Explore the beauty of the invisible world through the 2024 FBI digital calendar!

Enjoy the diversity of microscopy techniques, models and applications represented, one image at a time. All 12 images used for this calendar were submitted to France-BioImaging Image Contest 2023.

A big thank you again to all the participants!

You can download the A4 print version (one month per page) 2024 FBI digital calendar here:

If you wish to use it as your computer desktop, you can download a PNG version of each month here:

In order to answer image data analysis demands, France-BioImaging is launching its first data machine learning competition: welcome to the Light My Cells challenge!

The challenge

The Light My Cells France-Bioimaging challenge aims to contribute to the development of new image-to-image ‘deep-label’ methods in the fields of biology and microscopy. Basically, the goal is to predict the best-focused output-images of several fluorescently labelled organelles from label-free transmitted light input-images. And we need you for that!

More information about the challenge: lightmycells.grand-challenge.org/lightmycells

How to participate

We have defined the challenge as a single task with two phases:

  • preliminary test phase (on 30 images) to familiarize with the algorithm submission procedure, with the possibility to have five submissions (with a maximum of one by week)
  • The final test phase (on 300 images) with only one submission accessible will not give the possibility to evaluate their algorithms before submitting.

So, you have until the end of the first phase, on March 30, 2024, to register and participate at this Light My Cells challenge. Nonetheless, you can start working on your preliminary algorithm and tests on February 14st, 2024 (with the release of the training database)!

Register now! lightmycells.grand-challenge.org/lightmycells


For top 3 winners:

  • Award certificate
  • A challenge paper will be written with the organizing team’s members for submission to journals
  • Invitation to publish their methods in the proceedings of the IEEE International Symposium on Biomedical Imaging 2024s
  • Support and integration of open source code into open science image processing and analysis software (e.g. BioImage Model Zoo, Napari)

For the 1st: 

  • Invitation to 2024 France-Bioimaging annual meeting
  • Graphic card
  • Android tablet

For the 2nd:

  • Graphic card
  • Android tablet

For the 3rd:

  • Android tablet

Why launching a challenge?

To develop powerful methods that will then end up in creating public databases, standards & benchmarks in the field of bioimaging! The FBI challenge is hinged on a double contribution: from core facilities engineers and from data scientists. The first group acquired a large number of images to build a dataset, that will later be used by the algorithms. These images were produced by microscopy engineers & technicians from FBI’s platforms. As for the second contribution, this is where the challenge starts! The challenge is then published to have a maximum of data scientists to work on the algorithms that best fulfill the analysis task.

The first project is also based on four pillars:

  • Open source + FAIR (Findable, Accessible, Interoperable, Reusable)
  • Supervised learning, it involves annotated datasets to maintain control over performances.
  • In silico annotations, a computer labeling method to avoid manual annotation and its drawbacks.
  • Image-to-image analysis tasks, an image analysis tasks which aim to predict an output image from the input one.

For any questions, please contact Dorian Kauffmann: dorian.kauffmann@france-bioimaging.org.

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 2023:

  • 1st Place: Laurent LE, Lévêque-Fort Team, Institut des Sciences Moléculaires d’Orsay

In the blink of an eye

COS7 fixed cell. Alpha-tubulin labeled with DNA-PAINT and imaged with Atto 647N. Axial information is obtained by virtual-SAF measurement known as DONALD.

SMLM Fluorescence Microscopy with DNA-PAINT with DONALD detection

  • 2nd Place: Gonzalo QUIROGA-ARTIGAS, Team Contrôle cytoplasmique de la stabilité du génome, Centre de recherche en Biologie Cellulaire de Montpellier

“Tardigrade embryos protected by mother’s molt”

Tardigrades commonly align the time of molting with egg laying. In this image we observe a tardigrade molt covering three developing embryos (DNA in white). The microscopy technology applied was confocal microscopy, and the research aimed to investigate the synchronization of embryo development in tardigrades.

Confocal microscopy

  • 3rd Place: Hugues LELOUARD, Gorvel team, Centre d’Immunologie de Marseille Luminy

“Intestinal octopus”

Small intestine section from a LyzM-eGFP mouse containing one Peyer’s patch and stained for proliferative cells (Ki-67, yellow), Paneth cells (UEA-I, blue), epithelial cells (EpCAM, magenta), naive B cells (IgD, red), T cells (CD3, orange), helper T cells/macrophages (CD4, cyan), phagocytes (CD11c, turquoise), monocyte-derived phagocytes (GFP, green).

