technologique des Microstructures (CTµ)”, a microscopy core facility of University Claude Bernard Lyon1, where I have been working for 20 years now, mainly in the field of electron microscopy (SEM and TEM).
[Olivier Destaing]: I am DR2-CNRS and co-leader of a research team on the cell biology of invasion processes and their associated signaling regulations. Implicated in imaging development and optogenetics since many years, I am also the co-scientific leader of the imaging platform MicroCellof the Institute for advanced Biosciences (IAB).
Having organization with shared responsibilities is always a challenge and take time, but present the advantages of being potentially highly robust and well accepted by large communities.
Which platforms and R&D teams compose your node?
There are 2 main platforms on the nodes (ISDV and LyMIC):
For the Grenoble part, the ISDV (Imagerie Science du Vivant) network is composed by 7 platforms (LBFA, Liphy, PIC-GIN, ME-GIN, MicroCell-IAB, MuLife-CEA, TIMC, M4D-IBS)
For the Lyon part, the associated facility is LyMIC (Lyon Multiscale Imaging Center) which is the federation of 3 imaging platforms: PLATIM (south of Lyon), CIQLE (east of Lyon) and CTµ (north of Lyon).
There are both biology and Physics R&D teams:
ILM UMR5306 Team Dehoux – Unique expertise in Brillouin microscopy for imaging cells and tissues at various scales.
RDP UMR5667 Team Ingram – Measuring cell hydrostatic pressure and cell wall properties is challenging but of critical importance in the field of plant biology.
IGFL UMR5242 Team Enriquez/Ghavi-Helm – The Spatial-Cell-ID EQUIPEX facility enhance the spatial resolution of MERFISH by pinpointing transcripts of specific genes (ranging from a few to thousands) in situ, achieving cellular and subcellular precision over time.
IAB UMR5309 Team Destaing – the lab is focused on coupling optogenetics, biosensors and metabolism imaging through FLIM imaging.
Liphy UMR5588 Team Dupont – The OPTIMA team brings together expertise in imaging (optical, acoustic, X-ray) to develop new instruments, explore the physics of wave-matter interactions, and address biological and biomedical challenges where its scientific and technical know-how provides significant added value.
Liphy UMR5588 TeamDébarre – The MC2 team conducts interdisciplinary research at the crossroads of mechanics, physics, and life sciences to investigate, across scales, the dynamics and interactions of biological or bioinspired systems in complex environments.
GIN U1216 Team Pernet-Gallay– The electronic microscopy facility is located at the Grenoble Institute for Neuroscience (GIN, INSERM U1216, UGA) and proposes classic epoxy resin embedding for morphological analysis, as well as the Tokuyasu protocol for immunogold labeling on cryosections.
Which are the main application domains of your node?
Biomechanics: from single molecule to tissue, from animals to plants
Spatial cell transcriptomics
3D multiscale imaging through development in adaptive optics or original analysis of deep FIB-SEM acquisition
3D and high content image processing
Can you share a scientific or technical success achieved within your node?
Over the past two years, our node’s scientific impact is reflected by the co-authorship of our core facility staff in several high-profile publications, covering topics from immunology to molecular imaging and dermatology:
Functional diversity of NLRP3 gain-of-function mutants associated with CAPS autoinflammation (2024) J Exp Med. doi.org/10.1084/jem.20231200
Sperm motility in mice with Oligo-astheno-teratozoospermia restored by in vivo injection and electroporation of naked mRNA (2024) eLife. doi.org/10.7554/eLife.94514.1
Nanoassemblies of Chitosan-Based Polyelectrolyte Complexes as Nucleic Acid Delivery Systems (2024) Biomacromolecules. doi.org/10.1021/acs.biomac.4c00054
Dermal stiffness governs the topography of the epidermis and the underlying basement membrane in young and old human skin (2024) Aging Cell. doi.org/10.1111/acel.14096
Plasmacytoid dendritic cell sensing of hepatitis E virus is shaped by both viral and host factors (2024) Life Sci Alliance. doi.org/10.26508/lsa.202503256
On the technical side, our node has recently strengthened its infrastructure and expertise through major investments and upgrades, ranging from state-of-the-art microscopy systems to reinforced image analysis capacities and dedicated staffing:
Purchase and deployement of new and unique material at Lyon: AFM coupled to an inverted epifluorescence microscope, equipped with a motorized and piezoelectric stage (Hybrid Stage) that enables the acquisition of measurements on samples extended in the plane (e.g., tissue sections) or in height (e.g., whole tissues/organs).
