Discover the story of Jean-Baptiste Masson, recently honored in Le Point’s 2025 Palmarès des Inventeurs and a representative of the Pasteur Institute at French Tech London. As both the CSO of the startup Avatar Medical and the director of the Decision and Bayesian Computation – Epimethee laboratory, he shares his journey with us.

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.

We organize in Pasteur a training school on bioimage analysis at the Institut Pasteur, Paris, in May 2025.

The school will be in person only, from the 12th to the 16th of May 2025. All the details are on the course page, some details below.

The course lasts one week and is made of 2 tracks that run in parallel:

  • Early career investigators track (ECI): Learn to master the tools and techniques of bioimage analysis for your own research. From power usage to building analysis pipelines.
  • Analysts track: Learn to use and deploy advanced tools; learn to master high-performance computing for advanced bioimage analysis.

The number of available seats is 25 students max for the ECI track and 15 for the Analysts track. The selection is based on project description.

The keynotes are common to both tracks, and there is a bonus session on Friday afternoon: Work on your own data, with the help of colleagues and experts.

Program

The exact schedule is still being finalized. Here is a description of the course content.

Both tracks of the course have a specific focus on hands-on and interactive tutorials. They are meant to be convivial and foster a collaborative atmosphere between students and teachers. Each day begin with a common keynote, then the program for each track takes place.

Early-career investigator track

In this course you will learn how to use the most recent and common image analysis software tools. You will learn to master and use them for your own research project. The course will walk you from their installation, basic usage to building image analysis pipelines, from raw images to quantification results.

In the beginning we will explore the usage of software such as Fiji, Icy, QuPath, Ilastik, TrackMate, and Deep Learning tools… By the end of the course you will able to use and edit scripts and notebooks for batch processing and some advanced analysis.

The course will also offer fundamental introductions to the topics in modern image analysis, including machine learning / deep learning, ethics, …

You should apply to this course if you are a biologist and / or have no or little background in image analysis and do imaging in your research project. No knowledge of coding is required.

Analyst track

The strong focus of this track is the use of advanced algorithms, and mastering new tools and techniques. For every edition of this course, we pick a central topic in image analysis that we use to articulate the lectures and practical sessions of this track.

This year this topic is image analysis in the scope of spatially-resolved omics. Spatial-omics is a term used to describe a wide range of technologies focused on studying the molecular composition and interactions within tissues or cells while maintaining their spatial context. They all involve imaging and image analysis. We will use spatial omics as a theme to articulate several lectures and practical sessions on advanced image analysis topics that are central to these technologies. Importantly: we will restrict the topics to be on image analysis only, and won’t be dealing with the bioinformatics part. However, guest lectures by experts will help contextualize the course content within the broader scope of spatial omics.

In addition, the course will also focus on the use of artificial intelligence for bioimage analysis, using computational pathology and cell biology as topics to articulate the sessions and lectures.

Finally, a session will be dedicated to high performance computing in bioimage analysis, in the context of large images and large datasets.

The main tools of this track will be Python, Napari and Icy.

Basic experience with scripting and python is required.

Requirements

Bring your own laptop. We will spend time together installing everything needed and making sure they run for the course.

Also, absolutely bring a mouse with the laptop :) It’s painful to use the tools mentioned above with the trackpad.

Participants are encouraged to bring image data for the ‘Work on your own data’ sessions.

Registration

For registration visit the course webpage here : https://www.pasteur.fr/en/education/programs-and-courses/pasteur-courses?id_cours=32420

Deadline for registration: March the 31st 2025

Date for acceptance / rejection communication: April the 3rd 2025

Fresnel Institute, in collaboration with Imaris Software, is organizing the Imaris Workshop Day on Tuesday, March 11th.

This event includes a general presentation on Imaris, during which an Imaris expert will showcase various examples of its applications. Following the presentation, there will be an image analysis clinic where you can discuss the analysis of your own data*.

Workshop program:

  • 13:30-14:30: Imaris presentation
  • 15:00-17:30: Image analysis clinic

Location: Salle Pierre Cotton, Institut Fresnel, Faculté des Sciences – 52 Avenue Escadrille Normandie-Niémen, 13397 Marseille.

Registration is free of charge but mandatory. You can register here or click on the file below.

*If your data isn’t ready by then, we’ll find a similar dataset to discuss.

fresnel-imaris-invitation-110325Download

A recent study, led by the Advanced Molecular Virology Unit (Institut Pasteur) and combining virology, structural biology, and immunology, has uncovered a key mechanism involved in the establishment of an efficient infection and evasion of innate immunity of HIV-1 virus (responsible for AIDS disease) in the organism.

