L’institut CIML (Centre d’Immunologie de Marseille Luminy), membre du nœud marseillais de France-BioImaging, organise en mars 2025 une formation dédié à la microscopie confocale spectrale.

L’objectif de cette formation, ouverte aux ingénieurs et chercheurs utilisant la microscopie confocale, est d’acquérir en mode spectral un panel 10 couleurs sur coupe de tissu et analyser les images réalisées.

Pour vous inscrire, vous devez préalablement remplir le questionnaire disponible ici: https://france-bioimaging.org/wp-content/uploads/2024/12/Questionnaire_Formation-microscopie-confocale-spectrale-mars-2025.pdf

Retrouvez le programme de la formation ci-dessous:

Programme_Microscopie confocale spectrale mars 2025Download

Vous avez jusqu’au 27 janvier 2025 pour vous inscrire et retourner le questionnaire complété!

Contact:

Hélène Pastor: Chargée de formation et du développement des ressources humaines – Inserm
demat-form.dr-marseille@inserm.fr

Inscription (aucune demande ne sera prise en compte sans le questionnaire):

  • Personnels Inserm ou non Inserm dans une structure mixte Inserm : inscription via www.sirene.inserm.fr + envoi du questionnaire à : demat-form.dr-marseille@inserm.fr (Région : Paca – Domaine : TS3 – Imagerie)
  • Autres personnels : formulaire d’inscription + questionnaire à transmettre à demat-form.dr-marseille@inserm.fr

The NeurImag cellular and molecular imaging Facility, member of the Paris Centre Node of France-BioImaging, has initiated the development of a new tool called ExoJ, in collaboration with the teams of Guillaume Van Niel (CRCI2NA, Nantes University), Frederik Verweij (Utrecht University), Thierry Galli (IPNP, Inserm, Université Paris Cité) and Junjun Liu (Shandong First Medical University).

What is ExoJ?

ExoJ is a plugin developed for the Fiji/ImageJ2 software, specifically designed to automate the reliable detection and analysis of exocytosis events from fluorescence microscopy images. Exocytosis is a cellular process where molecules or substances contained within a cell are released to the extracellular environment. This process involves the fusion of a vesicle, a membrane-bound sac, with the cell membrane. Once fused, the contents of the vesicle are expelled into the extracellular space.

How does ExoJ work?

ExoJ automatically identifies user-defined exocytosis events. It extracts key quantitative information such as the intensity, apparent size and duration of each event. ExoJ is fully parameterizable and configurable, making it suitable for studying different types of exocytosis, whatever the imaging modality (TIRF [1] and/or spinning disk [2]). ExoJ is a robust and reliable tool for analyzing large datasets!

What are the benefits of ExoJ?

ExoJ automates the detection of exocytosis events, considerably reducing analysis time compared with manual annotation. Moreover, the results obtained are reproducible, facilitating comparisons between different experiments. Finally, ExoJ is based on Fiji/ImageJ2, an open-source software widely used in the scientific community.

To read the article, click here.

[1] Cois et al., 2024 https://pubmed.ncbi.nlm.nih.gov/39145986/

[2] Hessvik et al., 2023 https://pubmed.ncbi.nlm.nih.gov/37285022/

France-BioImaging members Fabrice Cordelières, Perrine Paul-Gilloteaux and Caroline Thiriet attended ANERIS first Annual Meeting in Seville on November 26-27. During two days, the project’s partners shared updates on the progress of various tasks and activities within the consortium. The event showcased significant progress, fostered collaboration, and charted the way forward in advancing marine biodiversity monitoring technologies.

Day 1 began with a project overview from the project’s coordinator, highlighting key achievements and the project’s aim to tackle the rapid loss of ocean biodiversity by developing innovative tools and technology for monitoring, research and management of marine life.

