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 IBDM and 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.

Read the full scientific article here: https://www.degruyterbrill.com/document/doi/10.1515/mim-2024-0024/html

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.

Click here to read the full scientific article!

We’re proud to announce the official integration of our two new cutting-edge imaging Nodes into the French Node of Euro-BioImaging: Normandie and Rhône-Alpes!

With this upgrade, the French Node now spans 10 geographical sites and provides access to 30 state-of-the-art imaging facilities, supporting both national and transnational users.

Why does this matter for the Euro-BioImaging community?

These new Nodes significantly expand the scope and excellence of the French Node:

Normandie Node (PRIMACEN – Rouen) brings unique expertise in:

  • Intravital imaging for vascular diseases, including brain and heart imaging
  • Microalgal biosciences and marine biology imaging
  • Advanced cryo-correlative microscopies (CLEM) and super-resolution imaging

Rhône-Alpes Node (LYMIC – Lyon & ISDV – Grenoble) enhances our capacity with:

  • Pioneering technologies in biomechanics and mechanobiology
  • Rare capacities in spatial transcriptomics, adaptive optics, and metabolic imaging
  • Deep expertise in large-volume 3D EM with integrated image analysis pipelines

These new capabilities fill critical technological and geographic gaps and will benefit users across Europe seeking access to next-generation imaging and expert support.

Users can expect powerful collaborations, robust training opportunities, and access to highly specialized platforms.

Researchers and imaging facility staff from low- and middle-income countries (LMIC) are invited to apply for access to cutting-edge biologicial and biomedical imaging technologies, training and hands-on experiences funded by the Wellcome Trust and coordinated by Global-BioImaging.

Why should you apply?

You should apply of you want to:

  • Explore new imaging techniques for your biological samples
  • Gain hands-on skills with advanced microscopy
  • Develop expertise in image analysis and imaging facility management

Imaging 4 All offers three grants and sub-tracks addressing different access needs and objectives:

  • i4A Access Grant: to access imaging facilities and laboratories of your choice to use imaging technologies and related services on offer, and to benefit from their imaging expertise.
  • i4A Pro Grant: to advance your skills in biological or biomedical imaging technologies and/or applying advanced imaging techniques to your research.
  • i4A Training Grant: to participate in a national or an international in-person training workshop or course of your choice

Who can apply?

Any researcher or imaging facility staff or management affiliated with a not-for-profit organisation (e.g. university, institute) located in a LMIC is welcome to apply.
Please check if the country of your home organisation is classified as an LMIC by using this link.

General informations

You will find more information in this article: https://globalbioimaging.org/i4a

To start the process, you must send an email at  i4a_support@embl.de before 15 August 2025.

The “Ecole physique des Houches” is hosting the 4th edition of its winter seminar dedicated to biophysical research, from March 15th to 20th, 2026. This year will be focused on the development and application of fluorescent markers for advanced fluorescence microscopy.

What is the objective?

This interdisciplinary training event aims to provide in-depth theoretical and practical knowledge on selecting and using fluorescent biomarkers for advanced microscopy techniques, such as high-resolution fluorescence imaging and single-molecule studies in living cells.

Who can apply?

The seminar is open to:

  • PhD students
  • Early-career scientists
  • Research engineers
  • Experienced researchers looking to explore new research areas

What is on the program?

A rich and interactive program including:

  • 2 introductory lectures
  • 12 advanced lectures by internationally renowned experts
  • A round table
  • A flash talk session*
  • 2 poster session evenings*

Find the complete program and all the experts below!

*All participants are required to bring a scientific poster showing their current scientific work and to participate in the flash talk session.

How to join?

When? March 15th-20th 2026
Where? Ecole de Physique des Houches
Fees? Participation is free of charge!

Applications are open until October 31th, 2025! Click here to fill your application.

The French Institute of Bioinformatics is organizing its next conference, focused on the use of generative AIs to support programming and scripting for biology, on June 13, 2025.

This event, intended for bioinformaticians and biologists, aims to share experiences, tools, and perspectives on the use of generative AIs (ChatGPT, Copilot, Devin, etc.) for developing scripts and software in biology..