The authors focused their work on HIV-1 condensates, called HIV-1 membraneless organelles (HIV-1-MLOs) which are tiny structures composed of viral genetic material and proteins that form in the nucleus of infected cells.

Key results

Researchers have discovered HIV-1 MLOs exist in vivo and act as a shield, allowing viral DNA to hide from cellular DNA sensors that trigger a pathway of our antiviral immune response when they detect a foreign DNA.

These structures can regulate the temporal and spatial conditions to create the perfect environment for reverse transcription (RNA to DNA conversion), a crucial step for the virus to replicate and spread in the organism.

New perspectives

These discoveries open new perspectives for:

  • Enhancing our understanding of how HIV-1 escapes immune detection.
  • Developing treatments targeting the formation of HIV-1 MLOs in the early stages of infection.
  • Exploring similar mechanisms in other viruses.

Microscopy imaging: a key player

Advanced microscopy techniques were essential in visualizing the formation and function of these structures, including:

France-BioImaging’s Pasteur PBI and UBI platforms (Paris-Centre Node) in collaboration with the Electron Microscopy Platform of the University of Tours provided cutting-edge expertise and equipment, playing a central role in unraveling this viral strategy. By enabling researchers to see what was once invisible, imaging technologies continue to be at the heart of discoveries that push the boundaries of infectious disease research!

Read the full article here: https://pubmed.ncbi.nlm.nih.gov/39623137/

On the occasion of the launch of France-BioImaging’s new challenge, Fuse My Cells, we reached out to the winners of the previous edition (Challenge – Light My Cells). Today, we invite you to meet Trang Le, PhD student in Bioengineering at Stanford University.

Hello Trang, I’m glad to meet you! Where are you from?

I’m originally from Hanoi, Vietnam. Then I moved to Europe for my bachelor and my master study, and now I’m finishing my PhD in the US at Stanford University.

What is your background and your professional activity?

I’m a PhD student in bioengineering focusing on machine learning for image analysis and modelling of single cell spatial proteomics, towards an AI virtual cell model. I’m also interested in citizen science and accessibility of AI models in biological research.

Why did you decide to participate in the France-BioImaging challenge “Light My Cells”?

I heard about the challenge from my advisor after she returned from a conference. Originally, I wanted to test out a different strategy of modelling complex joint distribution, which did not work for the task as intended. In the end, I opted for a more simplified solution, keeping only the essential network components and luckily that was enough.

What was the most challenging part of the competition for you?

Surprisingly it’s managing the submission format!

What are your thoughts about Challenge 2 “Fuse My Cells”?

It seems like an interesting and useful task, especially with the growing amount of multiview microscopy data. Ultimately, the developed models should learn meaningful biological features and generalize well to new imaging conditions. The challenge’s design and evaluation metrics will be crucial in guiding progress toward practical and robust solutions.

Do you have any advice for the participants of Challenge 2?

A few things come to mind:

  • Spend some time on dummy submission earlier
  • Think about the generalizability of your model (and create your validation set fairly) 
  • This competition is quite pressed for time, so keep your preprocessing simple at first
  • And have fun!

Thank you very much for your time, Trang! I’m sure your testimony will be useful for the participants of Challenge 2.

As the first-place winner of the competition, Trang had the opportunity to present her solution, VQGAN, to the entire France-BioImaging community at our last Annual Meeting in Strasbourg. We are delighted to share this moment with you!

For those interested in taking part in the “Fuse My Cells” challenge, find more information here!

On the occasion of the launch of France-BioImaging’s new challenge, Fuse My Cells, we reached out to the winners of the previous edition (Challenge – Light My Cells). Today, we invite you to meet Yu Zhou, research associate at the Leibniz Institute for Analytical Sciences (ISAS).

Hello Yu, I’m glad to meet you! Where are you from?

I am originally from Jiangsu Province, China. Currently, I live in Dortmund, Germany, where I work at the Leibniz Institute for Analytical Sciences (ISAS).

What is your background and your professional activity?

My professional background is in biomedical image processing, where I focus on applying AI algorithms to analyze and enhance imaging data. A key aspect of my work is improving efficiency, such as using model quantization and pruning to reduce inference energy consumption, as well as applying biomedical image compression to lower storage and bandwidth costs. Recently, I have also been exploring research in foundational models for omics data, aiming to bridge different modalities in biomedical research.

Why did you decide to participate in the France-BioImaging challenge “Light My Cells”?

I learned about the Challenge “Light My Cells” through my supervisor, who discovered the competition on X and shared it with me. I had never participated in a competition on the Grand Challenge platform before, so I wanted to experience the full process of such a challenge. Also we found the problem itself very interesting, and thanks to a previous project, we were already somewhat familiar with this topic.