Partners also presented updates on the 11 monitoring and life-sensing technologies and Perrine provided an in-depth overview on the latest developments in the AIES-MAC tool developed under the ANERIS project, which focuses on detecting and characterizing macro-organisms in underwater images. She highlighted the tool’s key features, improvements made since its initial development, and its ability to enhance the analysis of marine life captured in complex underwater environments.

The afternoon featured co-design sessions where teams defined Operational Marine Biology (OMB) products for the project’s four case studies and also worked on refining the draft infographics, combining input from across the consortium.

On Day 2, discussions shifted to cross-cutting topics such as infrastructure, training, communication, and exploitation. Ayoub El Ghadraoui, Euro-BioImaging Bio-Hub team member and ANERIS project task leader, presented a detailed overview of the training activities held in the frame of ANERIS WP3 Task 3.7, where FBI is involved. A first series of online workshops were held in 2023 with a focus on introducing the fundamentals of AI in image processing and the 2024 workshops focused on Underwater Imaging, Bio-optic, and Participatory Technologies. During the meeting, Ayoub also informed the partners that the ANERIS Workshop 2 was endorsed by the UN Ocean Decade, attesting to the relevance of this workshop for marine sciences.

The day concluded with work table sessions, where critical challenges were addressed, and consortium-wide priorities were established.

From February 6 to 7, 2025, the University of Rouen Normandie will host the 8th edition of the France Cerebellum Club Days. This year’s event will include a session dedicated to cerebellum bioimaging, highlighted by the Primacen imaging platform, a member of the Normandie Node of France-BioImaging.

The France Cerebellum Club is an organization aimed at promoting exchanges between scientists involved in the study of the cerebellum in all its modalities, using a variety of analysis methods.

This new edition will bring together researchers and industrials to discuss the latest advances in the study of the cerebellum. On the program: plenary lectures, thematic sessions and workshops highlighting recent work on the development, functions and pathologies associated with this cerebral region. This year’s topics include the development and evolution of the cerebellum, innovations in applied bioimaging, organoid models and studies of connections between the cerebellum and other brain regions.

Two keynotes will surround these scientific days. Mari Sepp (Heidelberg, Germany) will present her work on the development and evolution of the cerebellum using single-cell genomics, while Christian Hansel (Chicago, USA) will discuss cerebellar instructive signals and their role in neocortical plasticity.

For more information and registration details, click here.

Final Program 8th Cerebellum daysDownload

Le 3 décembre dernier, le Nœud Paris-Centre, membre de l’infrastructure France-BioImaging a organisé une journée intitulée placée sous le signe de la valorisation scientifique et du transfert de technologie. Accessible en mode hybride, elle a réuni une dizaine d’intervenants et une quarantaine d’auditeurs.

L’objectif de cette journée était de rendre accessible la valorisation de l’activité de recherche au plus grand nombre de chercheurs, étudiants, et acteurs du transfert technologique. À cette fin, les participants ont pu bénéficié d’une série de témoignages de chercheurs, de directeurs de startups (ABBELIGHT AVATAR MEDICAL, TWINCKLE FACTORY, INSCOPER) de responsables d’entreprises, et d’acteurs des services de valorisation qui ont converti un résultat scientifique dans le domaine de l’imagerie biologique en un produit ou un service commercialisé.

Ces témoignages ont permis aux intervenants de faire part de leur motivation et leur parcours de transfert technologique avec ses difficultés et ses satisfactions. Les directeurs de startups et responsables d’entreprises ont également présenté aux participants les temps clés de la valorisation d’une découverte scientifique, tels que les échanges entre industriels-chercheurs et la mise en place de la valorisation économique du travail scientifique initial.

Pour clore cette journée, une la table ronde finale a permis aux acteurs des services de valorisation de décrire la fonction, les moyens, ainsi que les modalités d’interaction avec les chercheurs et d’accompagnement du transfert technologique.

Restez connectés, les certaines sessions seront bientôt disponibles en replay!

Last days 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 28 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?

17, December 2024, 14:00 CET

How to apply?