10-color spectral confocal microscopy

Congratulations to the winners!

Explore all the images submitted here:

As stated in the Terms & Conditions of the contest, foreign participants non-affiliated to a French institution are featured in the gallery, but were not evaluated as part of the contest.

Launched earlier this year in coordination with the African BioImaging Consortium and Imaging Africa and within the framework of the Horizon Europe Programme, the Africa-France Joint Initiative for Biological Imaging aims at extending its partnership with colleagues in Africa that have interest in using advanced microscopy approaches for their own research programs and projects. With this in mind, we have previously designed two calls for funding: one for access to FBI’s bioimaging core facilities, the other as a twinning program.

Good news! Our first project has started! Granted by our second call, the Twinning program has begun between Stellenbosch University and FBI-Paris Node. A fantastic experience based on sharing practices, knowledge transfer and many fruitful discussions on image analysis and correlative approaches between light sheet and serial block face microscopy techniques. For the South African partner, Madelaine Frazenburg (Stellenbosch University), it is the opportunity to see how other microscopy laboratories in France works but also to learn more about cryo-SEM and to study new kind of sample preparation methods. From the French side, Ludovic Leconte (Institut Curie, FBI Paris-Centre node) is indeed very interested in gaining new experience in electron microscopy mainly in Serial Block Face, another tissue section imaging that is not available on his site and for which the Stellenbosch imaging platform has the mastery.

Our warmest thanks to Lize Engelbrecht, Professor Ben Loos and Janica Conradie for making this event possible and for the warm welcome they extended. The second stage of this “Twinning” project will take place at Institut Curie next spring. We look forward to welcoming Madelaine!

A key property of the human cornea is to maintain its curvature and consequently its refraction capability. Although we know that it is related to its stacked collagen lamellae structure, the distribution, size, and orientation of these lamellae along the depth of the cornea are poorly characterized up to now. A team from the Laboratory for Optics and Biosciences (LOB) has optimized a recent technology which combines Second Harmonic Generation microscopy and polarimetry (P-SHG) to image the lamellar microstructure of human corneas and more!

Acquire the structure in depth

Imaging the cornea is essential to understand how visual acuity works. This part of the eye is characterized by its transparency and refractive power but also by its unique mechanical properties. To answer the many questions of the cornea structure, the Second Harmonic Generation microscopy is the perfect technique. This technology is based on the sample capacity to generate second harmonic light, which has half the wavelength of the light entering the material. However, the SHG is working on well-aligned assemblies of non-centrosymmetric molecules which fits perfectly with the collagen!

Apart from being specific to this kind of macromolecules, the SHG microscopy offers multiple advantages. First of all, as it does not involve the excitation of molecules, molecules do not suffer from phototoxicity or photobleaching effects. Moreover, no markers are necessary which makes this type of microscopy noninvasive. Finally, Second Harmonic Generation microscopy allows the visualization of in-depth structure of thick samples. As a matter of fact, it is, nowadays, the gold standard technique for in situ visualization of collagen 3D organization in unstained biological tissues.

Add polarimetry and get orientation information

P-SHG first offers all the advantages of usual SHG microscopy: 3D optical imaging in depth and high specificity and sensitivity to collagen without any labeling. In this study, scientists took advantage of the light polarization to reveal the direction of the collagen fibrils that make up the lamellae of the cornea in their SHG microscopy acquisition. This recent technology is called: polarization-resolved SHG microscopy (P-SHG). The main novelty of this study was to implement P-SHG in depth to analyze intact human corneas along their full thickness (up to 600 µm). 3D reconstructions of P-SHG data show in a unique way the stacking of collagen lamellae with different orientations all along the thickness of the cornea. Here, imaging helped confirm that these lamellae are roughly organized parallel to the cornea surface, with different collagen orientations in sequential lamellae, and provided new information about the variation of these orientations along the depth of the cornea.