Upgrade of confocal microscopy ressources: We replaced our aging Leica SP5X with a Leica Stellaris 5, featuring TauSense temporal dimension imaging and a resonnant scanner. Funding was secured through a strategic partnership between the university, region, and internal investment. A new spinning disk system was integrated to a FastFLIM-TIRF module in order to provide new metabolic imaging possibilities in 4-5D.
Enhance STED FLIM capabilities: We equipped our Abberior STED system with a FLIM module, delivering super-resolved temporal imaging with < 40 nm spatial resolution while preserving excellent time and signal fidelity. This integration enables dynamic, quantitative imaging of molecular interactions and environments.
Strengthen image-analysis infrastructure: We deployed three dedicated workstations equipped with AI-assisted tools such as for segmentation and analysis. These platforms enable advanced processing, rapid 3D visualization, and robust quantification, empowering both academic and translational research workflows.
Launch of a permanent image-analysis engineer role: In 2025, we transitioned from temporary contracts to a permanent research engineer position specialized in image analysis. This ensures stable expertise in AI-driven segmentation, 3D visualization, and quantitative imaging. The engineer also leads user training and engages actively in national (FBI) and European (NEUBIAS) working groups.
What are your perspectives following your node’s integration into France-BioImaging?
Following our integration into France-BioImaging, we aim to foster stronger connections between AURA’s users (academic users and private companies) and the opportunities offered by the infrastructure. We also seek to highlight and transfer original technologies (Brillouin imaging and quantitative RICM), improve access to advanced data management and image analysis to our user, and democrate these cultures to the numerous biology laboratories of Rhône-Alpes. We also plan to contribute to Euro-BioImaging initiatives, all while enhancing our international visibility.
To achieve these goals, our node is committed to participating in expert working groups (RTmfm network and FBI), deploying nationally shared training modules and engaging in joint technology developments in 3D tissue imaging, sample clearing, and multimodal microscopy. We will also continue to strengthen data and AI workflows, and we are proud to be preparing the organization of the France-BioImaging Annual Meeting in 2027.
Your node has recently joined Euro-BioImaging, what added value do you think you bring to the European community?
As part of a Euro-BioImaging fellowship, the MicroCell platform at IAB Grenoble hosted Sarah Vorsselmans and Susana Rocha (KU Leuven, Belgium). Together, we worked on the development of innovative FRET-based multiplexing molecular tension sensors, strengthening transnational expertise in molecular imaging
In April 2025, the LYMIC platform welcomed a job shadowing candidate from Germany for ten days. This exchange provided an opportunity to share practices on biological sample preparation for electron microscopy, as well as image analysis, data storage, and quality management.
This autumn, two France-BioImaging microscopy platforms are inviting the public to dive into the fascinating world of microscopy! Discover their upcoming events.
“Temps d’Expo” in Pézenas – October, 24th to November, 2nd
IMAG’IC
IMAG’IC, the Institut Cochin imaging platform, will take part in the CNRS “Visites Insolites”, giving the public a rare chance to explore usually inaccessible scientific spaces and experience science in unexpected ways!
Applications are mandatory to join this visit and are open until September, 17th. Apply here
When? October, 8th – Starting from 13:30
These events offer the public a chance to discover the fascinating world of science, and microscopy in particular, through accessible and engaging formats, from art to playful experiences.
The NeurImag cellular and molecular imaging Facility, member of the Paris Centre Node of France-BioImaging, has initiated the development of a new tool called ExoJ, in collaboration with the teams of Guillaume Van Niel (CRCI2NA, Nantes University), Frederik Verweij (Utrecht University), Thierry Galli (IPNP, Inserm, Université Paris Cité) and Junjun Liu (Shandong First Medical University).
What is ExoJ?
ExoJ is a plugin developed for the Fiji/ImageJ2 software, specifically designed to automate the reliable detection and analysis of exocytosis events from fluorescence microscopy images. Exocytosis is a cellular process where molecules or substances contained within a cell are released to the extracellular environment. This process involves the fusion of a vesicle, a membrane-bound sac, with the cell membrane. Once fused, the contents of the vesicle are expelled into the extracellular space.
How does ExoJ work?
ExoJ automatically identifies user-defined exocytosis events. It extracts key quantitative information such as the intensity, apparent size and duration of each event. ExoJ is fully parameterizable and configurable, making it suitable for studying different types of exocytosis, whatever the imaging modality (TIRF [1] and/or spinning disk [2]). ExoJ is a robust and reliable tool for analyzing large datasets!