Program

  • 9:00 AM – 12:30 PM: Presentations and roundtable featuring developers, researchers, educators, and trainers sharing concrete feedback and experiences
  • 2:00 PM – 5:30 PM: Hands-on workshops and closing session

Workshops are optional and limited to 50 participants. If demand is high, selection will be based on responses provided in the registration form.

General Information

Date: Friday, June 13, 2025, from 9:00 AM to 5:30 PM
Location: Université Paris Cité, 5 rue Thomas Mann, 75013 Paris
Register and learn more: https://iabioscripting.sciencesconf.org/?lang=fr
Contact: iabioscripting@sciencesconf.org

Join us on June 3rd at 14:00 for the next FBI.data webinar, where the France-BioImaging team will share the latest updates and improvements to their data management solution, and answer all your questions!

Agenda

  • Project Background and History: Overview of deployments across the France-BioImaging’s Nodes
  • Théo Barnouin: System Security Enhancements – Implementation strategies at the Nodes and collaboration with Information Security Officers (RSSI)
  • Guillaume Gay: New Project Developments – Data import scenarios and insights from user testing

How to join?

Join us here: https://umontpellier-fr.zoom.us/j/97450221050

The Executive Board of the Rhône-Alpin Node of France-BioImaging is pleased to invite you to the event “Imaging & Microscopy Day in Rhône-Alpes – Image Analysis” – pre-program attached.

It will be held on Tuesday, July 1st at the Faculté Rockefeller, 69008 Lyon

Registration here: https://docs.google.com/forms/d/e/1FAIpQLScTyOV5tjfxZp2i4j-6OmXzdLUcHa7ByMOiJPnBMkEZZkAVBg/viewform?usp=header 


During registration, we will collect proposals for:

  • User Case Presentations (16 + 4 min questions) – Ideal for PIs and established researchers
  • Short Communications (8 + 2 min questions) – Perfect opportunity for students and early-career researchers

If you have any questions, please contact the organizers:

Jacques Brocard: jacques.brocard@ens-lyon.fr
Olivier Destaing: olivier.destaing@univ-grenoble-alpes.fr
Xavier Jaurand: xavier.jaurand@univ-lyon1.fr

As the number of seats is limited, please register as soon as possible to best organize the final program!

Last weeks to apply to the last canSERV Open Call, a unique opportunity designed specifically for early career cancer researchers worldwide. This initiative aims to provide these researchers with access to cutting-edge services and training, helping them advance their groundbreaking work in cancer research.

Who can apply?

This call is open to:

  • First-stage researchers: PhD students and junior researchers without a PhD.
  • Recognised researchers: Postdoctoral fellows, assistant professors or young investigators.

What’s on offer?

Selected applicants will gain free access to imaging services and expertise provided by 36 Euro-BioImaging Nodes, as well as state-of-the-art image data analysis resources. This support empowers researchers to elevate their projects through innovative technologies and expert guidance.

Research focus areas

Your project should address one or more of the following:

  1. Cancer research topics, spanning discovery science, translational research, personalised oncology or clinical studies.
  2. At least one of the four strategic goals of the EU Cancer Mission:
    • Understanding cancer,
    • Prevention and early detection,
    • Diagnosis and treatment,
    • Quality of life for patients and their families.

Deadline?

July 15th, 2025 at 14.00 CEST

How to apply?

Find all the informations here: https://www.eurobioimaging.eu/news/final-open-call-from-canserv-more-nodes-more-services/

Our colleagues from the National Biomedical Imaging Center (NBIC) in China are organizing a summer school focused on biomedical imaging. As International Research Network partner, France-BioImaging invites you not to miss this opportunity!

