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

For this second edition of Challenge, “Fuse My Cells”, we had 136 registrations and 6 participating teams. After a preliminary test phase, teams submitted their methods for evaluation on 32 images, with just one unique submission allowed!

We’re thrilled to reveal the top 3 winners of the challenge

• 1st place: Marek Wodzinski – FuseMyCells algorithm
• 2nd place: Shengyan Xu – Fuse_my_cells_dual algorithm
• 3rd place: Cyril Meyer – M²N² algorithm

What’s next?

Dorian Kauffmann, our Challenge Project Engineer, will present the results at the ISBI conference on April 17th, joined by challenge winner Marek Wodzinski!

Curious about the winning methods? You can explore the submitted algorithms here: https://fusemycells.grand-challenge.org/results/

To start, could you tell us a bit about yourself? What has been your academic journey so far, and what is your current role or area of work?

My name is Atitheb Chaiyasitdhi. I am a research fellow in Benjamin Warren’s lab at the University of Leicester in the United Kingdom. At the lab, we focus on auditory mechanotransduction and hearing loss in insects. Before joining the lab, I did my PhD at the Institut Curie in Paris, where I studied the biophysics of hearing in vertebrates.

What are you currently working on in your research? What is the main topic or challenge you’re exploring?

I have always been fascinated by how hearing works. Currently, I am investigating how insect ears operate. Unlike humans, insects possess ears in a wide variety of shapes and locations—sometimes on their legs, antennae, or abdomens. Despite this diversity, they all rely on a similar mechanosensitive structure known as a chordotonal organ. Interestingly, insects also use chordotonal organs to detect other mechanical cues, such as gravity or body position (proprioception), and these organs are located in different parts of the body as well. 

This raises two key questions:

How does the chordotonal organ convert such a broad range of mechanical forces into electrical signals? And do these organs share a common underlying mechanism?

To explore these questions, I am focusing on the chordotonal organ in the locust ear. On one front, I am using a high-speed camera to capture sound-evoked motion of the organ and electrophysiology techniques to measure electrical current in the chordotonal neurons evoked by the sound.

On another front, I am collaborating with Claire Boulogne at Plateforme Imagerie-Gif, using Focused Ion Beam Electron Microscopy (FIB-EM) to reconstruct the organ’s three-dimensional structure. These complementary approaches will provide insights into the mechanics of insect auditory transduction and bring us closer to solving the two questions I previously talked about.

At what point did you come across France-BioImaging, and what made you want to use its services or connect with the infrastructure?

I first learned about France-BioImaging during my PhD in France. At that time, I had the opportunity to collaborate with and use the excellent resources provided by one of the France-BioImaging Nodes—the Cell and Tissue Imaging Platform (PICT-IBiSA) at the Institut Curie. That experience left a strong impression on me, highlighting the expertise and support that France-BioImaging offers. Since then, I have been interested in collaborating with France-BioImaging platforms again.

Could you walk us through your experience accessing France-BioImaging? Which facility did you work with, how did the process go, and what stood out to you during your time there?

I worked with the Plateforme Imagerie-Gif in Gif-sur-Yvette, near Paris, using Focused Ion Beam Electron Microscopy (FIB-EM) with the support of Claire Boulogne, the lead engineer. Since I am based in the UK, and thanks to modern communication technology, our collaboration could start remotely. We discussed the experimental plan online, and I prepared the preliminary samples here before shipping them to the platform in France. Claire then carried out further sample preparation and image acquisition.

We worked closely, going back and forth to establish an optimal workflow, and soon began obtaining promising results afterwards. Despite the platform’s tight schedule, I always received prompt responses and consistent support from Claire.

What did microscopy bring to your project specifically? Were there insights or results you couldn’t have obtained otherwise?

The first ultrastructural image of a chordotonal organ was captured over 60 years ago, and it provided key insights into how the organ functions. In our lab, we have been able to resolve the mechanics of the chordotonal organ with unprecedented temporal resolution using high-speed cameras.

However, we still lack the spatial resolution to fully understand its structure. FIB-EM enables us to visualize the ultrastructure in three dimensions at a level of detail that has not been previously achieved. Seeing how each cellular component connects in 3D allows us to answer questions that arise from our high-speed recordings of sound-evoked motion in the organ.

At the same time, it opens up new questions and research opportunities. While there are other techniques, such as array tomography, they cannot match the spatial resolution of FIB-EM and would require hundreds of hours of manual effort.

Looking back, would you encourage other researchers to use France-BioImaging’s platforms and access program? What would you say to someone considering it?