Aside from being the first quantitative characterization of the lamellar structure of the human cornea continuously along its entire thickness with micrometric resolution, this imaging technique could be a huge step forward in vivo diagnosis as it uses the detection of the reflected signal. Furthermore, this study opens the way to promising new characterizations of the cornea, such as mapping the size and distribution of lamellae as a function of depth, but also as a function of position (center or periphery of the tissue). This information will feed into mechanical modelling of corneal behavior during variations in intraocular pressure or healing processes. Finally, the study of pathological tissues will clarify the role of the corneal defective structure in certain diseases.

These results show the unique potential of P-SHG microscopy for imaging of collagen distribution in thick dense tissues. And of course, this approach is readily applicable to more than just cornea! It may be used for instance to decipher the structure of collagen in fibrotic pathologies or in other proteins that exhibit SHG, namely myosin and tubulin, or in starch and cellulose in plants. This shows the unique potential of P-SHG microscopy for imaging thick collagen-rich tissues.

Three-dimensional reconstruction of the lamellae structure of a human cornea. Colors indicate the direction of the collagen lamellae in the imaging plane, as shown in the inset color wheel. The image size is 250 x 250 x 600 µm3. The anterior part (side outside the eye) of the cornea is at the top of the image.

Get access to one of our services!

Polarization SHG microscopy is not available in open access but we are open to collaborations!

You need classic SHG microscopy or another imaging technology or expertise that France-BioImaging provides? To get open access, please login via Euro-BioImaging website! You just have to choose the technology you want to use, then submit your proposal. All applications will be processed by the Euro-BioImaging Hub in close relation with France-BioImaging. And of course, all scientists regardless of their affiliation, area of expertise or field of activity can benefit from open access services! Users whose projects will be validated by Euro-BioImaging will benefit from a waiver for the access cost on France-BioImaging core facilities (https://france-bioimaging.org/access/).

Sources: https://www.inp.cnrs.fr/fr/cnrsinfo/cartographier-la-structure-de-la-cornee-humaine


Raoux, C., Chessel, A., Mahou, P. et al. Unveiling the lamellar structure of the human cornea over its full thickness using polarization-resolved SHG microscopy. Light Sci Appl 12, 190 (2023). https://doi.org/10.1038/s41377-023-01224-0


Starts: November 10, 2023 • Ends: December 31, 2023

FBI opens a call for the recruitment of its next Scientific Director (2024-2028)

(Deadline is 31st of December 2023)

France BioImaging-FBI (laureate of the INBS program of the PIA in 2011) is the National Research Infrastructure in Biological Imaging.  FBI is built on 8 geographical Nodes identified on the basis of strong relationships between R&D labs and imaging Core Facilities. Each Node shows a specialization of a local expertise in methods and biological topics. This crossover between imaging technologies and expertise in scientific topics is a characteristic of the complementarity between FBI Nodes. A 9th Transversal Node gathers FBI strengths and resources in Image Analysis and DATA management. The Operating Coordination is done under the umbrella of the UAR 3426.

Our motto is “Innovation-Training-Access”

(i) Invent and disseminate new imaging technologies
(ii) Training users and facility staff on existing and new technologies
(iii) Make them accessible to as many people as possible.

 Role of the Scientific Director of FBI

-He/She is the Strategic Manager of the Infrastructure

He/She leads the National Coordination (NC), composed of an adjunct director for international affairs, a manager of internal affairs and a manager of external affairs. The Infrastructure also benefits from several support functions: a communication officer, a business developer and an accounting officer. The NC leads the Executive Committee (EC) to manage the Infrastructure. With the Help of an international Scientific Advisory Board (SAB), he/she reports the overall Infrastructure policy and strategy to the Institutional Committee (Steering Committee, SC) which is the “decision maker”.

He/She is responsible for the arbitration of recruitment proposals (in interaction with the other governance bodies), equipment investments (PIA, TGIR, other National and International common actions…) and new service opening, in relation to the development objectives (R&D, service offers…) and the overall infrastructure strategy at national and international levels.

He/She is responsible, with the staff concerned, for the inventory of the different activities/tasks of the infrastructure: links with Europe and International, work with the different committees, web site/communication, training, animation of the “FBI-community”, scientific and financial reports…

He/She is responsible, in interaction with the EC, for managing interactions/collaborations (R&D, service providing, partnerships, technology watch…) with other PIA Research Infrastructures.

Entry into function is planned for the 1st of July 2024.

