Training

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