Training

La plateforme de microscopie Imagerie-Gif organise une formation autour de la microscopie confocale!

Au programme, 5 jours de cours théoriques pour approfondir ses connaissances en microscopie confocale, de la préparation d’échantillon à l’analyse d’image et découvrir des techniques de microscopie photonique avancées.

Jour 1

• Présentation de la formation, présentation des participants (Echanges)
• Primaires de microscopie (Cours/Echanges)
• Découverte de la microscopie confocale (Cours/Echanges)
• Présentation des éléments composant un microscope (Travaux pratiques)
• Découverte des bases de la microscopie confocale (Travaux pratiques)

Jour 2

• Présentation des bases de la fluorescence (Cours/Echanges)
• Bases en traitement et analyse d’images (Cours/Echanges)
• Présentation de l’imagerie spectrale (Cours/Echanges)
• Découverte de la microscopie confocale avancée (Travaux Pratiques)
• Introduction à la microscopie confocale Spinning Disk (Travaux Pratiques)

Jour 3

• Introduction à la préparation des échantillons pour l’imagerie (Cours/Echanges)
• Présentation des protéines fluorescentes et leurs propriétés (Cours/Echanges)
• Imagerie dynamique (Cours/Echanges)
• Présentation de la microscopie à feuillet de lumière (Cours/Echanges)
• Application des bases du traitement et analyse d’images (Travaux Pratiques)

Jour 4

• Présentation de la technique de FRAP (Travaux pratiques)
• Découverte de la mesure de durée de vie en fluorescence (Travaux Pratiques)
• Application de la microscopie à feuillet de lumière (Travaux Pratiques)
• Initiation à la métrologie (Travaux Pratiques)

Jour 5

• Initiation aux techniques de pointillisme (Cours/Echanges)
• Présentation de la microscopie d’expansion (Cours/Echanges)
• Présentation de la microscopie à illumination structurée (Cours/Echanges)
• Présentation de la microscopie STED (Cours/Echanges)
• Bilan de la formation (Echanges interactifs/Quiz)
• Imagerie de vos échantillons (Travaux Pratiques)

Plus d’information ici: https://cnrsformation.cnrs.fr/catalogue/formation/157/atelier-de-microscopie-confocale/

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The first Spatial-Cell-ID Summer School (SCID 2026) will be held from September 13th to 18th, 2026, at the Centre Paul-Langevin in Aussois (French Alps).

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This Summer School is designed to train students and researchers in the rapidly expanding field of Spatial OMICs.

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The program aims to provide an understanding of the field, ensuring that attendees can bridge the gap between wet-lab technologies and the complex bioinformatics workflows required to interpret high-resolution spatial data.

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Applicants are required to submit a motivation letter and may also include a poster abstract if they wish to present their work during the school.

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The registration fee covers access to all scientific sessions and hands-on tutorials, as well as full-board accommodation at the Centre Paul Langevin, including all meals and coffee breaks for the duration of the event. We are also pleased to confirm that registration is free of charge for all CNRS agents.

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All details regarding the scientific program, speakers, and the application process can be found on our website:
https://spatial-cell-id.github.io/scid2026/

Cette formation vise à maîtriser les contraintes d’acquisition 3D au FIB-SEM pour échantillons biologiques.

Elle allie théorie (fonctionnement du FIB-SEM, protocoles de préparation, montage des blocs de résine) et pratique (repérage par tomographie X/microtomie, acquisition FIB-SEM, gestion des problèmes).

Une 3ᵉ partie couvre l’analyse d’images (alignement, post-traitement) et les bonnes pratiques de gestion des données, avec manipulations sur les ordinateurs des participants.

QuPath is an open-source, multi-platform software dedicated to analysis of images originating from slide scanners, but not just that…

It offers a wide possibility for an easy and efficient way to detect, characterize and classify objects, from anatomical structures up to intracellular compartments.

The program of the training will be the following:

• Import of Data
• How to manipulate colored/fluorescent images
• How to create manual or automatic annotations (regions of interest)
• Extract and visualize measurements
• Creation and management of the different classes
• Pixel classification: How to create a model
• Automatic cell detection
• Object classification: based on statistics or by Machine Learning
• Bonus: Use StarDist as Cell Detection module

More info and registration file here: https://greta-cfa-aquitaine.fr/fiches/initiation-au-traitement-et-a-lanalyse-dimages-avec-qupath/

Le pôle photonique du Bordeaux Imaging Center organise une formation dédiée à la visualisation et l’analyse d’image 3D avec le logiciel Imaris.

Cette formation a pour objectif d’acquérir les bases du traitement et de l’analyse d’image microscopie en 3D ainsi que les possibilités du logiciel Imaris.

La session se déroule sur 3 jours et est composée de cours théoriques et d’ateliers pratiques.

Inscrivez-vous ici: https://cnrsformations.cnrs.fr/catalogue/formation/293/imaris-visualisation-et-quantification-dimages-3d/

PFIC, the Gustave Roussy’s microscopy platform, is hosting a practical workshop dedicated on high-resolution 3D label-free imaging using the Tomocube HT-X1Plus microscope, from November 17 to 19, 2025.

It will be a unique opportunity to discover the holotomopgrahy technique wich combines holography (imaging sample with the phase-shift of light) and tomography (Creation of a 3D image from different imaged cross-sections). This technique allows 3d lafel-free microscopy which is interesting for live cells and organoids imaging.

This workshop is open to all and the registration is free (but mandatory)!

Receive for info and secure you time slot sending an email to tudor.manoliu@gustaveroussy.fr

L’Association Française de Cytométrie organise une formation avancée sur la standardisation longitudinale de la cytométrie en flux les 13 et 14 novembre 2025 à Charleroi (Belgique).

L’objectif de cette formation théorique et pratique est d’apprendre à standardiser et optimiser les réglages des cytomètres pour garantir des résultats fiables et reproductibles.