If you are interested, please send a short CV and a letter of intent (2 pages) indicating your motivation, vision and strategy, at direction@france-bioimaging.org
BEFORE the 31st of December 2023

PDF version

In 2022, in a project funded by the Euro-BioImaging pilot User Access Fund, Andrew Boyce, postdoctoral fellow at the University of Calgary, used state-of-the-art microscopy techniques at the Bordeaux Imaging Center, part of the Bordeaux node of France-BioImaging, for panoptical visualization of brain tissue in vivo. His work just got published in a Nature Communications article!

The advantages that shadow imaging has in visualizing brain tissue

Progress in neuroscience research hinges on technical advances in visualizing living brain tissue with high fidelity and facility. Unfortunately, current neuroanatomical imaging approaches either require tissue fixation (electron microscopy), do not have cellular resolution (magnetic resonance imaging) or only give a fragmented view (fluorescence microscopy).

In this study, scientists have shown how regular light microscopy together with fluorescence labeling of the interstitial fluid in the extracellular space provide the information lacking in the previous techniques. Basically, it’s like looking at the negative of a photo! Called Shadow Imaging, they have demonstrated the power of this approach on revealing neurons, microglia, tumor cells and blood capillaries together with their complete anatomical tissue contexts.

The perfect combination between the right technology and the right expertise

How did Andrew Boyce contribute to this study? Interested in blebbing neuron dendrites during cell death caused by a stroke, he only had, at that time, results from how cells in culture reacted during this kind of events but no information about the neighboring cells.

Thanks to Euro-BioImaging pilot User Access Fund, he came to Bordeaux to use a combination of live cell 3D stimulated emission depletion (3D-STED) microscopy and super-resolution shadow imaging (SUSHI), and adapt shadow imaging approaches to conventional confocal microscopy (COSHI). Shadow imaging allows you to visualize fine details of cell-cell interactions and the extracellular space in an unbiased manner. Brain tissue is complex and shadow imaging is a technique that allows researchers to visualize all of the cells in this very complex architecture in an unbiased manner so it was the perfect match for Andrew’s research project!

A career-boosting experience

This has really been an incredible experience. It’s amazing to be trained by the person and team who pioneered this technique. I’m very thankful for this opportunity and humbled to be over here,”reflects Andrew from Bordeaux.

When asked how his visit to Bordeaux might impact his career, Andrew explains that he can certainly imagine doing shadow imaging in the future. He would eventually like to run his own lab at an academic institution in Canada. Being able to bring an exciting and novel technique like this back to Canada would be really impactful for his career, and for science in general.

Shadow imaging is a very exciting technique for studying brain tissue, but getting started on sample preparation and adapting this technique to your research question can be daunting. Coming to the Bordeaux Imaging Center to work with the person who developed this approach and get expert training is a dream come true and will make a big difference to my research. This is an amazing opportunity made possible by the Euro-BioImaging Pilot User Access fund with the goal of making shadow imaging more accessible across diverse platforms,” concludes Andrew.

Get access to one of our services!

You want to be the next user to get access to state-of-the-art technologies that France-BioImaging provides? Please login via Euro-BioImaging website! You just have to choose the technology you want to use, then submit your proposal. All applications will be processed by the Euro-BioImaging Hub in close relation with France-BioImaging. And of course, all scientists regardless of their affiliation, area of expertise or field of activity can benefit from open access services! Users whose projects will be validated by Euro-BioImaging will benefit from a waiver for the access cost on France-BioImaging core facilities (france-bioimaging.org/access)

Thanks to Marianna Childress and Andrew Boyce for the original article!

Dembitskaya, Y., Boyce, A.K.J., Idziak, A. et al. Shadow imaging for panoptical visualization of brain tissue in vivo. Nat Commun 14, 6411 (2023). https://doi.org/10.1038/s41467-023-42055-2

Microglial navigation through complex brain tissue is revealed by confocal shadow imaging (https://doi.org/10.1038/s41467-023-42055-2)

As the 2023 edition of the France-BioImaging Image Contest admissions is still running, we wanted to highlight our previous winners and their projects. Here is a quick throwback to our 2022 winners.

Before getting to the heart of the matter, we want to remind you that you still have time (before November 10th) to submit your best images and try to win your registration fees for one 2024 microscopy-related event! Please make sure you upload your images on the following link:

FBI Image Contest 2023

Last year, we enjoyed the winning images submitted for their artistic take and their quality. Thanks to Carole SIRET, Magalie BENARD and Frédéric FERCOQ for their beautiful images!

