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.

©French Embassy in China & 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, a shared 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.

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!

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

3rd Place: Simli Dey, Membranes and Cellular Functions Team, Institut Curie

Kaleidoscope

Directing branched actin filament growth from a curved lipid membrane site.
Total Internal Reflection Fluorescent Microscopy

Congratulations to the winners!

Explore all the images submitted here:

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The France volumeEM team will meet you on December 18th at 13:00 for its next webinar!

This edition will focus on 3D imaging of bone marrow megakaryocytes, featuring Dr. Anita Michel (Head of the EM plateform MicroEleCS – UMRS 1255).

Whether you work in hematology, immunology, or as a volumeEMengineer, don’t miss this opportunity!

When? December, 18th – 13:00
How to join? https://teams.microsoft.com/meet/3623066689014?p=k8pGQVBh5fYVVoxWga

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 receptor leads 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.

Access their article here: https://www.jneurosci.org/content/45/43/e0199252025

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 strand labelled 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 project support 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!

Last month, several members of France-BioImaging took part in the opportunities offered by Euro-BioImaging’s EVOLVE project, enabling valuable exchanges and inspiring experiences.

Through the Job Shadowing initiative, Guillaume Gay, Data Engineer for the FBI.data mission and Research Software Engineer at LIRMM (Montpellier), welcomed Kenneth Ho, Big Data Systems Engineer at the Francis Crick Institute (London).

They discussed their shared challenges and solutions in microscopy data management, and this week-long visit gave them the time to delve deeply into several technical topics.

Caroline Thiriet, Deputy Administrative Director for International Relations and Industry at France-BioImaging, hosted Virginia Pierini, Service Manager at the EMBL Imaging Centre. Their discussions focused on how France-BioImaging coordinates its distributed national infrastructure, which brings together 10 Nodes and more than 30 imaging facilities across France.

©Euro-BioImaging – Fabrice Cordelières and Eva Svecova interview

Finally, Fabrice Cordelière, Head of Training for France-BioImaging and Bio-Image Analyst at the Bordeaux Imaging Center, took part in the Train-the-Trainer event, where he mentored Iva Švecová from the Light Microscopy Facility at the Institute of Experimental Medicine of the Czech Academy of Sciences in Prague. Eva benefited from Fabrice’s extensive experience in team management, user training, coding practices, and user-driven data backup workflows.

©Euro-BioImaging – Group photo of participants, trainers and members of the Euro-BioImaging Hub team

We are delighted to contribute to the EVOLVE programme, which fosters collaboration, peer learning, and mutual inspiration among Euro-BioImaging Nodes. These initiatives reinforce our shared commitment to open, coordinated, and high-impact scientific services for the life science community.

The microscopy platform of Gustave Roussy is organizing a webinar dedicated to Huygens Software on Tuesday, November 25th, at 14:00 (CET).

This event will introduce the theory of deconvolution and image restoration through three main parts:

  • Principles of Deconvolution: Dive into the theoretical foundations to better understand this key process in microscopy
  • Demonstration of Deconvolution and Image Restoration: Discover the essential features of deconvolution and image restoration, and learn how to automate these processes
  • Benefits, Limitations, and Quality Control: Identify the strengths and limitations of deconvolution while ensuring the quality and robustness of your results

You can share your own images for the demonstration and receive a direct feedback on the improvements in your restored images!

To send your files, please use the secure link here: https://svi.nl/upload

Registration is free but mandatory by simply emailing tudor.manoliu@gustaveroussy.fr

Join the webinar here: https://us02web.zoom.us/j/89769358929?pwd=aOQhDkLhJXkZnackSrYc6Aii6ZsyeU.1

Mitochondria, often described as the bioenergetic powerhouses of our cells, and more broadly of our entire organism, play a central role in metabolism. These organelles are involved in multiple metabolic processes (including carbohydrate and lipid degradation) and produce ATP (adenosine triphosphate), an essential molecule for a wide range of biochemical reactions.

Maintaining mitochondrial integrity is therefore crucial, as dysfunctions can lead to severe pathologies such as myopathies, neurodegenerative diseases or metabolic conditions like diabetes. Better understanding mitochondrial function and dysfunction is key to addressing these challenges. This understanding partly relies on the observation of mitochondria and the analysis of their morphology under different conditions.