Intéressé par la formation? Retrouvez toutes les informations et les inscriptions dans le lien ci-dessous!

Don’t miss the chance to test the new confocal AX NSPARC (Nikon Spatial Array Confocal) detector on Gustave Roussy PFIC facility.

The NSPARC detector, combined with the Nikon AX R microscope, offers super-resolution 3D imaging, improved sensitivity, and fast acquisition for live-cell studies.

Content: Practical sessions on fixed or live samples (cells in culture for long-duration timelapses).

Practical Details: Application slots are two hours long and are limited to a maximum of three people per session, to ensure an optimal and personalized experience.

You have the option to run overnight timelapses. If this option interests you, please prioritize booking late-afternoon slots.

For any further information (technical details, logistics, etc.), please do not hesitate to contact:

Benoît Ferrandi : benoit.ferrandi@nikon.com
Tudor Manoliu : tudor.manoliu@gustaveroussy.fr
Flavien Berthou (Gustave Roussy) : flavien.berthou@gustaveroussy.fr

Book a session here: https://nikon.reservio.com/workshop-nikon-3?week=2025-10-27

La plateforme de microscopie I2BC organise une formation sur les bases de la microscopie électronique à transmission (MET) appliquée à la biologie cellulaire.

L’objectif de cette formation est d’acquérir les bases de la MET, découvrir et appliquer différentes techniques de préparation d’échantillons pour la MET.

La formation se déroule sur 4 jours et se compose de 8h de cours théoriques et 16h de cours pratiques, sous la forme d’ateliers.

Retrouvez le programme complet et pré-inscrivez-vous ici : https://cnrsformation.cnrs.fr/microscopie-electronique-en-transmission-pour-biologie-cellulaire?mc=microscopie

The Gustave Roussy Photonics Microscopy Platform is excited to announce a workshop dedicated to super-resolution microscopy using the Abberior STEDYCON system!

This workshop is a unique opportunity to explore the applications of super-resolution for your research projects. One-hour demonstration slots will be organized for small groups (2 to 3 people) to maximize everyone’s experience, depending on the number of registrations.

The event is open to all researchers, internal and external to Gustave Roussy.

To register, please contact Tudor MANOLIU or scan the QR code on the attached poster.

EMBL Heidelberg will host a practical course on advanced methods in bioimage analysis. This hands-on training focuses on cutting-edge concepts and tools to strengthen your skills, both in theoretical algorithm development and practical implementation.

With the exponential growth of new imaging techniques, software, and algorithms, bioimage analysis is becoming increasingly complex. As an expert in the field, you need to be able to guide life scientists in using the latest tools and methods to extract meaningful results from microscopy data.

What’s on the program?
* Image analysis workflows and data management
* AI and natural language processing for image analysis
* Deep learning for bioimage analysis
… and much more!

L’École Thématique “Organoïdes 2025”, organisée à Nantes, rassemble experts et passionnés autour des dernières avancées scientifiques et technologiques dans le domaine des organoïdes. Ces modèles tridimensionnels révolutionnent la recherche en biologie, santé et médecine de précision.

Pendant 5 jours, profitez d’un programme riche mêlant cours théoriques, travaux pratiques sur des plateformes de pointe, tables rondes interactives et échanges interdisciplinaires.

La préinscription est obligatoire et permettra de sélectionner les participants sur la base de leur projet et de leur motivation. Cette sélection est rendue nécessaire par le nombre limité de places disponibles. La pré-inscription est possible en cliquant sur le lien ci-joint dans “Link to training activity website”.

Téléchargez ci-dessous le programme général de l’événement!

This advanced training course aims to (1) present the theoretical foundations, (2) clarify and synthesize the various existing approaches to both sample and instrument preparation, and (3) provide an overview of solutions for handling and processing the data acquired. These objectives will be addressed through the prism of two important biological fields of application: Neuroscience and 3D Cell Cultures. Indeed, the versatility of light sheet methods means that questions in these two fields can be addressed at a wide range of scales, from the whole brain or organoid, to the study of the nervous system of small living organisms or brain slices, right down to the single molecule inside spheroids. To address these themes, we will draw on the expertise of the Bordeaux FBI site, whether in neuroscience or in the growth and imaging of 3D cell cultures.

The workshop is an exchange forum for best practices in teaching the use of ML & DL tools in bioimage analysis for a public of biologists i.e. the typical user of core facilities.
At the end of the workshop, the attendees will have:
– an understanding of the tools available for user friendly ML/DL image analysis
– learned how to manage AI project
– built a network of trainers for future collaboration and support for teaching
– built a training curriculum to teach back home

OBJECTIFS
– Acquérir et renforcer les bases théoriques de la microscopie photonique
– Approfondir et maîtriser l’utilisation pratique d’un microscope plein champ et confocal
– Intégrer les principes et possibilités des nouvelles applications et développements en microscopie photonique
– Comprendre les complémentarités des techniques de la microscopie conventionnelle à la super-résolution

PUBLICS
Chercheurs, ingénieurs, techniciens
Prérequis : une expérience en microscopie photonique est essentielle.

PROGRAMME
Cours (40 % du temps)
– Rappels de microscopie conventionnelle, vidéomicroscopie
– Introduction à la microscopie confocale (physique de l’instrument, acquisition, numérisation, échantillonnage, multiples marquages)
– Microscope confocal rapide à disque de Nipkow (Spinning-Disk)
– Comprendre et utiliser les fluorochromes en microscopie confocale, protéines et sondes fluorescentes
– Préparation des échantillons biologiques vivants et fixés
– Traitement et utilisation d’images 2D et 3D appliqués à la microscopie
– Applications particulières en microscopie confocale, FLIM, FRET, etc.
– Résolution augmentée et super-résolution (PALM, STORM, STED, SIM)
– Séminaires d’application
Travaux pratiques (60 % du temps)
Un cycle de dix travaux pratiques sur vingt heures permettra de renforcer le lien entre théorie et applications, de reconnaître les éléments mis en œuvre, d’acquérir des images, de les traiter et de les analyser avec ImageJ notamment.
Une journée sera également dédiée à la découverte de techniques avancées telles que l’excitation biphotonique, la microscopie en feuillet de lumière, les F-techniques (FRAP, photoactivation) et la déconvolution.