  • 1st Place: Carole SIRET, Van de Pavert Team, Centre d'Immunologie de Marseille-Luminy

"Little Monster"

The embryonic formation of lymph nodes, small organs essential for the immune response, is now known. Using light sheet microscopy, scientists were able to determine the dynamics at work in this 13.5-day-old mouse embryo. In blue, the lymphoid cells (LTi), derived from the haematogenous endothelium, a specific tissue of the embryo. They pass into the liver where they proliferate before migrating through the body to give rise to lymph nodes. The 3D information obtained thus makes it possible to follow the interactions of lymph nodes with their environment, in particular with nerve cells, in green, and blood vessels, in white. The lymphatic endothelial cells and some macrophages are visible in red.

Lightsheet Microscopy

Carole Siret is a Research engineer, expert in Lightsheet microscopy, at the Centre d’Immunology Marseille Luminy (CIML) since 2018. She is working in Dr Serge van de Pavert team where they study immune system development. They are particularly interested in the lymph nodes (LN) formation during mouse embryogenesis.

The image she submitted is a projection from a lightsheet acquisition on the UMII (Miltenyi). This image illustrates an E13.5 mouse embryo stained for neurons, LTi (Tissue inducer cells which are the precursor cells for the lymph node), lymphatic and blood vessels. This acquisition was done in the context of the study of the role of Cxcl12 in embryonic LN formation. From previous work it is clear that Cxcl13 and Ccl21 are not expressed present near blood vessels, but it likely that some chemokines, possibly Cxcl12, could be expressed on the endothelial cells. We focus on Cxcl12 since this chemokine has shown to be important for the attraction of several hematopoietic cells. Although it was shown that the receptor for Cxcl12, Cxcr4, is expressed by the mature hematopoietic inducer cells, it is not clear whether it also expressed by the progenitor hematopoietic inducer cells. Next to the possible attraction of hematopoietic cells towards the lymph node anlagen, Cxcl12 is involved in the attraction of nerve fibers. Therefore, the possible role of Cxcl12 could be to both attract hematopoietic cells as well as nerve fibers to initiate a region which is permissive to form lymph nodes.

Thanks to the France-Bioimaging Image Contest, Carole participated to the SFI Congress, where, this year, it was a special joint conference both between the Société Française d’Immunologie (SFI) and the Deutsche Gesellschaft für Immunologie (DGfI). It was a great opportunity to exchange with people at the cutting edge of the immunology field.

  • 2nd Place: Magalie BENARD, Plateforme de Recherche en IMAgerie CEllulaire de Normandie (PRIMACEN), Research infrastructure HeRacLeS, Inserm US 51, CNRS UAR 2026,

"The communication link with others"

Image of a cellular interconnection between two human tumor cells whose cytoskeleton has been labeled with anti-tubulin (ATTO-647N), anti-vimentin (AlexaFluor594) antibodies and with Phalloidin probe (AlexaFluor488). Scale bar 1µm.

Confocal microscopy

Magalie Bénard is a Research Engineer and the Technical Manager at the Cellular Imaging Facilty PRIMACEN (Plate-forme de Recherche en IMAgerie CEllulaire de Normandie).

The image she submitted is a confocal image representing a cellular interconnection tunneling nanotube (TNTs) between two human tumour cells. In a cancer case, some cells are able to express spontaneously TNTs with cytoskeleton protein composition corresponding to specific role of this communication mechanism. In the winning image, the TNT is composed of tubulin (magenta), actin (cyan) and vimentin (yellow) proteins. Called TNT1, this nanotube allows the transfer of intracellular elements such as RNA, proteins or organelles. Moreover, due to the thinness of TNTs, their photo-sensitivity and their fragility, live-cell imaging is technically challenging with regards to potentially damaging methods. Magalie and her team have developed an adapted method to observe TNTs in living cell with high resolution imaging (STED) enhanced by FLIM by using red and near infrared probes.

France-Bioimaging sponsored her participation to the ELMI (European Light Microscopy Initiative Meeting June 6-9, 2023) congress. During this event, she had the chance to present her project through a poster. This congress also offered a great opportunity to have an overview and the last updates on state-of-the-art imaging techniques.