Find all the informations here: https://www.eurobioimaging.eu/news/canserv-open-call-for-early-career-researchers/

The 11th French Society of Angiogenesis meeting that will be held the 4-6 June 2025.

This meeting will take place in Autrans (Vercors), in the mountains close to Grenoble.

The program delves into emerging fields in vascular biology, including blood vessel heterogeneity, their formation, stability, and dysfunctions in diseases such as cancer and cardiovascular conditions. It highlights recent advances in tools and models for rapid clinical applications.

The program will be supported by international experts, including two keynote speakers, Prof. Shahin Rafii of Cornell University, USA, and Prof. Martin Schwartz of Yale University, USA as well as renowned European guest speakers.

The conference will take place in the natural setting of the Vercors, fostering interaction through nature-based activities.

Please visit the website for more information and registration.

On September 6, the Cellular Imaging Master, created in 2004 by Delphine Burel and Ludovic Galas at the University of Rouen Normandie, celebrated its 20th anniversary in partnership with the IBiSA PRIMACEN imaging facility.

Over 50 alumni attended the event, along with the Master’s coordinators and several teaching staff members. The day began with a review of the program’s 20 years and a presentation on international collaborations with the Universities of Turku and Abo Academy in Finland, followed by a vote for the new Master’s logo!

In the afternoon, participants enjoyed fun activities such as karting, bowling, and karaoke at Espace Loisirs Rouen, fostering a convivial atmosphere among students and teachers. Everyone agreed to meet again in five years for future celebrations.

This successful anniversary was made possible thanks to the efforts of the M2 IMAC 2024 class and the support of their sponsors!

Find out more about the IMAC Master’s program here.

France-BioImaging recently participated in two major events dedicated to innovation and industrial collaboration: RDV Carnot and the Cosmetic 360 trade show. These gatherings highlighted the many applications of microscopy in addressing the specific needs of various industries, from pharmaceutical research to the cosmetics sector.

RDV Carnot: opportunities for applied innovation

For France-BioImaging, this event offers a unique opportunity to connect with companies from various sectors (pharmaceutical, food, textile) with advanced imaging needs.

Through direct exchanges, France-BioImaging members were able to better understand industry expectations in sample characterization and analysis, from immunology to textile fiber studies.

This event thus allows France-BioImaging to showcase its advanced microscopy technologies to companies seeking high-potential solutions for applied research.

Cosmetic 360: cosmetic innovation through the lens of microscopy

The Cosmetic 360 trade show is a key event for the cosmetics industry, bringing together companies from across the value chain: large groups, SMEs, start-ups, raw material suppliers, laboratories, and more.

In this sector, microscopy plays a vital role in analyzing natural ingredients, assessing cosmetic product efficacy, and ensuring formulation quality.

Beyond its scientific value, microscopy provides a marketing advantage with the high-quality images it produces, enabling brands to communicate transparently and attractively about product efficacy.

These two events underscored the strategic role of microscopy in addressing the challenges of innovation across various industries. Whether for applied research needs or marketing value, France-BioImaging continues to develop and provide cutting-edge technologies to support companies in their R&D projects.

As the infrastructure evolves, the ongoing identification of industrial needs and emerging sectors will enhance the impact of France-BioImaging’s imaging technologies, fostering collaborations that align with the goals of diverse industries. If you have already identified some needs and potential collaborations, please contact us.

Global BioImaging organizes annual international workshops called Exchange of Experience (EoE), which represent key moments for the international imaging community to come together and discuss common goals, trends and challenges in running open access imaging facilities across the globe.

This year’s host has been our Japanese colleagues from ABis (Advanced Bioimaging Support). We took the opportunity to take part in their annual meeting, one day ahead of the GBI EoE. The program highlighted groundbreaking research, including studies on genome structure in single human cells (Jan Elleberg) and new methods for analyzing multi-cellular dynamics (Tomomi Nemoto). Other high-interest topics included big data acquisition (Hideharu Mikami), expansion microscopy (Xiaoyu Shi) and cognitive biases in neuroimaging (Makiko Yamada).