What are the benefits of ExoJ?
ExoJ automates the detection of exocytosis events, considerably reducing analysis time compared with manual annotation. Moreover, the results obtained are reproducible, facilitating comparisons between different experiments. Finally, ExoJ is based on Fiji/ImageJ2, an open-source software widely used in the scientific community.
We are pleased to introduce Ludovic Galas, head of the Normandie node, which has recently joined Euro-BioImaging as part of the French node. In this interview, Ludovic shares his background and presents the unique strengths of the Normandie node, from its state-of-the-art imaging platforms to its scientific expertises. He also reflects on the significance of integrating into the France-BioImaging and Euro-BioImaging communities and how this connection enhances visibility, fosters collaboration and provides new opportunities for users at both national and international levels.
Could you introduce yourself and your role within the Normandie node?
Attached to the Inserm Health TechnoIogies Institute, I am a cell biologist (PhD, HDR) with a research engineer position (IR HC HEB) and former international scientific experience in the Netherlands, the United States and Japan.
I am also author and co-author of more than a hundred publications in various fields due to facility activities, awarded from the French Society of Neuroendocrinology (2003) and from Inserm (Prix Innovation, 2017), co-founder of the international master program in Cell Imaging (University of Rouen Normandie, 2004), and reviewer for international journals and national « equipment » calls. I joined in 2025 the IBiSA scientific committee and the 2026 INBS roadmap working group (MESRI).
In 2022, I was appointed as director of HeRacLeS (Inserm US 51, CNRS UAR 2026, University of Rouen Normandie) with 7 facilities or services including the cell imaging platform of Normandie so called PRIMACENof which I am the scientific leader. I am also the head of the Normandie node of France-BioImaging managing together with Isabelle Bardou (PhD, HDR, University of Caen Normandie), applications to calls, organizing meetings and seminars of the node and finally defining the scientific and technological node signatures but also the strategies for new equipment and associated human resource profiles. I also identify needs from Normandie node users that can be found in other FBI nodes.
Which platforms and R&D teams compose your node?
At that time, the Normandie node is composed of a single platform so called PRIMACEN which offers both advanced light and electron microscopy approaches. Thanks to expertise of human resources, we propose a full workflow from living and fixed sample preparation and labelling, image acquisition and image processing and analyses.
6 complementary R&D teams are also integrated in the Normandie node including a chemobiology CNRS team (UMR 6064-Rouen, Dr Xavier Franck), 3 Inserm teams in vascular sciences (UMR 1096-Rouen, Pr Jérémy Bellien and Dr Ebba Brakenhielm ; UMR 1237-Caen, Pr Denis Vivien ; UMR 1245-Rouen, Pr Gaël Nicolas and Dr Bruno Gonzalez), an ecotoxicology INERIS team (UMR-I 02-Le Havre, Prs Céline Boulangé-Lecomte and Frank Le Foll) and a team in microalgae biosciences (UR 4358-Rouen).
Historically, PRIMACEN and R&D teams have several common publications facilitating exchanges and collaborations within the Normandie node.
Which are the main application domains of your node?
Within the Normandie node, the first main application domain is « vascular sciences » including neurovascular dysfunction in the pathophysiology of neonatal brain, physiopathology of thrombosis/ischemic neurovascular disorders, inflammatory responses in hearts and vessels, vascular anatomy, immune cell migration and blood/hemolymph tissue perfusion in marine invertebrate models.
The second main application is related to the biosynthesis and secretion of glycoproteins with a special focus on N-glycosylation in microalgae models used as cell factories for biotherapies.
Finally, two more transversal domains are the development of new fluorescent probes and the investigation of intercellular, including cell-to-cell, communication modalities.
Can you share a scientific or technical success achieved within your node?
As a recent technical success, US 51 PRIMACEN platform (Rouen) has recently published a series of papers describing the combination of FLIM, confocal microscopy and STED nanoscopy for multi-labelling experiments in living samples (Bénard M et al.: Int J Mol Sci. 2021; Life Sci Alliance, 2024; Bio Protoc. 2025). Indeed, cell-to-cell communication via tunneling nanotubes (TNTs) is a challenging topic with a growing interest. Several innovative tools that use red/near-infrared dye labeling and employ lifetime-based imaging strategies were proposed to investigate the dynamics of TNTs in a living mesothelial H28 cell.
