Advanced microscopy workshop in Bordeaux from November 4th to 7th, 2024.

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.

Description
Programme
Registration
Venue

AT A GLANCE

The course will be structured around 4 main thematic tracks, addressing the issues of sample preparation and data analysis for given samples. Participants will have the choice of following one of these tracks, or navigating between them according to their interests. The tracks will be :

  • P1: Large sample imaging – Clearing & Expansion
  • P2: 3D cellular models Culture & Imaging
  • P3: Neuronal network imaging
  • P4: Image Analysis

The format of the course will include lectures and seminars in the morning, providing a theoretical grounding in the various areas covered (sample preparation, imaging, image processing) and presenting the latest developments in these fields, and practical workshop in the afternoon on the various sites of the Bordeaux node (IINS, BIC, VoxCell).

affiche fbiat 2024Download

Invited Speakers

Laura Batti, (Wyss Center for Bio and Neuro Engineering, Geneva Switzerland)

Julien Colombelli, (Institute for Research in Biomedicine, Barcelona Spain)

Adam Glasser (Allen Institute for Neural Dynamics, Seatle USA)

Farida Hellal (Institute for Tissue Engineering and Regenerative Medicine, Munich Germany)

Alfred Millet-Sikking (Calico Life Sciences LLC, San-Francisco USA)

Gaelle Recher (Institut d’optique Graduate School, Bordeaux France)

Ihssane Idrissi / Rémi Galland (Interdisciplinary Institute for Neurosciences, Bordeaux, France)

Vincent Studer (Interdisciplinary Institute for Neurosciences, Bordeaux France)

Gustavo de Medeiros (Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland)

Georges Debrégeas (Jean Perrin Laboratory, Paris France)

Thai Truong (University of Southern California, Los Angeles USA)

Angela Getz / Mathieu Ducros (Bordeaux Imaging Center, Bordeaux France)

Alexandra Fragola (Institut des Sciences Moléculaires d’Orsay, Orsay France)

Emmanuel Faure (Laboratory of Computer Science, Robotics and Microelectronics, Montpellier France)

Johannes Roos (Johannes Kepler University, Linz Austria)

Philippe Girard (IJM, Paris, France)

Carole Siret (CIML, Marseille, France)

Guillaume Maucort (BIC, Bordeaux France)

Workshops on

  • Whole brains imaging by Ultramicroscopy
  • 3D imaging of neuronal expanded samples by AxL (3i) microscope
  • 3D entire small animal imaging
  • 3D Cellular models culture and imaging using the soSPIM technology
  • Micro-niche creation for 3D cell culture and 3D imaging using the HS-ISM technique 
  • Neurospheres culture and imaging using the MuViSPIM
  • Brain slices imaging using a Lattice Light Sheet Microscope
  • Single Cell electroporation for Brain slices labelling
  • Functional neuronal network imaging in ZebraFish
  • Orchestrating complex bioimage workflows using the Arkitekt solution
  • Napari for 3D data handling
  • How to segment a 3D dataset in just a few clicks?

Organizing committee

Coordinators: Mathieu Ducros & Rémi Galland

& FBI Work Group on « Multiscale Light-Sheet Microscopy »

Sponsors

1st Interdisciplinary Summer School on Chemical and Physical Probes for Biology

July 3rd to 7th

The fine understanding of molecular mechanisms in native biological systems is an important step in rationalizing, preventing and ultimately curing diseases. Photonic imaging plays an important role in this field. Quantitative imaging experiments designed to answer complex biological questions require the implementation of efficient probes and adapted imaging setups and data processing workflows.

This interdisciplinary school will provide an overview of these different chemical, physical and biological aspects. It will offer also interactive and interdisciplinary workshops to learn how to communicate effectively between disciplines as well as two half-days of hands-on.

Program and registration on: https://chemphysbio2023.sciencesconf.org/

This is the first edition of our Summer School outside of France, going to South America in synchrony with the IEEE SPS-EMBS ISBI Conference in Colombia.

The spirit of our Summer School was established in French Brittany in 1994 (by Christian ROUX and Jean-Louis COATRIEUX). This Summer School has become a worldwide reference with international lecturers from 20 countries and accessible to young scientists from all around the world. Our Summer School is an open yet privileged place for exchanges and discussions on major on-going research and technologies. Informal and warm, we always select a location and design a program where ample time is dedicated to interactions between lecturers and students.

The Summer School is open to graduate students (MSc., PhD), post doctoral scientists, radiologists, biologists, researchers and engineers in industry.

France-BioImaging, with its partner the GDR IMABIO, organizes the 4th edition of the FBI-AT: an advanced microscopy workshop to be held in Paris from November 21st to 25th, 2022.