La formation portera sur les préparations des échantillons pour la microscopie (de la prise en charge de l’échantillon jusqu’à la coupe sur lame) et les méthodes de vérification de la qualité des échantillons préparés en vue de leur quantification par analyse d’image. Les caractéristiques de préparation de différents types d’échantillons seront présentées (tissus durs – os, biopsie, organe entier…) et mises en pratique.
OBJECTIFS
– Acquérir des bases théoriques et pratiques sur la préparation des échantillons pour la microscopie photonique (lumière visible et fluorescence) et la quantification du signal
– Savoir préparer un échantillon en histologie (coloration – immuno-marquage)
– Connaître les différents types de préparation en fonction de la question biologique posée
– Savoir adapter la préparation des échantillons pour une analyse du signal solide et reproductible
– Savoir reconnaître les artefacts de préparation les plus courants et savoir vérifier la qualité de ses marquages à l’aide de logiciels d’analyse d’image

Ecole de Physique des Houches, in the french Alps, from March 17th to 22th, 2024

This school aims at training students and researchers to master fluorescent markers used in advanced fluorescence bioimaging: their diversity, how they actually work and what are their current development.

Objectives of the school :
Fluorescence microscopy techniques play an essential role in biology and medicine. A very rapidly developing field concerns nanoscale imaging (“nanoscopy”), which today ties together different fields of biology such as structural and cell biology. Similarly, “single molecule” imaging and spectroscopy techniques are in rapid development and play a central role in life science research. All fluorescence microscopy methods are based on labelling samples with appropriate markers: fluorescent proteins, organic fluorophores or nanoparticles. All these type of markers are characterized by very complex photophysical behaviors, leading to blinking, chromatic conversion, photoreactivity, etc… However, nanoscopy and single molecule spectroscopy or imaging, specifically rely on the ability to understand and control these properties.

The school we offer is motivated by the fact that more and more laboratories around the world are committed to implementing advanced microscopy techniques, especially super-resolution, with an increasing number of dedicated platforms. However, there is a lack of overall knowledge about the selection of fluorescent markers, their properties and mechanisms, and the type of artifacts they can create. The school’s objective, through interdisciplinary teaching between physics, chemistry and biology, is to overcome this gap by transferring knowledge to the participants’ laboratories. Our school also aims to make participants aware of new developments in the field in order to prepare them to become major players in the breakthroughs that may result from them.

More information: fluorescenceleshouches.wordpress.com

OBJECTIFS
– Acquérir les bases théoriques de la microscopie électronique en transmission (MET) nécessaires pour une exploration fonctionnelle de la cellule
– Appréhender les différentes techniques de préparation des échantillons associées à la MET
– Apprendre à préparer son propre échantillon

PUBLICS
Chercheurs, ingénieurs et techniciens des secteurs public et privé, intéressés par la résolution ultrastructurale de la MET et les approches de microscopie corrélative en biologie cellulaire

Afin d’adapter le contenu du stage aux attentes des stagiaires, un questionnaire téléchargeable ICI devra être complété et renvoyé au moment de l’inscription.

PRÉREQUIS
Stage ouvert aux débutants et aux utilisateurs réguliers

PROGRAMME
Cours et séminaires d’application (8 h)
– Les électrons en imagerie
– Préparation des échantillons, immunomarquages
– Traitement des petites particules : coloration négative et cryo-microscopie
– La 3D en microscopie électronique
– Séminaires d’application par 2 invités extérieurs

Ateliers (16 h)
– 1 : fixation chimique, déshydratation et inclusion en résine (4 h)
– 2 : ultramicrotomie (coupes semi-fines et ultra-fines) (4 h)
– 3 : coloration négative et microscope électronique (2 h)
– 4 : cryofixation sous haute pression et cryo-susbtitution (2 h)
– 5 : charte de préparation des échantillons (2 h)
– 6 : TP à la carte (au choix : cryo-microscopie, cryo-ultramicrotomie, tomographie, initiation à ImageJ, préparation des grilles – Formvar, microscopie électronique à balayage – applications) (2 h)

Les stagiaires, après concertation avec les responsables du cours, pourront apporter leur matériel.

EQUIPEMENTS
2 microscopes JEOL1400 120kV et autres équipements Leica pour la préparation des échantillons
Voir le site internet de l’I2BC pour une description détaillée des équipements

INTERVENANTS
Membres du pôle de microscopie électronique de la plateforme Imagerie-Gif (responsable : Claire Boulogne) et 6 intervenants extérieurs

Expansion microscopy (ExM) is a relatively new super-resolution method based in the isotropic dilatation of the biological sample in order to overcome the diffraction limit of conventional microscopy. Since its development in 2014, many laboratories have been implementing and adapting the technique to their needs, and the biological applications of ExM grow exponentially.

The ExM working group from the French fluorescence microscopy network (RTmfm), with the support of France-BioImaging, is organizing a workshop on ExM at Bordeaux on October 2, 2023. During the workshop, we will cover different aspects of ExM protocols with experts in biochemistry and biology, and we will present examples of biological applications.

Invited speakers:
– Marine Laporte (Institut NeuroMyoGène, Université Claude Bernard, Lyon).
– Sven Truckenbrodt (E11 Bio, Alameda, California, US).
– Maxence Wisztorski (University of Lille, Inserm, CHU Lille, U1192).

You can register here to enjoy the ExM community during a day, and to show you work with a poster or a short talk. We have limited seats!!! To send abstracts please contact monica.fernandez-monreal@bordeaux.fr and jim.dompierre@ibgc.cnrs.fr.