In a recent scientific advance, UMR 1237 PhIND (Caen) recently demonstrated that during aging, central nervous system-associated macrophages(CAMs; i.e., resident immune cells located along the brain vasculature at the interface between the bloodstream and the parenchyma) become key coordinators of the neuroimmune responses following stroke. Moreover, CAMs ensure a long-term fine-tuning of the immune responses triggered by stroke (Levard et al., Nat Neurosci 2024).
What are your perspectives following your node’s integration into France-BioImaging?
Following integration of the Normandie node into France-BioImaging, Damien Schapman, Christophe Chamot and Magalie Bénard (PhD) have contributed respectively to integration working group, training mission and Africa-France joint initiative. Marc Ropitaux, Sophie Bernard and Philippe Chan are involved in the organization of CLEM working group days (Rouen, 2026). We also stimulate the internship of Rouen master’s students in other nodes including Paris-Centre (2024), Bordeaux (2025) and Toulouse (2025)… We also developed reciprocal participation of node members to PhD monitoring committee (Audrey Salles, Paris-Centre/Normandie ; Jeremy Teillon, Bordeaux/Normandie ; Ludovic Galas Normandie/Bretagne-Loire).
Among France-BioImaging nodes, we currently envision particular collaborations with Ile-de-France Sud andBordeauxnodes.
In 2023, I benefited from a EuBi/FBI user access for FIB-SEM imaging at Imagerie-Gif. In 2024, the consortium “UR4358 (R&D Team, Dr Elodie Rivet, Rouen), Imagerie-Gif (Dr Claire Boulogne) and PRIMACEN (Dr Ludovic Galas) facilities” applied to the 2025 ANR PRC program to unravel N-glycoproteins biosynthesis and secretion in Chlamydomonas reinhardtii microalga. The project so called « Secret Story » is currently under assessment (Phase 2 ANR). Since 2023, Christophe Chamot also contributes to the Confocal microscopy training organized by Sandrine Lecart and Romain Lebars at Imagerie-Gif. Damien Schapman, Christophe Chamot and Ludovic Galas were recently invited to the OV cytology and imaging R&D team (INRAe, Versailles) to share experience in metrology and image analysis and will contribute to the next « Journées Microscopie INRAe» in November 2025.
The Normandie node has also tight collaborations with the Bordeaux node including members of the Bordeaux Imaging Center (BIC; Dr Fabrice Cordelières, Dr Christel Poujol, Jérémy Teillon, Dr Magalie Modin, Sébastien Marais, Dr Etienne Gontier, Melina Petrel and Sabrina Lacomme). Dr Magalie Bénard contributed to the STED workshop which took place in Bordeaux (2024). Dr Bruno Gonzalez benefited (Inserm UMR 1245) in 2024 from a EuBi/FBI user access for TEM imaging at BIC and a manuscript entitled « Involvement of the Endothelial N-Methyl-D-Aspartate Receptor on Vessel-Associated Positioning and Differentiation of Cortical Oligodendrocytes and on Motor Activity » is under revision in Journal of Neuroscience. Dr Etienne Gontier was invited in Rouen on June 18th 2025 to give a seminar on « 3D EM » to initiate new project on cell-cell contacts in retina and brain tissues.
If time will be sufficient, we would like to stimulate collaboration with the Alsace node (Dr Mayeul Collot, CNRS UMR 7199) as slightly initiated through a recent paper of Pfister et al. (Angew. Chem. Int. Ed. 2025, e202425276) on photoactivable fluorescent probe and Tunneling Nanotubes. We also would like to develop mechanobiology projects for vascular sciences and cell-to-cell communication.
Thanks to the FBI business developer Samy Al-Bourgol, PRIMACEN (Dr Ludovic Galas) and the Alga Biologics start-up (Pr Muriel Bardor) plan to apply next September to a “First Collaboration” call proposed by the Région Normandie in order to share knowledges and technologies. Finally, with the precious help of Caroline Thiriet (External Affairs Manager) and Marine Béraud (Communication Assistant), the Normandie Node is very enthusiastic to organize the next Annual Meeting of France-BioImaging during the second 2026 trimester.
Your node has recently joined Euro-BioImaging, what added value do you think you bring to the European community?