This 9th edition brought together the global imaging community in Okazaki to discuss shared goals, trends and challenges in managing open-access imaging facilities worldwide. The focus of this edition, “Image Data Horizons – Global Strategies for Accessible Knowledge”, encouraged a rich exchange on practical approaches to data sharing, management, and accessibility.

France-BioImaging’s Data mission co-officer, Perrine Paul-Gilloteaux, presented the FBI.Data project, showcasing France-BioImaging’s leadership data management – recognized as a model approach within the international community.

We also attended the first FoundingGIDE meeting, where we delved more deeply into the steps that image data scientists, supported by funders, decision-makers, and corporate partners, can take to advance towards a Global Image Data Ecosystem (GIDE).

As always, it was a pleasure to meet all the colleagues from the international bioimaging community!

As the 2024 edition of the France-BioImaging Image Contest is still running, we wanted to highlight our previous winners and their projects. Here is a quick throwback to our 2023 winners.

Before getting to the heart of the matter, we want to remind you that you still have time (before November 8th) to submit your best images and try to win your registration fees for one 2025 microscopy-related event! Please make sure you upload your images on the following link:

FBI Image Contest 2024

Last year, we enjoyed the winning images submitted for their artistic take and their quality. Thanks to Laurent LE, Gonzalo QUIROGA-ARTIGAS and Hugues LELOUARD for their beautiful images!

  • 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

Laurent LE is a Post-Doc researcher in the Sandrine Lévêque-Fort Team at Institut des Sciences Moléculaires d’Orsay. His goal is to develop new techniques for time-resolved microscopy and single molecule localization microscopy. During his PhD he especially learned to perform 3D SMLM with SAF light measurement named DONALD. This technique enables to have an isotropic three-dimensional localization precision of 20 nm within an axial range of around 150 nm above the coverslip.

During one of his trainings on the DONALD setup, he acquired this image with a nice round shape that looks like an eye. This image represents the alpha-tubulin of a fixed COS7 cell, labelled with DNA-PAINT and imaged with Atto 647N. The axial information is obtained by DONALD.

Thanks to the France-Bioimaging Image Contest, Laurent participated to the international conference FOM (Focus On Microscopy) in Genoa (Italy). This event is the most important one for his research community.

  • 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

Gonzalo QUIROGA-ARTIGAS is a Post-Doc scientist in the Team “Cytoplasmic Control of Genome Instability” of the Centre de Recherche en Biologie cellulaire de Montpellier (CRBM-UMR5237). His research background is centered on Evolution and Developmental Biology (EvoDevo), a broad field that integrates knowledge from phylogenetics, cell and molecular biology, genetics and genetic engineering, as well as developmental biology and evolution. He is currently undertaking his second postdoctoral position, focusing on the study of the tardigrade Hypsibius exemplaris. Tardigrades are microscopic animals known for their extreme resistance to various stressors, and his research aims to uncover the mechanisms that enable them to endure such conditions. He is conducting this research in Dr. María Moriel-Carretero’s lab at the CRBM in Montpellier. His goal is to become a CNRS researcher in the years to come.

His image depicts the cuticle (or exoskeleton) of a tardigrade protecting three developing embryos. Tardigrades typically couple the moment of cuticle shedding with that of egg laying, a strategy designed to provide an extra layer of protection, ensuring the eggs survive and successfully develop into the next generation. The study aimed to assess the synchrony of embryonic development in eggs laid by the same mother within the same cuticle. This image was captured after staining the animal with a live dye (MemBrite Cell Surface Staining Kit), which highlights the cuticular structures, and a DNA stain (DAPI). A confocal Z-stack of each channel was processed using different depth LUTs in ImageJ, then merged to create the final image.