Deadline for applications is July 15th 2023.

Preliminary program: download here.

OBJECTIFS
– Acquérir des bases théoriques et pratiques sur la préparation des échantillons pour la microscopie photonique (lumière visible et fluorescence) et la quantification du signal
– Savoir préparer un échantillon en histologie (coloration – immuno-marquage)
– Connaître les différents types de préparation en fonction de la question biologique posée
– Savoir adapter la préparation des échantillons pour une analyse du signal solide et reproductible
– Savoir reconnaître les artefacts de préparation les plus courants et savoir vérifier la qualité de ses marquages à l’aide de logiciels d’analyse d’image

PROGRAMME
La formation portera sur les préparations des échantillons pour la microscopie (de la prise en charge de l’échantillon jusqu’à la coupe sur lame) et les méthodes de vérification de la qualité des échantillons préparés en vue de leur quantification par analyse d’image. Les caractéristiques de préparation de différents types d’échantillons seront présentées (tissus durs – os -, biopsie, organe entier…) et mises en pratique.

EQUIPEMENTS
Microtomes ; cryostat ; automate de coloration ; serial block face ; scanner de lame (fond et fluorescence) ; microscope champ large et confocal ; ordinateurs avec QuPath et ImageJ Voir le site internet de la plateforme MicroPICell pour une description détaillée des équipements

Les techniques d’imagerie photoniques ont longtemps été limitées à l’étude d’échantillons biologiques sortis du contexte physiologique et métabolique de l’animal comme les lames de cellules ou les boîtes de culture. Désormais, il est technologiquement possible de visualiser les interactions biologiques au sein même de l’animal vivant par la microscopie in vivo (animal entier) ou in situ (coupe épaisse de tissus vivant). Des verrous technologiques existent qui peuvent être levés avec l’avènement des technologies d’impression 3D et autres outils open source à bas coûts, permettant de faciliter grandement la mise en place de la microscopie intravitale dans les laboratoires de recherche.

Objectifs de la formation : mettre en place différents moments d’échanges entre les chercheurs, les ingénieurs formateurs et les stagiaires autours des thématiques scientifiques et techniques sous-tendues par la microscopie intravitale.

Fin des inscriptions le 20/06/2023

Plus d’informations : https://institutcochin.fr/formations/anf-microscopie-intravitale-situ-petit-animal

Objectifs
1. Rappeler et/ou fournir les éléments de base de la microscopie par FLIM : qu’est-ce que c’est le FLIM ? Le FLIM est-il la bonne méthode pour répondre à ma question ?
2. Établir des « lignes-guide » pour tout utilisateur et/ou personnel de plate-forme souhaitant démarrer des expériences de microscopie par FLIM : quel type d’échantillon ? Pour quelle application ? Comment bien préparer son échantillon ? Quels sont les limites des échantillons ? Quels sont les contrôles indispensables à intégrer pour chaque expérience et quoi faire si les contrôles présentent des problèmes ?
3. Illustrer, avec des ateliers pratiques, des applications en FLIM pour la biologie qui sont susceptibles d’être l’objet d’une large diffusion au sein des laboratoires de recherche et des plateformes de microscopie : comment déterminer la présence d’interactions protéine-protéine à l’échelle sous-cellulaire (par ex. à la mitochondrie ou dans le cytoplasme des cellules), la concentration de certains métabolites intracellulaires (par ex. NAD(P)H, FAD) et l’activité d’une voie de signalisation intracellulaire (kinase ; autophagie)

Programme
➢ Axe 1 : principes du FLIM
➢ Axe 2 : préparation d’échantillons et contrôles des expériences en FLIM
➢ Axe 3 : FLIM pour déterminer les interactions protéine-protéine
➢ Axe 4 : FLIM en mode biosenseurs (activation de voies biochimiques intracellulaires)
➢ Axe 5 : FLIM en mode autofluorescence (activation de métabolites intracellulaires)

Super-resolution light microscopy (SRLM) is a dynamically evolving field of biomedical approaches. The knowledge of these approaches enables scientists to apply the suitable type of SRLM to their own research projects.

The main goal of this course is to practically demonstrate a broad variety of SRLM methods. During the course, a majority of available SRLM systems will be demonstrated and available for hands-on experience. Leading experts of the field will present their research and methodology. Many opportunities for discussions and social networking will provide a unique and highly efficient environment to support sharing of skills and knowledge. This promotes establishing of contacts and communication channels within the in-field scientific SR community.

The focus of the course is on the practical part with a lot of hands-on sessions supported by theoretical lectures and complemented by presentations of ongoing scientific projects presented by leaders of the field.

OBJECTIFS DE LA FORMATION
Acquérir les bases théoriques des pratiques en microscopie de super-résolution et s’initier aux méthodes d’analyses :
– Microscopie de déplétion par émission stimulée : STED
– Microscopie par localisation de molécules uniques (SMLM) : (spt)PALM, (d)STORM et (u/DNA)-PAINT
– Analyse d’images

CONTENU DE LA FORMATION
Cours théoriques :
Présentation générale des techniques de super-résolution : STED et SMLM
Description du montage expérimental
Intérêts, avantages et limites de chaque technique
Sondes fluorescentes et stratégies de marquage pour la super-résolution
Autres techniques de super résolution : Microscopie d’expansion, iSIM, ISM, AiryScan, et SRRF
Techniques de super résolution utilisant une illumination par feuille de lumière
Séminaires d’application : Présentations scientifiques d‘applications biologiques par des utilisateurs avancés des certaines techniques de super-résolution

Phase pratique :
Pour les techniques, d’Expansion, de STED et de SMLM, des TP de 2h permettront de renforcer le lien entre théorie et application sur différents échantillons biologiques. Des systèmes de laboratoire et commerciaux seront mis à disposition. Des démos seront aussi proposées au choix sur les techniques alternatives de super-résolution.