There are maybe two major added values the Normandie node can bring to European community. The first one is the clear opening to European and international users, whether it is collaborators or not of the R&D teams, in accordance with the strategies of the University of Rouen Normandie and the Région Normandie offering access to technological and scientific expertises. The 2024 France BioImaging call for external users led to PRIMACEN access for Dr Hamed Abbasi from the Department of Otorhinolaryngology, Head and Neck Surgery, Erasmus Medical Center, Rotterdam, The Netherlands(an interview is coming soon).
In the future, the granted open access to the new Norman imaging facility will surely:
Help to explore the complexity of physiological and pathological processes and possibly unravel new therapeutic targets,
Reinforce existing collaborations between French and international teams,
Increase the worldwide visibility of R&D teams/facility,
Increase the income of PRIMACEN through diversification of users and the associated billing process.
Thanks to our technological and scientific signatures, we are planning to offer complementary approaches to study vascular sciences in the field of Neuro- and Cardio-vascular sciences. In particular but not exclusively, Drs Zheng and Denes (USA, Hungary) will be interested in two-photon microscopy for scientific projects related to stroke or central nervous system diseases while Dr Laguesse (Belgium) will have access to ophthalmic imaging to examine post-natal development of the retina. Our new fast intravital heart imaging (2025) is already very attractive for our Canadian (Dr Ruiz) and German (Dr Zernecke) collaborators. A paper entitled “Molecular determinants of cardiac lymphatic dysfunction in a chronic pressure-overload model” submitted by Dr Ebba Brakenhielm (U1096, Rouen, Normandie Node, France) and Dr Zernecke (Institute of Experimental Biomedicine, Würzburg, Germany) is currently under revision in EMBO Mol Med. This study revealed that loss of lymphatic valves and dysregulated lymphatic barrier may underly poor drainage capacity during pressure-overload, despite potent lymphangiogenesis and preserved lymphatic endothelial cell immune attraction. This work provides tractable targets to restore lymphatic health in cardiovascular diseases.
Our workflows for CLEM will be very helpful for functionalized nanoparticles characterization (Dr Khalin, Germany) and subcellular imaging of plant (Dr TeH, Taiwan) and microalgal (Dr Strasser, Austria; Dr Pandhal, UK and Dr Molinaro, Italy) samples. Finally, our skills in FLIM-STED imaging will have a valuable impact to determine, in cellulo, the photophysical properties of new organic fluorescent probes developed by Dr Karuso in Australia, Dr Guieu in Portugal and Proimaging (Dr Urbain, french SME). Besides Norman users, fluorescence lifetime imaging and nanoscopy will also be very useful for user (Dr Kantati, Togo) needing multiplexing experiments and super resolution imaging. Dr Kantati will apply to the Global Imaging call namely “Imaging 4 all” for a project aiming at identifying molecules from plants used in traditional medicine including those with neuroprotective effects.
We also want to stimulate Master student exchanges between the University of Rouen Normandie and the University of Turku/Åbo Akademi University in Finland. Amina Berredjem (IMAC, Rouen) is currently following a 6-month internship in the Viral Oncogenesis Laboratory under the supervision of Pr Sylvia Gramolelli (Åbo Akademi University, Biocity, Turku) to optimize immunocytochemical protocols while Tehreem Fatima spent 2 months on PRIMACEN (supervisors: Dr Ludovic Galas, Thomas Bance) for FIB-SEM image processing and analysis of microalgae. Such student exchanges could also be spreat out to other French nodes.
Fluorescence microscopy allows researchers to explore the living world at the cellular and subcellular scales with remarkable precision. However, as time passes, microscopes inevitably degrade: detectors become noisy, optical systems lose alignment, and image quality declines. This aging process can hinder long-term biological studies and quantitative analysis.
To address this challenge, a team of Engineers from IBDMand LIS (France-BioImaging Marseille node) developed μPIX, a new deep-learning algorithm based on generative artificial intelligence.
A smarter way to restore microscopy images
μPIX uses a specific type of AI called a Pix2Pix conditional Generative Adversarial Network (cGAN): this algorithm learns how to transform low-quality or noisy images into clean and high-quality ones, based on examples.
