Training

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.

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.

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