Table ronde et discussion : La formation se terminera par une table ronde-discussion

Test sur échantillons : Journée optionnelle dédiée aux échantillons des participants sur l’ensemble des systèmes mis à disposition (nous contacter)

Plus d’informations sur : https://greta-cfa-aquitaine.fr/fiches/microscopie-de-super-resolution-des-bases-a-la-pratique/

The Institut de biologie intégrative de la cellule (I2BC) is organizing a Cytometry Workshop from March 28 to March 30, 2023.

By the end of the workshop, you will know the theoretical bases in flow cytometry (analysis and sorting, experimental strategies), the different applications and developments in a wide variety of fields of application and be able to learn how to use cytometers.

Open to researchers, engineers and technicians, the program is divided between lectures and practical sessions.

What will you learn? The EXCITE summer school is dedicated to teaching the basics and wider context necessary to understand recent advances and current challenges in biological and medical imaging. Cutting-edge techniques using a wide range of image-formation mechanisms — including magnetic resonance imaging, positron emission tomography, infrared and optical microscopy, electron microscopy and X-ray imaging — will be discussed, with a focus on multimodal and multiscale imaging methods, together with supporting technologies such as computer-aided image analysis and modelling.

What is the structure? The summer school will provide different tracks for participants with a background in life sciences and physical sciences, respectively. The students will have lectures in the morning and hands-on sessions in the afternoon. The highlight is a full-day project in a topic of choice within an academic institution or institute. The program is rounded off with the EXCITE Symposium on “Bringing algorithms close to
data and scanner: distributed learning for biomedical imaging” and an industry day.

How do I attend? Admission is decided based on the applicant’s curriculum vitae, a statement of purpose and applicant’s references. Students who have not yet started a PhD program may apply for a stipend. Interested students are kindly asked to submit their application pack including their study grades and reference letter on our homepage (https://excite.ethz.ch/education/summer-school/Application2022/Application2022.html)

APiL is an advanced management course in Life Sciences and Health, developed by the Institut Pasteur (IP) and the Ecole Supérieure de Commerce de Paris (ESCP). APiL aims to provide the keys to develop Biotech, Medtech, AI for Health, or even a connected medicine application. It is an intensive and demanding training involving teachers from two institutions, each renowned in their field.

It is a part-time course for professionals, doctoral students, and Postdocs in Life Sciences and Health who want to learn from startup creation to its business & management.

The academic year starts in September. Students follow business courses, capsules modules on entrepreneurship and start-up creation in healthcare, workshops, companies visits, capsules, and other seminars.

Students will obtain a diploma from both Institutions and will become ESCP & Institut Pasteur Alumni.

At the end of the program, students have a global vision allowing them to become successful entrepreneurs, innovation leaders, or top managers in life sciences and health through an intensive, specialized, carefully-crafted, advanced program co-created and designed by Institut Pasteur & ESCP Business School.

Besides complex networks of protein interactions, the life of the cell is also governed by biophysical parameters. The objective of this course is to disseminate practical knowledge concerning recent quantitative fluorescence microscopy methods aiming at characterizing biophysical properties of the living samples. In the present practical course, we wish to introduce recent imaging methods allowing participants to assess three essential biophysical components of the intracellular environment:

– the diffusion-reaction dynamics
– the physico-chemical state
– the mechanical tensions

Each component will be assessed in living cells and tissues using complementary methods. Hands-on sessions will focus not only on data acquisition but also on the methods available to quantitatively analyze and model these data.

The applicants will be able to register either for on/site or online participation. Online participants will have access to all talks and round tables as well as interactive discussion via chat. Practicals will only be accessible to onsite participants. If along the selection process, some applicants cannot be selected for on/site participation due to the limited number of people that can participate in the practicals, we will offer them the possibility to participate online.

This workshop will present the principle of light-sheet fluorescence microscopy (LSFM). Seminars will
cover basic principles, applications, and challenges of LSFM, while practical sessions will allow to test different
LSFM implementations and to learn sample preparation and data processing methods.
The workshop will be divided in two parts:
A first theoretical part in Bordeaux from the 16th to the 18th of May 2022 which will cover basic principles, applications and challenges of LSFM imaging through seminars,
A second practical part along June 2022 where you will have the possibility to choose the set-up on which you want to be trained amongst many systems available within the France BioImaging community.

Fluorescence microscopy techniques play an essential role in biology and medicine. A very rapidly developing field concerns nanoscale imaging (“nanoscopy”), which today ties together different fields of biology such as structural and cell biology. Similarly, “single molecule” imaging and spectroscopy techniques are in rapid development and play a central role in life science research. All fluorescence microscopy methods are based on labelling samples with appropriate markers: fluorescent proteins, organic fluorophores or nanoparticles. All these type of markers are characterized by very complex photophysical behaviors, leading to blinking, chromatic conversion, photoreactivity, etc… However, nanoscopy and single molecule spectroscopy or imaging, specifically rely on the ability to understand and control these properties.

The school we offer is motivated by the fact that more and more laboratories around the world are committed to implementing advanced microscopy techniques, especially super-resolution, with an increasing number of dedicated platforms. However, there is a lack of overall knowledge about the selection of fluorescent markers, their properties and mechanisms, and the type of artifacts they can create. The school’s objective, through interdisciplinary teaching between physics, chemistry and biology, is to overcome this gap by transferring knowledge to the participants’ laboratories. Our school also aims to make participants aware of new developments in the field in order to prepare them to become major players in the breakthroughs that may result from them.

Workshop on Expansion Microscopy – ANF RT-MFM

Programme available here: https://sites.google.com/view/microscopie-par-expansion/programme

The event will take place from November 15 to 19, 2021 at the PFIC UMS AMMICa imaging Facility of Gustave Roussy.

Registrations are free but required.