Figure: µPIX architecture is based on a Pix2Pix generative network. µPIX consists of two subnetworks: a generator, based on a UNet architecture with an EfficientNet-b0 backbone, and a discriminator (PatchGAN). During supervised training, a noisy image is input to the generator, which generate an image. This output is compared to the real clean image using a pixel-wise loss function (MSE). Pairs of real and generated images are then passed to the discriminator, which classifies them as real or fake using a binary cross-entropy loss (BCE). Both subnetworks are progressively refined through adversarial loss during training. In the inference phase, only the trained generator is used to generate clean images. (Bon, Gabriel, Sapède, Daniel, Matthews, Cédric and Daian, Fabrice. “μPIX: leveraging generative AI for enhanced, personalized and sustainable microscopy” Methods in Microscopy, 2025. https://doi.org/10.1515/mim-2024-0024)
Unlike conventional image processing algorithms, μPIX adapts its training to the characteristics of the microscope, making it personalized and highly precise.
It improves image quality while preserving fine structures and intensity relationships, which is essential for quantitative imaging.
Thanks to its capacities, it extends the usefulness of old equipment, offering a cost-effective and sustainable alternative to replacement.
Better results than existing tools
In their publication, the authors show that μPIX outperforms both traditional denoising methods and popular deep learning tools such as CARE or Cellpose3.
It also improves downstream applications: using μPIX as a pre-processing step enhances segmentation accuracy by up to 3% compared to existing pipelines.
Reviving aging detectors
The team went one step further and applied μPIX to an ambitious task: restoring images from an outdated Multi-Alkali photodetector so they resemble those acquired with a high-performance GaAsP detector.
The results are impressive: μPIX manages to compensate for signal loss along the z-axis (represents the depth), recover structural information, and maintain a near-linear relationship between the predicted and original intensities, enabling quantitative analysis on images that would otherwise be considered obsolete.
From user-centered to hardware-centered AI
Unlike most AI tools that require users to train their own models, μPIX proposes a platform-centered paradigm: platforms train one model, tailored to their equipment, and provide it to their users. This approach reduces redundancy, improves consistency, and aligns with the principles of frugal and shared AI development.
The code and models are freely available on GitLab, and μPIX is already proving to be a useful asset for microscopy platforms seeking long-term performance with limited hardware budgets.
Recently, Pierre Bourdoncle, head of the IMAG’IC platform at the Cochin Institute (Paris Centre Node), and his team published a new protocol for intravital imaging of calvarial bone marrow. Today, he tells us more about their research and how it can enhance the study of diseases like leukemia.
Could you tell us a little about yourself and the project?
As the head of the IMAG’IC platform at the Cochin Institute, we have consistently advanced intravital imaging through multiphoton microscopy. For the past 25 years, we have been dedicated to enhancing intravital imaging at the Cochin Institute, with a focus on improving synchronization, laser technology, and OPO (Optical Parametric Oscillator, ed.) systems.
Why is the calvarial bone marrow such an interesting model to study hematopoiesis and vascular dynamics?
The calvarial bone marrow is an interesting model for studying hematopoiesis and vascular dynamics due to its unique anatomical features. Its thin structure allows for high-resolution imaging, facilitating the observation of cellular interactions and vascular networks. Additionally, it is easily accessible, making it ideal for experimental manipulations and real-time monitoring. This model provides valuable insights into the complex processes of blood cell formation and vascular development.
z-projection of tile scan view of the calvaria vasculature labeled by cdh5-DSRED – 2-photon microscope
Your team has developed a custom-made titanium cranial implant. What advantages does it offer compared to existing methods?
The stability of the imaging area has always been a major challenge in intravital microscopy. Indeed, the animal’s breathing and temperature variations complicate long-term acquisitions. Moreover, precise repositioning of the acquisition area over several days is essential for observing the evolution of the cellular environment. The development of titanium implants, as opposed to traditional resin 3D printing, allows for more robust fixation of the system to the microscope stage and, most importantly, limits the deformation of the implant.
(A) Parts of the implant in situ: 1 observation ring, 2 cementing feature, 3 stabilizing anchor, 4 tail, 5 dovetail, 6 threaded hole, 7 Bregma. (B) Connection of the head implant to the holder: 8 fixation body, 9 clamp, 10 eccentric lever, 11 structure, 12 microscope objective.
What perspectives does this method open for the understanding of hematological diseases, such as leukemia?
This method opens significant perspectives for understanding hematological diseases like leukemia by enabling detailed visualization of disease progression and cellular interactions. It allows researchers to study the impact of treatments in real-time, enhancing the development of targeted therapies. Additionally, it facilitates the exploration of the bone marrow microenvironment’s role in disease pathogenesis.
What are your upcoming projects?
Following the same principle, we are collaborating with the company Ymetry to develop similar appendages adapted for soft organs. Our goal remains to maintain the acquisition area for as long as possible without any drift.
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