Electron microscopy (EM) is the gold-standard technique for visualizing mitochondria, as it provides high-resolution imaging of cellular ultrastructure. However, segmentation and morphological analysis remain challenging due to the lack of contrast and color information in EM images. Existing pipelines to overcome these limitations are often time-consuming or too complex for users without experience in advanced deep-learning models.

To tackle this challenge, a research team from the Restore Institute in Toulouse, led by Mathieu Vigneau and Jean-Philippe Pradère, has developed EMito-Metrix, a computational tool designed for the automatic segmentation and analysis of mitochondria from 2D EM images.

The team created six species-specific models and one generalist model by training a segmentation algorithm with their own annotated EM images. Their results demonstrate that the tool enables highly specific detection of mitochondria according to their species of origin. With its user-friendly interface, EMito-Metrix allows users to easily visualize and analyze 26 mitochondrial metrics, presented through automatically generated graphs. In addition, EMito-Metrix includes a machine learning module that provides predictive analytical capabilities to assess how experimental factors, such as genetic mutations or drug treatments, may affect mitochondrial morphology and ultrastructure.

To validate their tool, the researchers analyzed mitochondria across the entire tree of life. More than 35 000 mitochondria were processed, with over 800 objects per species. The results obtained with EMito-Metrix are compelling, enabling precise segmentation of mitochondria by species and efficient quantitative analysis of their metrics.

The AI algorithm is capable of accurately detecting mitochondria (in colour) from tissues from different species imaged in ME (left). For each segmented mitochondrion, the tool extracts 26 morphology and ultrastructure metrics that can be displayed using graphs. The radar plot (centre) illustrates striking differences in metrics between vertebrates and invertebrates. Based on these metrics, the neural network is able to predict the class to which each mitochondrion belongs with 94% accuracy (right).

In conclusion, EMito-Metrix supports mitochondrial research by simplifying morphological analysis, saving researchers valuable time and reducing the risk of bias.

Access to EMito-Metrix solution here: https://www.emitometrix.org/

The RIC Paris-Saclay is pleased to announce the conference “AI & Image Analysis”, which will take place on Thursday, November 20, 2025, from 1:00 p.m. to 4:30 p.m. at the Paris-Saclay Faculty of Medicine (Research Building).

Organized in collaboration with the Interdisciplinary Object “BioProbe” (University Paris-Saclay), this half-day event is open to researchers, engineers, clinicians, faculty members, PhD students and students.

It will highlight recent advances in Artificial Intelligence and Deep Learning applied to cellular and tissue imaging, through presentations by both academic and industrial experts (University Paris-Saclay, University of Nantes, Institut Pasteur, École Polytechnique, Sartorius, and Nanolive).

The event will be recognized as doctoral training for the graduate schools BioSign, Cancerology (CMBS), and Therapeutic Innovation (ITFA) of UPSsaclay.

Invited speakers and titles

  • Perrine Paul-Gilloteaux (BioCore – University of Nantes) – AI in Correlative Microscopy: Unlocking the Potential of Multimodal Imaging.
  • Olivier Schwartz (Institut Pasteur) & Mathieu Fréchin (Nanolive SA) – Life in Motion: From AI-Enhanced Imaging to Cellular Process Simulations.
  • Anatole Chessel (LOB – École Polytechnique) – Understanding Complex Tissues from Microscopy Images.
  • Catherine Guettier (AP-HP / University Paris-Saclay) – Computational Pathology: From Code to Patient.

General information

Date: Thursday, November 20, 2025 – 1:00 p.m. to 4:30 p.m.
Location: Paris-Saclay Faculty of Medicine, Kremlin-Bicêtre
Free but mandatory registration: www.ric-paris-saclay.fr

Affiche_Conference_IA et AI_2025Download

Organization committee: Larbi Amazit, Régis Bobe, Laurent Combettes, Cécile Denis, Marie Erard, Evelyne Ferrary, Isabelle Garcin, Anne Guiochon-Mantel, Aude Jobart-Malfait, Valérie Nicolas, Oliver Nüsse.