The number of places being limited to 15 people, we will select the candidates according to their motivations.

The registration deadline is September 15, 2021.

Vous avez entendu parler de la révolution du machine learning, mais ne savez pas par où commencer pour vous y mettre ?
Vous avez tenté d’utiliser des logiciels clé-en-main mais peinez à comprendre comment ils fonctionnent ?
Vous suivez avec minutie les tutoriels disponibles sur le net mais n’avez pas réussi à installer cette *** de bibliothèque qui débloquerait votre problématique de segmentation ?

Si au moins l’une de ces phrases décrit votre situation actuelle, l’ANF du RT-MFM “Machine learning pour les microscopies” est faite pour vous ! Elle vise à vous faire monter en compétence sur les problématiques de machine learning.
A l’issue de la formation, vous serez en mesure d’utiliser ces techniques dans votre activité quotidienne, mais aussi de partager les outils, savoirs et bonnes pratiques aux utilisateurs de votre plateforme.

Nous avons réuni la fine fleur du ML pour vous !
• Olivier Buri, Bioimaging and Optics Platform, EPFL
• Romain Guiet, Bioimaging and Optics Platform, EPFL
• Guillaume Jacquemet, The cell migration lab, Åbo Akademi University
• David Rousseau, Université d’Angers
• Daniel Sage, Biomedical Imaging Group, EPFL
• Bertrand Vernay, IGBMC

L’ANF se déroulera en 3 temps:
• Une pré-formation vidéo en amont pour acquérir des bases et un vocabulaire commun avec débriefing en visio;
• Une formation de 3 jours en présentiel à la Rochelle
• Un retour d’expérience post-formation sous la forme d’une table-ronde dédiée à MiFoBio

> Quand ?
Du mardi 19 (14h) au vendredi 22 octobre 2021 (12h)

> Où ?
Résidence La Fayette La Rochelle

> Pour qui ?
– BioImage Analysts en plateforme
– Participants maitrisant un language de scripting (Python, macros ImageJ …)
– Limité à 14 participants (une sélection des participants est prévue)
NB: la formation se déroulera sur les ordinateurs des participants

> Pour quoi ?
• Acquérir le vocabulaire
• Acquérir la maitrise des outils “clé-en-main”
• Repartir avec sa machine configurée
• Transférer ce savoir-faire

The aim of this workshop encompasses most of the workflow steps from the 3D-sample preparation (organoids, spheroids, encapsulated 3D cultures), how to process them (histology, staining), how to mount them (for upright, inverted etc…), and finally how to image them with various microscopy techniques (from super resolution microscopies -liveSR or STED- to microscopies dedicated to thick samples (two-photon, ultramicroscope), from fast optical scanning spinning-disk to High Content Screening -HiTech and LowTech-).

Bench work is possible thanks to the TBM Core Facility, and the microscopes are provided by the BIC facility and the LP2N (home-made setup).

The number of attendees will depend on the rules that will prevail at this time.
Seats will be limited.
Registration is free but mandatory https://wkshpimageoids.sciencesconf.org/
Registration deadline: 6th Sept at noon
The organisation committee will then select participants and contact them shortly after registration closure.

There will be 4 seminars with the following keynote speakers:
• Xavier Trepat -link- (IBEC, Barcelone)
• Fanny Jaulin -link- (Institut Gustave Roussy, Paris)
• Laura Broutier -link- (CRCL, Lyon)
• Charlotte Rivière -link- (ILM, Lyon)

Each seminar will be preceded by a talk from our industry partners: Corning, StemCell, TreeFrog Therapeutics and Idylle.
They will be accessible freely on a dedicated streaming platform, upon ad-hoc registration which will be set soon.

We presume there will be restrictions due to the sanitary circumstances, therefore we strongly encourage you to anticipate about your own protection and sanitary status.

Who should apply? The summer school addresses excellent MSc and PhD students as well as scientists from industry with background in biology, chemistry, computer science, engineering, mathematics, medical science or physics. It follows a challenging and demanding schedule. We plan to admit about 60-80 participants (internally and from abroad).

What will you learn? The EXCITE summer school is dedicated to teaching the basics and wider context necessary to understand recent advances and current challenges in biological and medical imaging. Cutting-edge techniques using a wide range of image-formation mechanisms — including magnetic resonance imaging, positron emission tomography, infrared and optical microscopy, electron microscopy and X-ray imaging — will be discussed, with a focus on multimodal and multiscale imaging methods, together with supporting technologies such as computer-aided image analysis and modelling.

What is the structure? The summer school will provide different tracks for participants with a background in life sciences and physical sciences, respectively. The students will have lectures in the morning and hands-on sessions in the afternoon. The highlight is a full-day project in a topic of choice within an academic institution or institute. The program is rounded off with the EXCITE Symposium on “Digital Twins: generating predictive models from imaging data” and an industry day.

How do I attend? Admission is decided based on the applicant’s curriculum vitae, a statement of purpose and applicant’s references. Students who have not yet started a PhD program may apply for a stipend. Interested students are kindly asked to submit their application pack including their study grades and reference letter on our homepage (www.excite.ethz.ch/education/summer-school/Application2021.html)

Virtual course: Course Overview

Correlative Light and Electron Microscopy (CLEM) allows precise localisation of an event of interest within cells and tissues. During this course, we will focus on a specific method that has been developed at EMBL that enables the location of fluorescent proteins with high accuracy at the ultrastructural level. The course will cover both the theory and practicals of high precision CLEM, as well as opportunities to discuss their research with CLEM experts and receive practical and troubleshooting advice.
Audience

This course is intended for scientists with experience in EM who want to further develop their skills in high-accuracy correlated microscopy.

Modules/Resources
The course will combine lectures and remote hands-on practical work covering all steps in the work flow including cryogenic sample preparation, ultramicroscopy, image registration and electron tomography.