The aim of this France-BioImaging-Advanced Training is to train microscopy users on the most advanced imaging techniques that will allow them to perform molecular studies at the cellular level as well as in thick samples. In particular, recent developments on fluorescent probes will be highlighted. The workshop will benefit from state-of-the-art equipment available on several of the Parisian Node Imaging facilities.

This year’s edition will have plenary lectures given by experts in the microscopy development field. These seminars will be advertised as a series and will be broadcasted for a large audience.  In addition, specific techniques will be introduced.

Hands-on practicals will train attendants on these techniques every afternoon in different sites in Paris including Institut Curie, Institut Pasteur, Institut Cochin, Institut Jacques Monod, Institut de Psychiatrie et Neurosciences de Paris and ENS Paris. Access to this part of training will be restricted to selected and registered trainees.

To guaranty access to set-ups and proper training, each practical session will host only 3-4 persons. The sessions will be run in parallel.

Apply now, attendance will be limited to 25 participants! 

FBI-AT is ideal for researchers with a basic training in microscopy willing to become familiar with advanced techniques to answer their specific biological questions, or to be exposed to new developments that will allow them to tackle new questions in their project. We will consider applications from early career researchers (PhD students, post-docs), technical staff members and more senior scientists.

Description
Programme
Registration
Venue
Gallery

AT A GLANCE

The workshop contains plenary lectures and specific training sessions. Plenary lectures will be on hybrid mode and largely open.

Invited Speakers

Emmanuel Beaurepaire

Giulia Bertolin

Joerg Bewersdorf

Peter Dedecker

Claire Deo

Marie Erard

Ricardo Henriques

Christophe Leterrier

Sandrine Lévêque-Fort

Gustavo Quintas

Gaelle Recher

Jean-Baptiste Sibarita

Lothar Schermelleh

Practicals on

  • Combining micro UV-irradiation and Single Particle Tracking in living cells
  • SMLM multi-color: from sample preparation to quantification
  • FRET-based molecular tension sensors and FLIM
  • Imaging of cellular ultrastructures with expansion microscopy
  • SIM, STED or STORM ? : from sample prep to 3D imaging
  • 3D STED : Comparing flat cells vs thick samples
  • Culturing and imaging multicolour 3D live brain organoïds
  • Combining fast live 3D imaging with Z resolution preservation
  • Light sources for optogenetics
  • Non-classical genetically modified fluorescent probes for biological imaging
  • Imaging biological structures in 3D using double helix-STORM and 3D-SIM

Organizers

Florence Niedergang, Lydia Danglot, Chloe Guedj, Mickael Lelek, Pierre Bourdoncle, Audrey Salles, Xavier Baudin, Nicolas Borghi, René-Marc Mege, David Geny, Ludovic Jullien

Poster

FBI-AT-2022-poster-V2Download

Sponsors

The first practical workshop « Imaging Organoids: from the bench to the microscope » will take place in Bordeaux, from Mon 27th Sept to Fri 1st Oct 2021.

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). 

This workshop is open to all (PhD students, Postdocs, Engineers, Technicians, Researchers and Teaching Assistants) who would like to learn how to prepare their 3D samples for photon microscopy.

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.

This workshop is organized with the support of the GdR ImaBio, the GdR Organoids and France Bio-Imaging.

Grant Applications for organizing Virtual/Hybrid Training Schools are open!

COMULIS is now launching a call to financially support virtual and hybrid training schools fulfilling the following conditions:

  • the training school has to take place between the 1st of June and 30th of October 2021;
  • it has to be virtual (or hybrid);
  • it has to cover topics of the COMULIS network;
  • led by a COMULIS member or someone who is willing to become one;
  • COMULIS and COST support will have to be diplayed on the program, website, or any related document to the training school;
  • fees that can be covered by this grant include the technical setup of these training schools and training material:
    • If engaging a conference organiser, technician hourly rate if required on specific openings days before and during the event to assist with technical support, attendee management and monitoring, configuration and setup, communication.
    • customer support for attendees, live-stream tech support via email and/or chat.
    • pre-recording of keynotes/teaching sessions for training schools.
    • post-event process management: video editing, recording management.
    • Rental of rooms and audio-visual material
    • Consumables purchased for Training Schools
    • Photocopying and the printing of programmes, handouts, event materials, book of abstracts, book of proceedings, flyers etc

Maximum amount of a grant is 10000 euros, that will be reimbursed on presentation of invoices strictly related to eligible fees above.

Procedure

Filling an online form https://forms.gle/tJqaLmauZDA5V58o6 with check of the above conditions, (pedagogical) program, list of organizers, speakers and trainers, dates, provisional budget including usage of the COMULIS financial support in regards of one or several of the above categories of eligible expenses.

Deadline 1st of June. Notification of acceptance: 15th of June. (if needed earlier please do tell us, and we will do our best to meet you own deadline in case of co-funding).