France-Bioimaging sponsored his participation to the Euro Evo Devo congress (EED) in Helsinki, Finland, in June 2024. This event brought together nearly 700 researchers from around the world, all sharing a passion for this research focus, to gather here for several days and share their ongoing projects. He attended the Arthropod satellite meeting, where he presented a current project using tardigrades as experimental models and received plenty of feedback. He also presented a poster at the main meeting and unlocked numerous potential collaborations, as many researchers showed interest in this animal model.

“Altogether, this meeting has been a fantastic opportunity for me. I was able to share my ongoing projects with the EvoDevo community, which has greatly stimulated my research progress. Additionally, the excellent atmosphere throughout the congress, the impeccable organization, and the collaborations I unlocked have made this experience wonderful both personally and professionally, opening new networking possibilities for my present and future endeavors” says Gustavo Quiroga-Artiguas.

  • 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

Confocal microscopy

Hugues LELOUARD is a CNRS research director working in the field of mucosal immunology at the Centre d’Immunologie de Marseille Luminy (CIML). His research focuses on understanding the role of Peyer’s patch phagocytes in initiating the intestinal immune response.

His image depicts a section of the small intestine from a LyzM-eGFP mouse, featuring a Peyer’s patch, captured using a Zeiss LSM 980 spectral confocal microscope with a mosaic setting of 20 tiles. Spectral confocal microscopy enables the simultaneous imaging of multiple parameters without requiring iterative acquisition steps. Here, staining highlights proliferative cells (Ki-67, yellow), Paneth cells/goblet cells/mucus (UEA-I, blue), epithelial cells (EpCAM, magenta), naïve B cells (IgD, red), T cells (CD3, orange), helper T cells/macrophages (CD4, cyan), phagocytes (CD11c, turquoise) and monocyte-derived phagocytes (GFP, green). This image illustrates the spatial distribution of phagocytes (green and turquoise) within the complex microenvironment of Peyer’s patches. Understanding their role in pathogen uptake, degradation and antigen presentation to effector immune cells is crucial for unravelling the mechanisms that initiate the intestinal adaptive immune response. 

Want to be the next winner of our FBI Image Contest? Apply through the following link before November 8th, 2024: france-bioimaging.org/fbi-special-events/france-bioimaging-image-contest-2024

In a highly competitive call part of the National France 2030 Plan, France-BioImaging was selected to receive special funding to upgrade its technology offer and implement tomorrow’s imaging technological and methodological developments.

Securing Next-Generation Instruments for Biological Imaging 

In recent decades, innovations in microscopy have led to technological revolutions that had strong impacts in important societal fields such as agronomy, marine biology and human health. Life scientists need to have easy access to these technologies and France-BioImaging, with 30 top-notched facilities and thousands of users, is best placed to develop, implement and give access to the latest imaging technologies to the national and international community. 

In 2024, the French Ministry of Higher Education and Research allocated 80 M€ for a call dedicated to the National Research Infrastructures in Biology and Health (Programme Investissement d’Avenir)  to keep their research and technologies at the highest level of excellence.

France BioImaging was a laureate of the call with its project Biological Imaging Next-Generation Instruments (BIOGENI).

In this project, 1.9 M€ will be invested to rejuvenate and upgrade existing technologies and 7.3 M€ will serve to implement new technologies, paving the way for the use of next-generation imaging methods by our users.

The BIOGENI project will both strengthen the visibility and attractivity of France-BioImaging, and provide our researchers access to the most powerful and needed imaging technologies. This includes new technologies in super-resolution and single molecule tracking, multiscale correlative microscopy, light sheet microscopies, high-content and multiplexed imaging, new contrasts and preclinical microscopy. The equipment purchased thanks to BIOGENI will be complemented by new human resources dedicated to data management and image analysis, provided by the Partner Institutions of the infrastructure. This will enable proper data management and analysis, as many of the new technologies deliver very large datasets requiring dedicated tools.

2023 and 2024 were busy years for France-BioImaging. The infrastructure not only made a winning grant proposal to ensure the upgrade of existing technologies and the implementation of new ones, but successfully passed the evaluation of the 2020-2024 period, ensuring allocation of its running budget for the next few years.