Learning Outcomes
Participants will gain hands-on experience with the CLEM methods and learn tips from the people who developed the methods.

This webinar series will focus on the overarching topic of light microscopy areas including latest advances in light microscopy ecosystem covering state-of-the-art technologies, efficient workflows, and sample preparation methods.

Imaging core facility staff including personnel of light and electron microscopy core facilities and biomedical imaging units are invited to attend the webinars. Principal investigators, post-doctoral researchers, and graduate/PhD student who utilize imaging and microscopy technologies are also invited to attend. Webinar series are free of charge and we invite everyone from around the globe to attend the webinars.

Introduction to Confocal Microscopy (Tuesday, 30th March at 15:00 CEST)

Confocal Microscopy is one of the central pillars of the imaging facility. This training will provide a basic overview of how a confocal microscope works and why this is beneficial for Life Science imaging.

La formation portera sur les préparations des échantillons pour la microscopie (de la prise en charge de l’échantillon jusqu’à la coupe sur lame) et les méthodes de vérification de la qualité des échantillons préparés en vue de leur quantification par analyse d’image. Les caractéristiques de préparation de différents types d’échantillons seront présentées (tissus durs – os -, biopsie, organe entier…) et mises en pratique.
Cours et tables rondes (40 %)
– Préparation des coupes :
. détails des étapes de préparation des coupes histologiques paraffine et congelées
. présentation des diverses colorations, des protocoles, de cas d’écoles et d’erreurs typiques à éviter
– Immuno-marquages :
. préparations en immuno-histochimie sur coupe (DAB – Red chromogène…)
. éléments de traitement du signal et d’analyse d’image pour validation de la bonne préparation des échantillons
. aspects quantitatifs
. immunofluorescence – multiplexing
– Introduction à la préparation des gros échantillons : spécificités liées aux marquages et à la préparation des gros échantillons pour observation en microscopie
Travaux pratiques (60 %)
– Préparation des échantillons histologiques (mise en œuvre des protocoles présentés)
– Visualisation au microscope des échantillons préparés
– Acquisition et analyse des images dans les meilleures conditions (logiciels gratuits QuPath et ImageJ)
Possibilité de faire les TP, à des fins pédagogiques, sur des échantillons apportés par les stagiaires.

EQUIPEMENTS
Microtomes ; cryostat ; automate de coloration ; serial block face ; scanner de lame (fond et fluorescence) ; microscope champ large et confocal ; ordinateurs avec QuPath et ImageJ
Voir le site internet de la plateforme MicroPICell pour une description détaillée des équipements

France BioImaging (FBI) is organizing a remote training on Light-Sheet Fluorescence Microscopy (LSFM), which enable 3D imaging of biological samples with unprecedented spatio-temporal resolutions and low perturbing effects.

LSFM methods actually cover a large variety of implementations which allow imaging a wide range of sample types, from single cell to whole organs or organisms both live and fixed. These new imaging capabilities are revolutionizing the way we visualize our samples and address biological questions. However, imaging with a light-sheet microscope raises many questions about the choice of the set-up depending on the sample to image, the sample preparation and mounting protocols or the data management (storage, visualization, quantification). Thus, it can be difficult to find its way through the numerous microscope implementations, protocols and tools that have been extensively developed over the last 20 years. We therefore decided to review all those questions in a remote training.

Our goal is to help people who want to jump into the world of 3D imaging and are seeking the best solution for their samples and biological questions. In that perspective, we will provide a comprehensive picture including all the possibilities and challenges regarding LSFM.

The training will be divided in 3 parts:

– Theoretical courses on LSFM
– Practical demonstrations of several LSFM implementations available throughout the FBI infrastructure
– Live online question and answer session

For the two first parts, videos will be available on a Youtube FBI channel. The participants will have 3 weeks, from the 15th of February to the 5th of March 2021, to watch those videos and will be invited to ask questions or comment.

FBI experts will then answer all questions during a live interactive video chat on the third week of the training (5th of March where participants will have the opportunity to directly interact with the experts.

Expansion microscopy virtual workshop.

For the convenience of our global attendees, we will be conducting two sessions: Session one (10:00-12:30 UTC), Session two (16:00-18:30 UTC).

This online course will focus on several key areas including data management of image data using OMERO open source data management solution, cloud-based sharing of image data using next-generation image file format, and image data repositories including Image Data Resource (IDR) and EMPIAR (Electron Microscopy Public Image Archive) as well as new developments within BioImage Archive.

The workshop will last 3 ½ days and is built on the basis of an alternation between theoretical and practical sessions. Both will be in English and provided by national expert trainers.
On day 2 a mini-symposium will be organized to present the last developments in different LSFM domains (instrumentation, sample preparation and data analysis) done by international experts. This mini-symposium will be open to a larger audience in order to promote LSFM approaches to the local research community.
The workshop will encompass various theoretical aspects of LSFM from sample preparation, to image acquisition and first post-processing steps (3D reconstruction, visualization).
The workshop will span various scales that can be imaged with LSFM based on at least 4 different LSFM set-ups.

S’initier à ImageJ
-Qu’est-ce qu’Image J ? Où le trouver ? Comment l’installer ?
-Qu’est-ce qu’une image ? Comment ouvrir les formats d’images propriétaires ?
-Qu’est-ce que l’histogramme d’une image ? Comment le manipuler ?
-Le cas des images couleur : notion de table de couleurs, les différents types d’images couleur (overlay,
composite…). -Calibration en distance d’une image
-Montage de planches. -Travailler avec des images 3D : projections et visualisation 3D.
Quantification d’images
-Manipulation de régions d’intérêt et mesures simples en 2D.
-Amélioration d’image en préalable à la quantification : les filtres (linéaires, de rang, fréquentiels).
-Travailler sur une image binaire : notions de morpho-mathématiques.
-Analyse en composante connexe, dénombrement et quantifications d’objets en 2D et 3D.
-Calibration d’images en intensité. -Segmentation d’images (N&B et couleur).
-Quantifications avancées (co-localisation, pistage). -Introduction à l’automatisation de tâches.