Program overview

Five modules covering cutting-edge technologies applied to the biomedical field:

  • Optical Super-resolution Imaging
  • Fluorescent Probes and Optogenetics
  • Illuminating the Mechanobiology
  • In Vivo Imaging
  • Computational Imaging & Visualization

General informations

  • Training Schedule: July 14 – July 27 (2 weeks), combining lectures and hands-on workshops
  • Application Period: April 1 – June 30
  • Application Requirements: Personal statement + two recommendation letters + academic transcripts. Please send your application to beiliu@pku.edu.cn
  • Participants: Graduate students (Master and PhD students), selection of 30 students + 10 internal students
  • Training Fee: Application fee of 5000 RMB (approximatively 620€). Accommodations and meals throughout the two-week training will be fully covered by the center

Detailed schedule

NBIC-summer school v3 – EgDownload

A research team from the Laboratoire de Biogenèse Membranaire (CNRS/University of Bordeaux), in collaboration with the Bordeaux Imaging Center, has recently developed ROOT-ExM, a novel protocol enabling the application of expansion microscopy to plant tissues, specifically the primary root of Arabidopsis thaliana. This method overcomes key limitations that had so far prevented the use of expansion microscopy in plant systems.

Zoom in on expansion microscopy

Expansion microscopy (ExM) is a super-resolution imaging technique that relies on the physical enlargement of biological specimens embedded in a swellable hydrogel. By expanding the gel, the distance between fluorescent labels increases, thereby enabling nanoscale resolution with conventional microscopes.

©Donatelle Liens

The challenge of plant tissue rigidity

Plant cells are embedded in a dense network of polymers (cell walls) that provide mechanical strength and prevent expansion. These structural barriers are especially problematic for expansion microscopy, as they hinder both the penetration of labeling molecules and the isotropic expansion of the sample.

ROOT-ExM: Tailoring expansion microscopy for plants

To adapt ExM to plant roots, the team developed a two-step strategy combining:

  • A mild cell wall digestion, sufficient to relax the cell wall structure and facilitate labeling,
  • And a plant-optimized ExM protocol, compatible with common fluorescent markers and preserving tissue architecture during expansion.

Promising results

  • ROOT-ExM achieves an approximately 4-fold linear expansion of Arabidopsis roots with minimal deformation.
B) Confocal microscopy images of the same root with the same field of view before expansion and after ROOT-ExM.
– In yellow: Endoplasmic Reticulum
– In blue: Cell wall
C) Expansion factor quantification. The diameter of nuclei was measured before and after expansion.
  • When combined with confocal microscopy, this technique enables nanoscale visualization of intracellular (nuclei, Golgi apparatus) and intercellular (plasmodesmata, microtubules) structures with resolution comparable to advanced super-resolution methods.
Representative images of acquisitions in confocal on nonexpanded samples (left), super-resolution lifetime-STED on nonexpanded samples (middle) and confocal after ROOT-ExM (right). Labelling of Golgi apparatus.
  • In addition, coupling ROOT-ExM with lattice light-sheet microscopy (LLSM) allows 3D reconstructions of cellular processes at nanometric resolution and across large tissue volumes.
Volume acquisition of a root cell labeled with anti-KNOLLE (membrane marker during cell division) after ROOT-ExM and imaged by LLSM.

Looking ahead

ROOT-ExM demonstrates that super-resolution imaging of plant tissues is possible using conventional microscopes and accessible labels. While currently limited to the primary root of Arabidopsis thaliana, this protocol lays the groundwork for expanding ExM to more complex plant organs and other species. Rather than replacing high-end super-resolution techniques, ROOT-ExM stands as a complementary approach, providing an accessible, scalable alternative for plant imaging at the nanoscale.

A French-Danish team (Jacques Monod Institute — FBI Paris Centre Node & Niels Bohr Institute) has recently highlighted a new regulator of cell competition: cadherins!

How it works?

These proteins, which promote cohesion between cells, appear to facilitate the transmission of mechanical stress from one cell to another. The researchers demonstrated that colonies of cells capable of transmitting these mechanical forces are more likely to “win the cellular competition” compared to other colonies with similar characteristics but fewer cadherins — and therefore less ability to share the stress caused by mechanical forces.

These new findings open up new perspectives for understanding how cells compete within healthy tissues, and also during the proliferation of cancer cells.

As the journalists at Le Monde nicely put it: “unity is strength”!

Want to know more? Read the article here: https://www.nature.com/articles/s41563-025-02150-9

Article Le Monde figuresDownload