What was the most challenging part of the competition for you?

The most challenging part of the competition was data processing. We used a semi-automated approach that combined an automated pipeline with manual curation for data filtering. This process was quite time-consuming.

How did you manage your time during the competition?

For the experimental phase, our team worked in parallel on several tasks: data cleaning, trying different network architectures, and conducting hyperparameter searches. However, when it came to writing the final paper, we were somewhat rushed as we had only about two weeks left to complete it.

What are your thoughts about Challenge 2 “Fuse My Cells”?

What excites me most about this challenge is its innovation. Predicting a fused 3D image directly from a single view bypasses some potential issues of multi-view fusion, such as light toxicity. Additionally, with a well-constructed dataset, the solution could be more generalizable, enabling models to perform image restoration across all the various 3D perspectives.

Do you have any advice for the participants of Challenge 2?

  1. Pay attention to the data.
  2. Keep an open mind and be willing to explore different strategies, including model selection and training methods.
  3. Manage your time wisely by balancing the experimental phase and paper writing.

Thank you very much for your time, Yu! I’m sure your testimony will be useful for the participants of Challenge 2.

For those interested in taking part in the “Fuse My Cells” challenge, find more information here!

On the occasion of the launch of France-BioImaging’s new challenge, Fuse My Cells, we reached out to the winners of the previous edition (Challenge – Light My Cells). Today, we invite you to meet Marek Wodziński, a post-doc in the Institute of Informatics at HES-SO Valais-Wallis in Switzerland.

Hello Marek, I’m glad to meet you! Where are you from?

I am from Poland – currently working both in Poland (AGH University of Kraków) and Switzerland (HES-SO Valais).

What is your background and your professional activity?

I have a PhD in Biomedical Engineering & Computer Science from AGH University of Kraków and I am currently working as PostDoc in HES-SO Valais. I have worked in the field of medical image analysis, computer vision, machine & deep learning for more than 7 years so far.

Why did you decide to participate in the France-BioImaging challenge “Light My Cells”?

Taking part in scientific challenges is a great way to explore previously unknown subfields and gain valuable experience in new topics. When I came across the challenge on the IEEE ISBI website, I immediately recognized it as an opportunity to deepen my expertise in biological imaging and expand my research network.

What was the most challenging part of the competition for you?

As in every challenge – to fully understand the goal, the data, and the associated challenges. The most time-consuming part in scientific challenges work is to explore the dataset and understand which challenges related to the data are the most important, e.g. in the Light My Cells challenge it was connected with significant dataset imbalance, both at the study and organelles level.

How did you manage your time during the competition?

I started with exploring the data and thinking how the problem should be addressed. The process took me more than half of the time I spent on the challenge. Then, I implemented and debugged the training and evaluation scripts. Finally, I queued all ablation studies on our supercomputing platform (ACK Cyfronet Athena) and chose the best model.

Do you have any projects or aspirations related to imaging or research after this competition?

The competition improved my experience related to image-to-image translation tasks that could be further used in different downstream applications I am working on, e.g. MR-to-CT translation in radiology. I continue to work both in digital pathology and radiology where I develop novel deep learning techniques.

What are your thoughts about Challenge 2 “Fuse My Cells”?

Definitely the most difficult aspect of the Fuse My Cells challenge is the timeline – there is only 1.5 months to develop and evaluate the solution.

Do you have any advice for the participants of Challenge 2?

I suggest starting with exploring the data and understanding the associated challenges. Then, it is wise to explore the current state-of-the-art to understand the best-performing solutions and improve them. The practical part related to developing the scripts and  performing ablation studies is usually significantly less influential.

Thank you very much for your time, Marek! I’m sure your testimony will be useful for the participants of Challenge 2.

For those interested in taking part in the “Fuse My Cells” challenge, find more information here!

Gustave Roussy Microscopy Facility, in collaboration with Imaris Software, is organizing the Imaris Workshop Day on Friday, February 14th.

This event includes a general presentation on Imaris, during which an Imaris expert will showcase various examples of its applications. Following the presentation, there will be an image analysis clinic where you can discuss the analysis of your own data*.

Workshop program:

  • 11:00-12:00: Imaris presentation
  • 13:00-16:00: Image analysis clinic

Location: Salle 2, Espace Maurice Tubiana, 20 Rue du Dr Pinel, 94805, Villejuif.

Registration is free of charge but mandatory. You can register here or click on the file below.