Within the context of the COST action COMULIS (Correlated Multimodal Imaging in Life Sciences, CA17121) we are organising a training event on ‘Image processing for correlated and multimodal imaging techniques’.

COMULIS (Correlated Multimodal Imaging in Life Sciences) is an EU-funded COST Action that aims at fuelling urgently needed collaborations in the field of correlated multimodal imaging (CMI), promoting and disseminating its benefits through showcase pipelines, and paving the way for its technological advancement and implementation as a versatile tool in biological and preclinical research.

Cours (40 % du temps)
– Rappels de microscopie conventionnelle, vidéomicroscopie
– Introduction à la microscopie confocale (physique de l’instrument, acquisition, numérisation, échantillonnage, multiples marquages)
– Microscope confocal rapide à disque de Nipkow (Spinning-Disk)
– Comprendre et utiliser les fluorochromes en microscopie confocale, protéines et sondes fluorescentes
– Préparation des échantillons biologiques vivants et fixés
– Traitement et utilisation d’images 2D et 3D appliqués à la microscopie
– Applications particulières en microscopie confocale, FLIM, FRET, etc.
– Résolution augmentée et super-résolution (PALM, STORM, STED, SIM)
– Séminaires d’application
Travaux pratiques (60 % du temps)
Un cycle de dix travaux pratiques sur vingt heures permettra de renforcer le lien entre théorie et applications, de reconnaître les éléments mis en œuvre, d’acquérir des images, de les traiter et de les analyser avec ImageJ notamment.
Une journée sera également dédiée à la découverte de techniques avancées telles que l’excitation biphotonique, la microscopie en feuillet de lumière, les F-techniques (FRAP, photoactivation) et la déconvolution.

Une séance pratique d’acquisition d’images peut être programmée sur les échantillons apportés par les stagiaires à des fins pédagogiques. Pour connaitre les possibilités de stockage des échantillons, veuillez prendre contact avec le responsable de la formation. “Happy Hour”, le mardi à 18h15

Bioimage analysis has become a keystone of biological research: the deluge of data produced by increasingly advanced microscopes calls for experts able to guide life scientists in the methods and software to be used to produce quantitative knowledge from this data. Due to the complexity of the data, without such expert guidance, it is very likely that image analysis algorithms may be applied incorrectly, possibly even producing erroneous results. Moreover, the diversity of imaging modalities, analysis algorithms and software solutions is growing so rapidly that even experts are overwhelmed.
This advanced course concentrates on teaching cutting-edge concepts and tools for quantitative image analysis, and will seek to upgrade the competencies of future bioimage analysis experts on both theoretical algorithm advancements as well as on practical implementation skills.

This one-week school provides a hands-on introduction to image processing and analysis, with an emphasis on biologically relevant examples.
Covered topics will encompass :
– Basics in Image Formation
– ImageJ, from everyday use to advanced applications
– State-of-the-art analysis procedures like e.g. co-localisation
– Machine Learning including Deep Learning
– Stitching and registration
– Data analysis using KNIME

This training session will cover the basics of super resolution in photonic microscopy, principally: STED microscopy (STimulated Emission Depletion) and single molecule localization microscopy. We will also present alternative solutions for super resolution like SRRF (Super resolution Radial Fluctuations), Airy Scan, or Computer based pixel-reassignment like ISM (Image Scanning Microscopy), and solution based on light sheet illumination. The mornings will be dedicated to theoretical lectures and application seminars. The afternoons will allow the participants to see demonstrations of these different techniques in front of home-made or commercial systems. The fourth day will be a full hands-on day, as participants will be invited to bring their own samples and test them on the different systems available, like STED microscope, STORM, lattice light sheet, ISM, SRRF….

Rapid advances in live imaging of targeted cellular morphologies and functions underpin the emerging revolution in our understanding of synapses, circuits, and behaviour. In keeping with its long-established tradition, this Cajal course will assemble at its international faculty leading experts in developing and exploiting cutting-edge imaging techniques that have been propelling such advances. How to combine genetically encoded fluorescence labelling with behavioural designs, micro-circuit monitoring, or single-molecule tracking, how to avoid pitfalls of having false-positive observations and inherent noise, how to best analyse your multi-dimensional data will be, among others, the recurrent subjects of the Course.

The use of fluorescence microscopy (wide field, confocal, multiphoton, and now superresolution) in combination with genetically encoded fluorescence probes comprise a powerful set of scientific tools to study live cells. However, surprising little practical and theoretical training in such methods exists within standard curricula, particular at the early stage of training (Masters or Doctorate level). This course offers to cover basic optics principles necessary to understand the origin of microscope resolution and design. Participants will get hands-on experience implementing simple optical configurations to illustrate these fundamental principles. Subsequently, participants will perform experiments on state-of-the-art imaging equipment provided by microscope vendors.

This training school will cover the basics of image analysis using ImageJ/Fiji, as well as image analysis workflow automation using ImageJ macro programming. In addition, it will be taught how to use the software package ilastik for machine learning based image segmentation and object classification, and how to integrate ilastik into ImageJ macro based workflows. Moreover, an overview of further relevant bioimage analysis software packages will be given and there will be ample time for “Work on Your Own Data” sessions assisted by experienced Analysts.

This school targets bioimage analysts, who are willing to enhance their professional scope and techniques for improving the quality of their analysis, as well as willing to contribute with their knowledge and experience to the school. Prerequisite is a proficiency in at least one programming language (we do not train coding). The school focuses on workflow designing. This year, we will have a particular emphasis on statistics for bioimage analysis and related tools e.g. R and Python libraries. In addition, we will overview machine & deep learning components.

Microscopie à épi-fluorescence et microscopie confocale: Des bases à la pratique