Criteria among eligible proposals (fulfilling the above checklist) will be based on matching COMULIS objectives (www.comulis.eu) and scientific excellence. Proposal will be ranked by grade following this criteria, and funded until the available budget is used up. Three to ten possible grants, according to budget.

Contact: Perrine.paul-gilloteaux@univ-nantes.fr, andreas.walter@vbcf.ac.at

Cette action nationale de formation regroupe 160 personnes, techniciens, ingénieurs, chercheurs de centres de recherches, voulant approfondir leurs connaissances en microscopie corrélative.

L’objectif de cette formation est de présenter différentes techniques de microscopie corrélative en essayant de présenter les techniques et les appareils utilisés le plus précisément possible.
Les corrélations abordées concerneront les techniques de microscopie optique classique et à fluorescence, la microscopie électronique à balayage et à transmission, le NanoSIMS, la Fluo-RX et le synchrotron.
Des présentations et des ateliers permettront de bien approfondir les outils utilisés de la préparation des échantillons à la corrélation des images.

Date limite pour les inscriptions : 15 Avril 2021

Crédit image header: Cosenza, M. R. et al. Asymmetric Centriole Numbers at Spindle Poles Cause Chromosome Missegregation in Cancer. CellReports 20, 1906–1920 (2017)

Important information for the registered participants: an email with the links to access the training videos was sent on February 15th, 2020. Please check your inbox and SPAM folder!

If you did not receive it, please send us an email to contact@france-bioimaging.org

If you registered after February 14th, 2021, you will receive an email with the links within two days.

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.

Format:

The training will be divided in 3 parts:

  1. Theoretical courses on LSFM
  2. Practical demonstrations of several LSFM implementations available throughout the FBI infrastructure
  3. 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.

Program:

1.      Theoretical aspects of LSFM (15th to 26th of February 2021)

Here are the three main questions concerning the imaging with a light-sheet microscope: (1) what LSFM type should I use for my experiment, (2) How do I prepare and mount my sample, and (3) how to visualize and analyze my data sets. The first part of this training will address these three questions through three theoretical courses:

  • Course 1: Theoretical principles and numerous implementations overview of LSFM
    • P. Girard (Institut Jacques Monod, Paris-Centre)
  • Course 2: Sample preparation and mounting principles – highlight on clearing approaches
    • Carol Siret (CIML, Marseille)
  • Course 3: Reconstruction, Visualization and Analysis software overview.
    • Cesar Augusto Valades (Institut Curie, Paris-Centre),

2.      Practical demonstrations of several LSFM implementation and experiments (15th of February to 5th of March 2021)

In the second part of the training we will propose several videos on various systems available in the FBI laboratories and imaging platforms covering diverse types of LSFM design and applications.

Each video will feature a specific set-up and experts will present how to run an experiment on them focusing on three main aspects: (1) sample preparation and mounting methods, (2) image acquisition processes, and (3) visualization of the data-sets.

  • Lattice Light Sheet Microscope – (Home-made  and 3i versions)
    • Mathieu Ducros (BIC, Bordeaux)
    • Ludovic Lecomte, Jean Salamero and Cesar Valaldes-Cruz (Institut Curie, Paris-Centre)
  • Single-objective Single Plane Illumination Microscope (soSPIM) – Home-made
    • Rémi Galland (IINS, Bordeaux)
  • Dual inverted Single Plane Illumination Microscope (diSPIM) – 3i (Marianas)
    • Elric Esposito et Julien Fernandes (Institut Pasteur, Paris-Centre)
  • MuviSPIM – Luxendo
    • Sylvain De Rossi (MRI, Montpellier)
  • Ultramicroscope – LaVision Biotech
    • Carol Siret/Mathieu Fallet (CIML, Marseille)

3.      Questions & Answer interactive session (March 5th, 2021)

An online video session will conclude the training where FBI experts will answer all participants’ questions. You can ask questions either in advance in the comment box of the Youtube video, or during the Q&A session in a chat box. The Q&A session will be divided in sections, each related to a specific video.

To register:

In order to register to the Light-Sheet Fluorescence Microscopy remote training, please fill out the registration form available here.

Registration is free but mandatory in order to receive the links to the training videos.

Extended deadline: February 19th, 2021

We look forward to your participation !

During this year 2020, the MicroPICell facility from the Bretagne Loire Node acquired several imaging systems, some of which offer access to new technologies on the Nantes health research site:

  • a complete Zeiss Lighsheet 7 light sheet microscope associated to an X-Clarity clearing system and an Arivis Vision 4D Offline station,
  • a motorized Nanolive holotomographic microscope,
  • a high-end Nikon confocal microscope (resonant, spectral, FLIM, large field of view),
  • an Akoya CODEX system of multiplex fluorescent tissue labeling.
Holography offers a unique means to measure cells in their native environment: label-free, non-invasive, manipulation-free, and interference-free.