Yes, I would. I would tell them that I have extensive experience working with France-BioImaging platforms, and the collaborations have always delivered reliable results. I trust their expertise and the quality of their support. In fact, I’ve already recommended France-BioImaging to colleagues here in the UK, as well as from the US and Germany. We are currently exploring the possibility of continuing our collaboration with Imagerie-Gif to investigate the diversity and evolution of chordotonal organs in various insect ears, even those involved in proprioception in the legs.

Celebrate the four seasons through imaging! Submit your best scientific images that capture the essence of each season, from electron micrographs of flu viruses in autumn to heat shock proteins in summer!

Who can participate?

This contest is open to all members of the Euro-BioImaging community and anyone involved in scientific imaging and research worldwide. The contest has four quarterly sessions, each linked to a season.

How to participate?

Register, submit as many entries as you like, and upload your images. Only images captured with a microscope or other imaging devices are eligible (macrophotography is not allowed).

What can you win?

Quarterly winners will receive reimbursement for travel expenses (up to 1000€) to attend a scientific conference or event. Runner-ups get up to 500€. Selected images will be featured on Euro-BioImaging’s website and social media.

Contest timeline:

• Spring: 31 Mar – 20 Jun 2025
• Summer: 21 Jun – 21 Sep 2025
• Autumn: 22 Sep – 20 Dec 2025
• Winter: 21 Dec 2025 – 20 Mar 2026

You are interested? Find more information and detailed rules here.

Last week we attended Euro-BioImaging All Hands Meeting at EMBL in Heidelberg (25-28 March 2025). It was a pleasure to gather with all our colleagues from the Euro-BioImaging nodes and discuss imaging technology innovation, data, access, training & international collaboration.

All Hands Meeting recap!

The second day, co-organized with the Euro-BioImaging Industry Board (EBIB), featured updates from Euro-BioImaging, several presentations focusing on innovations in imaging technologies, including new approaches to multispectral optoacoustic tomography, FLIM imaging modalities, and advanced 3D multiplex imaging,  high-resolution imaging, cryogenic sample preparation, and correlative imaging techniques. The day concluded with a session on Industry User Experience at Euro-BioImaging, where discussions focused on industry collaborations and access to research infrastructures.

On Thursday, the day started with an inspiring keynote lecture by Lisa Yen from Microscopy Australia on the role and impact of open-access research infrastructures in scientific collaboration. This was followed by sessions on Global BioImaging and the Imaging4All initiative, highlighting international opportunities for Euro-BioImaging Nodes. The morning also featured presentations from various imaging nodes, including insights into new services, methodologies, and applications in imaging research. Later in the day, the focus shifted to Euro-BioImaging’s User Access Experience, featuring an interactive session where Yves Lutz (IGBMC) presented France-BioImaging Alsace Node experience. The afternoon was dedicated to Euro-BioImaging’s data services, with updates on AI-driven image analysis, medical imaging, and data-sharing initiatives. A session on the FoundingGIDE project concluded the day.

The final day of the meeting highlighted training opportunities under the EVOLVE program, with presentations on job shadowing experiences from different imaging nodes. The morning also included breakout sessions on topics such as training, communication strategies for engaging with funders and the general public, data management, and core facility performance evaluation.

This annual gathering offers an essential platform for the EuBI nodes to exchange on key topics, current challenges and best practices with European colleagues and build on new transnational collaborations.

Thanks to the Euro-BioImaging hub team for organizing and hosting this inspiring event! We are glad to be part of this amazing community and working together as a European Research Infrastructure!

Hi Dorian! Thanks for this interview. Let’s start with your professional journey. How did you end up managing the Challenge project?

It’s a long story! I’ve always been curious about many things, which made choosing a path difficult. I wasn’t particularly gifted in one subject, but rather reasonably good at everything—whether it was math, life sciences, physics, or even literature and ancient Greek. With no clear distinction to guide me, I felt torn between scientific and literary studies.

So, I chose a compromise: an Economic and Commercial Scientific Track (ECS) preparatory class, which allowed me to study various fields. 

Then, as I developed a real interest in mathematics and its applications, I moved towards a third-year degree in mathematics and computer science at Paris 1 Panthéon-Sorbonne University.

I continued with an interdisciplinary Master’s degree, focused on applied mathematics, economics, and finance. But here’s the thing: I hated finance. However, I didn’t quit—I kept going, because even in what seemed like a mistake, I knew there was something to learn.

During that time, I discovered data science and deep learning (AI), which fascinated me. In my second year, I specialized in optimization and data science, choosing courses in machine learning and AI.

And then came the turning point: an internship in histology image processing. Histology is the study of biological tissues (animal and plant) at the microscopic level, and my role was to develop an algorithm to help detect cancerous cells in histology slides, assisting anatomopathologists (doctors who analyze patients’ biological samples: cells, tissues and organs) in their diagnosis.

That’s when it all clicked.