*If your data isn’t ready by then, we’ll find a similar dataset to discuss.

igr-imaris-invitation-140225Download

It is with deep sadness that the France-BioImaging community learned of Spencer Shorte’s passing.

Spencer Shorte was a highly esteemed member of France-BioImaging. As Director of the Institut Pasteur platform Imagopole at the time, then UTechS Photonic BioImaging, Spencer was involved right from the initial project of France-BioImaging (2011-2014), especially in the Paris Centre node structuration, where the connection between the Parisian platforms of Imagoseine (Institut Jacques Monod), Imagopole (Pasteur), PICT (Institut Curie) was key, notably for user transfers and the sharing of technical facilities in EM. He also was one of the driving forces behind the French RIO platform label, forerunner of the IBiSA quality label.

His contributions to the bioimaging landscape and platforms at the international stage, particularly in the coming of ELMI, the foundation of CTLS and more recently within Global-BioImaging, played a pivotal role in fostering the creation of a global network connecting all imaging stakeholders and promoting the dissemination of knowledge.

France-BioImaging will remember his energy, his active advocating for imaging core facilities and his important contributions to the French and international imaging community.

Our heartfelt condolences go out to his family and colleagues.

Here is the memorial link to pay tribute to Spencer Shorte by sharing a personal message: https://hommage.inmemori.com/sshorte-e45je

France-BioImaging’s “Preclinical Microscopy” Working Group is organizing its next webinar on February 6th, 2025, from 14:00 to 16:00. The main objective of this Working Group is to advance multimodal microscopy of thick samples for preclinical studies.

During this webinar, you will have the opportunity to discuss the latest research, technologies, and regulatory frameworks related to photonic microscopy, spanning from the scale of organs/organoids to live animals.

Program:

14:00 – Welcoming and introduction

14:05 – “Exploring Mammary Gland Remodeling and Breast Cancer Therapies Through 3D Organoid Imaging” by Thomas Pelé (CRCI2NA, Nantes)

14:55 – Presentation on animal ethics (title to be confirmed) by Magali Jacquier (IPBS, Toulouse)

15:45 – Open discussion

Join the webinar:

Click here to join the Microsoft Teams meeting.

Please connect using your last name and first name so we can update the participants’ list.

France-BioImaging, the french national research infrastructure for biological imaging, offers external users* access to its state-of-the-art microbiological equipment and cutting-edge expertise. Simply submit your request by registering through the Euro-BioImaging portal to benefit from a wide range of advanced technologies and personalized support from our specialists!

Access: the benefits

  • Access more than 30 biological imaging facilities and specialized R&D laboratories across 10 regional nodes and 1 transversal bioinformatics node,
  • Receive funding to cover France-BioImaging equipment usage costs, up to €750 per week for a maximum of 3 weeks,
  • Explore a wide range of cutting-edge technologies and methodologies, including Single Particle Tracking & Super Resolution / Multimodal & Quantitative fluorescence Microscopies / Multiscale & Correlative Microscopy / New Contrast & In-Depth Imaging…
  • Benefit from personalized support to assist you with the computational analysis of your data.

How to benefit from access?

To take advantage of the Access benefits, you need to fill out an online form via the Euro-BioImaging portal to create a research proposal. The entire application process takes around 2 to 3 weeks, and submissions can be made at any time of the year.

At certain times of the year, special calls for access are published, with specific criteria and deadlines. Stay tuned to catch these opportunities!

To learn more, visit our dedicated access web page!

*This registration process is open to:

  • any users from outside the institutional perimeter of France-BioImaging nodes (i.e. from outside the partner university of the Node) who would like to use imaging technologies in one of FBI nodes: Alsace, Toulouse, Paris Centre, Paris Ile-de-France-Sud, Marseille, Montpellier, Bordeaux, Bretagne-Loire, Normandie, Rhône-Alpes. They can be French or international users – EU and non-EU
  • or users from one France-BioImaging regional Node who want to access an equipment available in another FBI regional node.

On November 20 and 21, the France-BioImaging community gathered in Strasbourg for its Annual Meeting.

This event provided an opportunity for members from different nodes to discuss the future and latest updates of the infrastructure, as well as to discover each other’s projects, all centered around this year’s theme: “Live functional imaging: From chemical synthesis of the probes to instrumentation.” It was also the perfect occasion to introduce the recently joined nodes to the FBI community: Strasbourg, Rhône-Alpes, and Normandie.

If you couldn’t attend the event or would like to rewatch one of the presentations, the 2024 Annual Meeting videos are now available on YouTube!
Finding the presentation you’re interested in is easy — each video includes chapters with the titles of the topics presented and the speakers.

Enjoy watching!