  • 3rd Place: Frédéric FERCOQ, Parasites et Protistes Libres (PPL), Museum National d'Histoire Naturelle


Stage 25 cuttlefish embryo (Sepia officinalis) observed under a confocal microscope.
The cuttlefish was cleared and the tissue autofluorescence was captured.

This image was produced in collaboration with Laure BONNAUD-PONTICELLI and Luis MOLINA from the BOREA laboratory.

Confocal microscopy

Frédéric Fercoq is a postdoc scientist in the Parasitology laboratory of the Muséum National d’Histoire Naturelle (MNHN) in Paris. My main interest is on how myeloid cells participate to the control of parasitic infections, but sometimes at the price of collateral tissue damage. This project involves a lot of microscopy of immune cells, parasites and host tissues to analyse the complex interactions taking place at the site of infection.

The image he submitted has nothing to do with his main project! As he has the chance to work on very different topics and models, this image was acquired as a proof of concept for imaging full embryos of the cuttlefish Sepia officinalis for Frédéric's colleagues Laure BONNAUD-PONTICELLI and Luis MOLINA (BOREA laboratory, MNHN). They work on the nervous system of cephalopod and on the influence of environmental factors during its development. They are now optimizing fluorescent staining for neuronal markers to test the effect of light on the nervous system in situ.

France-Bioimaging sponsored his participation to the FOM (Focus on Microscopy) 2023 congress in Porto. He had the chance to be granted the opportunity to both present his current project through a poster and to give an oral presentation. He was also amazed by the new avenues opened up by the cutting-edge imaging techniques presented throughout the conference.

Want to be the next winner of our FBI Image Contest? Apply through the following link before November 10th, 2023: france-bioimaging.org/fbi-special-events/france-bioimaging-image-contest-2023

You can now apply for a new call to get free open access to instruments and services at one of our nodes’ core facility!

We are happy to announce the first Open Call from the Horizon Europe-funded canSERV project! Cancer Researchers are invited to apply for FREE state-of-the-art services and training at several European Research Infrastructures, including Euro-BioImaging ERIC. Within this project, 28 Euro-Bioimaging Nodes (- Yes, France-BioImaging is part of it too! -) offer access to their expertise. It’s an amazing opportunity for the cancer research community to access a wide-ranging portfolio of services.

CanSERV invites applications covering the entire range of the oncology developmental pipeline, from supporting discoveries in fundamental research to translational science and personalized oncology, addressing at least one of the four strategic goals of the Cancer Mission:

  • Understanding of Cancer
  • Prevention and Early Detection
  • Diagnosis and treatment
  • Quality of life for patients and their families

Researchers from academia, industry and SMEs may apply for several service categories including:

  1. disease models,
  2. cutting-edge imaging and structural biology technologies,
  3. biomarker research and development,
  4. new therapeutic solutions,
  5. complex clinical trial design and support,
  6. personalized oncology implementation pipelines and recommendations and
  7. regulatory support and tools to analyse the socioeconomic dimension of research activities.

Launch of the first call is today, Thursday, October 12, 2023.

Submission deadline is January 4, 2024 at 14.00 CEST.

For more information and call text please visit their CanSERV project website www.canSERV.eu/Calls or contact them at canservprojects@eurobioimaging.eu.

To know which Euro-Imaging’s technologies can help your research project, visit their website www.eurobioimaging.eu/service

In order to answer image data analysis demands, France-BioImaging is launching its first data machine learning competition! The idea? To develop powerful methods that will then end up in creating standards & benchmarks in the field of bioimaging.

The FBI challenge is hinged on a double contribution: from core facilities engineers and from data scientists. The first group will acquire a large number of images to build a dataset, that will later be used by the algorithms. These images will be produced by microscopy engineers & technicians from FBI’s platforms. As for the second contribution, this is where the challenge starts! The challenge will be later published to have a maximum of data scientists to work on the algorithms that best fulfill the analysis task.

The first project is also based on four pillars:

  • Open source + FAIR (Findable, Accessible, Interoperable, Reusable)
  • Supervised learning, it involves annotated datasets to maintain control over performances.
  • In silico annotations, a computer labeling method to avoid manual annotation and its drawbacks.
  • Image-to-image analysis tasks, an image analysis tasks which aim to predict an output image from the input one.

We need you!