For the first time, I found a field that combined everything I loved: mathematics and data science, but applied to bio-imaging, which brings together biology (the subject of the images) and physics (the imaging and acquisition process); and a literary dimension, through scientific writing and discussions with professionals from different backgrounds.

After graduating, I looked for a way to stay in this field, which led me to my current position at France-BioImaging.

To the younger generation: it’s okay if your path isn’t straightforward! You may make choices that don’t turn out as expected, but everything can be connected in unexpected ways. If you feel lost, just keep moving forward and stay true to yourself—you’ll find your way!

What is your role at France-BioImaging?

As a research software engineer, I am the referent and project coordinator for the FBI Challenges.

How did the idea for the first Challenge come about?

Thanks to discussions within the FBI community, we identified a critical question:

“How can we find four common organelles (i.e. cell components as nucleus or mitochondria) in living cells by fluorescence microscopy without the constraints of the acquisition process?”

After several exchanges and exploratory imaging sessions, we built a robust dataset and defined a specific challenge topic—the two essential pillars of any bioimaging competition.

This led to “Light My Cells”, a challenge focused on using deep learning (AI) to reconstruct sharp fluorescence images from transmitted light images.

Why are competitions like Challenge valuable for bioimaging?

Advancing data science applications in bioimaging requires a deep understanding of both the imaging process (biology and microscopy) and data science techniques tailored to specific tasks.

For example, in our context, it is crucial to understand the advantages and limitations of fluorescence microscopy vs. transmitted light microscopy:

• Fluorescence microscopy, widely used in cell imaging, relies on biochemical fluorescent labeling to highlight specific cellular structures. While effective, this technique is time-consuming, costly, and potentially harmful to the cells, as it can cause damage ranging from minor alterations to complete cell death. To preserve biological samples, it is essential to minimize the number of fluorescent labels used in live-cell experiments.
• Transmitted light microscopy—including bright field, phase contrast, and DIC (Differential Interference Contrast) microscopy—offers a non-invasive alternative. These label-free techniques reduce phototoxicity and cell alteration, while still providing valuable structural information.

This raises an important question: Can we computationally generate fluorescence microscopy images using only transmitted light microscopy?

This was the goal of the “Light My Cells” Challenge. With “Light My Cells”, we sought to:

• Develop deep learning methods capable of generating multi-channel fluorescence images from a single transmitted light image.
• Encourage innovation in AI architectures and loss functions to handle challenges such as missing organelles and microscope variability (e.g. magnification, depth of field, numerical aperture).
• Promote open science by providing a publicly available training dataset and integrating winning AI models into bioimaging software.

Beyond this competition, Challenge encourages participants to push the boundaries of AI, innovate, and contribute to bioimaging research. The ultimate vision? Achieving fluorescence imaging in silico—generating fluorescence-like images directly from transmitted light data, without the need for physical labeling.

What has been the most challenging part for you as the organizer?

The entire challenge was challenging!

What are your hopes for the future of the Challenge?

If I can dream a little, I’d like to achieve at least 2 things:

1. Develop a large-scale, open-source bioimaging dataset in open format (ome.zarr), covering diverse biological models (fauna and flora) under a standardized acquisition framework with comprehensive metadata—like a smaller ImageNet for biology (ImageNet is a large heterogeneous dataset used to train AI for image recognition).
   
2. Launch a ‘Microscope Metrology’ challenge to develop methods for accurately recovering the Point Spread Function (PSF) directly from microscopy images. In fluorescence microscopy, images are inherently blurred, and the PSF defines how a single point appears in an image. However, current methods rely on approximations between: Theoretical PSF (ideal, physics-based model), Experimental PSF (measured from calibration samples), Real PSF (true system response), Effective PSF (influenced by optics, noise, and reconstruction). By improving PSF estimation, this challenge may enable technicians to assess microscope quality faster and standardize calibration while helping biologists optimize imaging parameters and enhance quantitative analysis.

Thank you, Dorian! Good luck with the evaluation phase of the ‘Fuse My Cells’ Challenge and the selection of the three winners. See you in April for the results announcement and ISBI 2025 participation!

The Pasteur Education Center and the Pasteur Advanced Light Microscopy Initiative organize a 1/2 day symposium dedicated to recent advances in Life-Sciences and Light Microscopy.

The symposium is followed by a week-long demonstrations by innovative microscopy companies, showcasing their latest technology. 

The event and demos are open to all, free, but registration is mandatory.

