Training

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.

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