The first challenge is still under preparation. It will predict the fluorescence image of cell culture from a bright field, phase contrast and/or DIC microscopy label-free image. Nevertheless, we need you to contribute to the dataset that will supply the machine learning! The more images we have, the better the prediction algorithm will be.

If you are interested, please contact Dorian Kauffmann: dorian.kauffmann@france-bioimaging.org.

Going to Rendez-Vous Carnot 2023? Drop by our booth U10 and say hello! 18 & 19 October – Lyon

In a few days, we will be travelling to Lyon for the Rendez-Vous Carnot 2023! This is the fifth time that we will attend the forum as an exhibitor, in the Research Infrastructures Village. We are going to present France-BioImaging R&D ecosystem and the multiple advanced biological imaging technology developments taking place on FBI imaging platforms and R&D teams.

If you are in Lyon between October 18 and October 19 attending the Rendez-Vous Carnot as well, be sure to drop by our booth U10 (at the Research Infrastructure Village) and meet some of our colleagues at the venue:

  • Caroline Thiriet , France-BioImaging External Affairs Manager
  • Etienne Henry, France-BioImaging R&D and Tech-Transfer mission Officer
  • Alban Belloir, France-BioImaging Communication Officer

We will be happy to discuss with you!

  FBI opens a call for the recruitment of its next Deputy Director for Internal Affairs


The Deputy Director for Internal Affairs will help infrastructure management team to oversee several of its key missions: implement a strategic vision for France-BioImaging, encompassing our three pillars, Innovation, Training, Access; develop a roadmap for next generation imaging technologies and services; increase funding opportunities and develop a sustainable cost model; update and improve infrastructure communication goals and actions; develop ours links with the private sector.
The Deputy Director will work closely with the Manager of Internal Affairs to tailor specific activities, prepare strategic decision-making and prioritize needs for initiatives.

Mandate of the Deputy Director for Internal Affairs

  • Help to develop and implement the strategic vision of FBI’s core activities, in Innovation, Training and Services; synthesize and prepare elements to assist in decision-making
  • Advise the management team to improve cooperation across FBI geographical Nodes; promote the scientific and structuring activities of the infrastructure at the national level, to seek out and federate potential partners, initiate and manage national cooperation programs, and provide expertise and advice.
  • Develop a roadmap for technological developments and their implementation as FBI services
  • Help to develop funding opportunities and develop a sustainable cost model for Innovation and Services
  • Develop links with the private sector, as users of FBI services or partners in FBI core activities including methodological innovations
  • Organize a prospective reflection on the development of new initiatives to be carried out to improve FBI communication


  • Senior scientist (DR or equivalent) with a strong motivation and willingness to strengthen FBI core activities in Innovation, Service and Training;
  • Knowledge of the national landscape in biological imaging, including in innovation and services;
  • Experience in the management of research units or facilities, and projects in the science and innovation domain;
  • Demonstrated experience in fund raising operations for research and innovation projects in biological imaging;
  • Knowledge of the national and international research infrastructures in Biology and Health environment
  • Experience in interdisciplinary scientific and stakeholder networking;
  • Demonstrated ability to work collaboratively with diverse stakeholders;
  • Excellent communications and public relations skills;
  • High proficiency in English language


France-BioImaging is a national research infrastructure distributed throughout France that provides researchers with access to the latest innovations in biological imaging and aims to accelerate the transfer of technological and methodological innovations in biological imaging to the 22 platforms
that constitute the infrastructure. The Deputy Director for Internal Affairs will contribute to the development and strengthening of France-Bioimaging.
The Deputy Director for Internal Affairs will work within the national coordination of the France BioImaging infrastructure. He/she will work within a team distributed between Montpellier and Bordeaux, composed of 4 people: the Scientific Director and the Deputy Director for International Affairs, the Internal Affairs Manager, and the External Affairs Manager.

Time Commitment

FBI’s Deputy Director for Internal Affairs should commit approximately 20% of his overall working time to this mission. Virtual coordination meetings (Directors + Managers) occur weekly, and the FBI Executive Board meets virtually monthly. FBI steering committee meets bi-annually. The Deputy Director is appointed for a 5-year mandate and is eligible to renew his service.


Frequent travels in France and abroad.

Entry into function is planned as soon as possible / November 15th, 2023.

If you are interested,
please send a short CV and a motivation letter at direction@france-bioimaging.org