All informations are on the event page: https://research.pasteur.fr/en/event/symposium-and-workshop-pushing-the-frontiers-of-dynamic-imaging-2025/

Some details below

Symposium

Monday, March the 24th

Location: Auditorium Francois Jacob, Institut Pasteur, 28 rue du Docteur Roux, 75013 PARIS

Time	Speaker	Institute	Title
14:00 – 14:15	Introduction
14:15 – 14:45	Viktorija Glembockyte	Max Planck Institute for Medical Research, Heidelberg	DNA origami tools for sensing and imaging single molecules
14:45 – 15:00	Company presentation – Bruker & Coherent
15:00 – 15:30	Jens Bosse	Centre for Structural Systems Biology, Hamburg	From in silico to in cellulo: Illuminating viral morphogenesis
15:30 – 15:45	Company presentation – Evident
15:45 – 16:15	Magali Suzanne	Centre de Biologie Intégrative, Toulouse	Non-invasive approaches to decipher morphogenetic forces at different scales
16:15 – 16:45	Coffee break
16:45 – 17:00	Company presentation – Leica
17:00 – 17:30	Oliver Kepp	Centre de recherche des Cordeliers, Paris	Automated high-throughput high-content autophagy and cell stress fingerprinting
17:30 – 17:45	Emna Ouni, on behalf of ImagXcell, Tomocube	Institut Gustave Roussy, Paris	Engineering tumoroid nests at a scale for detailed profiling of mechanosensitive drug responses

Workshop

Tuesday the 25th of March to Friday the 28th of March.

Participants will be able to book one or several demonstration slots to test cutting edge microscopy equipments in the Pasteur Education center microscopy room. You can directly contact the company representatives to set up one or more demo slots for you to test the systems.

For reminder, the event and demos are open to all, free, but registration is mandatory.

In a nutshell, how would you describe your work today?

My work is divided between my primary activity—research—as the director of the Decision and Bayesian Computation – Epimethee laboratory (Pasteur Institute, Inria, CNRS, UPC); my involvement with the Pr[AI]rie Institute; and my role as the CSO of Avatar Medical, a spinoff from our laboratory.

What is your academic and professional background? Was there a defining moment or a key encounter that shaped your career?

I am a theoretical physicist by training, and I completed my PhD at Polytechnique under the supervision of Guilhem Gallot. Thanks to Antoine Danchin, I had the opportunity to meet Massimo Vergassola, whom I later joined at the Pasteur Institute. This was an extraordinary encounter—working for and alongside him was an incredibly formative experience. Another key meeting was with Marta Zlatic (Janelia Research Campus), who introduced me to the Drosophila larva as a model system in neuroscience. I have been leading a laboratory at the Pasteur Institute since 2017, and in 2024, we also became an Inria project team.

Could you briefly explain what Avatar Medical is? Who is this technology for, and what problem does it solve?

Avatar Medical is a spinoff from the Pasteur Institute and Curie Institute, originating from the postdoctoral research of Mohamed El Beheiry team. It provides solutions for medical image visualization and analysis using volumetric rendering on various platforms, including virtual reality and 3D screens. The startup addresses several challenges, such as surgical planning for surgeons, patient engagement strategies that help doctors explain procedures to patients, and medical education at all levels.

What motivated you to take the leap into entrepreneurship in the healthtech sector?

A company must back an algorithmic solution to reach patients and doctors. We embarked on this adventure with Mohamed and Elodie Brient Litzler, who supported our project within the Pasteur Institute’s technology transfer office, led by Isabelle Buckle.

Have you used France-BioImaging services?

For me, France-BioImaging is above all a discussion community. Throughout this project—originally called DIVA and initially focused on microscopy—I benefited from the network for discussions, publications, and access to alpha and beta testers for our technologies and algorithms.

What were the main technical or regulatory challenges in transitioning from a lab technology to a commercial solution?

With a strong team, challenges become manageable. Under the leadership of the founders—Xavier Wartelle (CEO), Elodie Brient Litzler (COO), Mohamed El Beheiry (CTO), Marie Buhot-Launay (Sales), and myself—Avatar Medical built a highly competent team. There were a few technical challenges, as the technology was already mature. The main focus was on developing the right strategy and expertise first to obtain FDA approval and then CE marking. The real challenges lie in integrating our solution into hospital workflows, maximising its usefulness for doctors and patients, and positioning it effectively within the industrial value chain.

You are a researcher at the Pasteur Institute, a lab director, and the CSO of Avatar Medical. How do you balance all these responsibilities?

It depends on the period—sometimes better than others! The workload is significant but manageable with good organisation, allowing me to remain relatively efficient. Occasionally, the accumulation of different pressures and the desire to do everything as well as possible can be challenging.

What are the next challenges and ambitions for Avatar Medical?

This is a particularly exciting time (which helps me take my mind off current events), as Avatar Medical is experiencing significant growth with numerous new clients, successful projects, and new installations. We now offer several software solutions across multiple platforms, and we need to build on this momentum. The major challenge for 2025 will be less about algorithms and more about expanding our “patient engagement” solutions in the United States.