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

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

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/

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!

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’s roadmap for managing and analyzing data produced by the infrastructure spans several areas, supported by the transversal node Image Processing and Data Management (BioImage Informatics), as well as engineers and researchers distributed across various nodes.

Two geographically distributed teams are developing solutions: FBI.data for managing microscopy data, from metadata management to using data centers and regional computing centers, pooling efforts for the entire infrastructure; and F-BIAS to develop image analysis as a national service offering within the infrastructure. These distributed groups meet frequently via video conferencing and twice a year in person.

The FBI.Data and FB-IAS teams at the FBI Data Sprint Spring 2024 Edition

The Bordeaux Spring 2024 Edition allowed progress on the test deployment of the FBI.data solution, welcoming the latest F-BIAS recruits, and offering a live open desk. It also involved joint sessions between the two teams to address the challenge of making powerful but complex infrastructure accessible to our users, as well as discussing upcoming and ongoing challenges like the Lightmycells – Grand Challenge at grand-challenge.org. 

The event also featured a public progress update via videoconference, with recordings available here:

FBI.Data

https://youtu.be/PpuVRh8f-uw?si=WQaiq-sRyuHraCzL

FB-IAS

https://youtu.be/TO6ZFlYewX0?si=Upb0HUD3Bo0-uPqa

As the FBI Correlative Light-Electron Microscopy workshop is currently happening at the Bordeaux Imaging Center (FBI Bordeaux node), what a better occasion to highlight a correlative microscopy technique: The Array Tomography.

​Correlative Light and Electron microscopy (CLEM) increases our capacity of biological investigation. By combining light microscopy and electron microscopy, this complementary approach takes advantages of both techniques. In fact, light imaging provides valuable functional information thanks to its labeling power, whereas Electron microscopy excels at high resolution.

Where array tomography (AT) is special is that this technique is based on serial ultramicrotomy (cutting many sections less than a micrometer in thickness) of the sample, section collection onto support, and serial scanning EM (SEM) imaging.

An array of microscopy modes

Array tomography is a versatile microscopy method that offers opportunities to explore cell and tissues in three dimensions. This technique is well suited to image large tissue volumes of your sample with fine structural and molecular details.

Different modes are available, each having its own specificity and benefits:

  • The fluorescence microscopy AT mode (FM-AT) delivers volumetric resolution and molecular marker multiplexing highly superior to traditional fluorescence microscopies.
  • The electron microscopy AT mode (EM-AT) captures three-dimensional ultrastructure at size scales that would require prohibitive effort using traditional serial-section EM methods.
  • And of course, you can combine both modes in a unique one FM/EM-AT with three-dimensional light and electron images acquired in perfect volumetric data.

Why you should consider this technique next time?

The use of FM-AT should be considered for volumetric fluorescence imaging of fixed tissue specimens whenever there is need for very high resolution, high-order molecular multiplexing and/or rigorously depth-independent quantification of fluorescence signal intensities. Use of EM-AT offers perhaps the most convenient approach to volumetric electron microscopy available. Moreover, even though fields of applications are numerous, these attributes establish AT as an ideal choice for the most demanding analyses of diverse cellular architectures within mature and developing tissues such as brain tissue (neuroscientists, this technique is for you!).

Finally, while originally developed for EM, physical cutting of ultrathin sections was found to improve the axial resolution and provide accessibility to the sample for molecular labeling, beneficial for both, EM and light microscopy. Need another argument? The same or adjacent sections can be imaged with different modalities in correlative or even conjugate microscopy!

Get access to one of our services!

You need Array Tomography 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/).

Technical information: https://www.arraytomography.org/

Smith SJ. Q&A: Array tomography. BMC Biol. 2018 Sep 6;16(1):98. doi: 10.1186/s12915-018-0560-1

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!