Moreover, the MicroPICell facility, in collaboration with the training organization of the CNRS, is organizing in March 2021 a training on histology: from sample preparation to markers validation by image analysis. This training (lectures, workshops) will take place over 4 days between 03/22/2021 and 04/24/2021.

Link: https://cnrsformation.cnrs.fr/stage-21290-Histologie–de-la-preparation-dechantillons-a-la-validation-des-marquages-par-analyse-dimage.html?stage=21290&axe=138

Dear Bioimaging colleagues,

NEUBIAS, the Network of European BioImage Analysts (www.neubias.org), is delighted to announce two new Training Schools on BioImage Analysis:

  • for Early Career Investigators (life scientists)
  • for Facility staff (imaging & analysis staff from core-facilities)

The focus of training will be on construction and automation of BioImage Analysis workflows, using as examples more than one toolbox and different exercises. The schools will be held in Edinburgh, 16-19th of October 2018, hosted by the MRC Center for Regenerative Medicine/Imaging facility and co-organized by the University of Edinburgh and University of Dundee.

NEUBIAS schools are an excellent opportunity to learn from many experts in Bioimage Analysis (we are expecting >30 specialists at the event) and “….a great mix of intensive learning and community networking” (former trainee testimonial!). The schools will include practical sessions and seminars on ImageJ for analysis and publication, scripting/macros in ImageJ and Matlab, Omero, CellProfiler, QuPath, Ilastik, Ethics in Image Analysis and work on own data.

  • Applications are now open (each school has 20 available seats and ~7 trainers)
  • Applicants are highly encouraged to bring their own laptops and data.
  • Within the COST framework (funders of NEUBIAS), 7 travel grants per school are offered to applicants who qualify.
  • Registration requires a “letter of motivation” (filled in application form) and later a confirmation of status.
  • Application deadline:  May 11th 2018
  • Selection notification: 1st week of June 2018.

More information about schools (programme & trainers) and venue, travel & lodge available at our website:
www.neubias.org -> “Training Schools”

http://eubias.org/NEUBIAS/training-schools/eci/ts8-edinburgh-2018/

http://eubias.org/NEUBIAS/training-schools/staff/ts9-edinburgh-2018/

We kindly ask that you help us reach all potential interested applicants.

on behalf of all NEUBIAS members, of local organizers (Bertrand Vernay & Graeme Ball) and programme organizers (Anna Klemm, Laura Murphy, Graeme Ball and Sebastien Herbert)

_______________________________

NEUBIAS is an European network of >220 members and 41 countries, which aims to promote the communication between Life Scientists, Instrumentalists, Developers and BioImage Analysts and to establish and promote the role of Bioimage Analysts in Life Science. Our mission includes:
– A training programme for 3 different target audiences:”Early Career” researchers, (core) Facility Staff and Bioimage Analysts (running until 2020 – expected 400 trainees and 15 training schools).
– Promote different yearly events (NEUBIAS Conference, workshops [training schools], Taggathons)
– Online Resources: Repository of tools and workflows e.g. biii.eu, Benchmarking and Sample datasets, Training material and Open Textbook.
– A Short Term Scientific Mission mobility programme for Scientists to visit Host Labs and get in depth insights into cutting edge Image Analysis technology.
– A “ITC conference grants” programme to support travel for Early career Investigators from Inclusiveness Target Countries to present their work at conferences.
– Outreach material.
… more at www.neubias.org

L’I2BC organise un atelier à destination des chercheurs curieux de se perfectionner ou de s’initier aux techniques spécifiques à la microscopie confocale.

Le programme détaillé et les modalités d’inscription sont disponibles à l’adresse suivante : http://cnrsformation.cnrs.fr/stage-17090-Atelier-de-microscopie-confocale.html?axe=72

La pré-inscription se fait en cliquant sur le bouton orange “S’inscrire” en haut à droite de la page.

Pour plus de renseignements, contacter imagerie@i2bc.paris-saclay.fr.

Comité d’organisation : Sandrine Lécart, Romain Le Bars & Laëtitia Besse.

(This training session will be taught in French only).

Formation CNRS
Objectifs :
 Apprendre les fondamentaux de la microscopie photonique
 Acquérir les bonnes pratiques
 Découvrir les techniques avancées
 Acquérir de l’autonomie sur un ensemble de techniques de microscopie fréquemment rencontrées dans les laboratoires de biologie

Inscription avant le 9 octobre 2017 via le portail de formation du CNRS, Rubrique “Connaissances scientifiques” : https://admin.core-cloud.net/ou/SMUT/PFM/Lists/OFFRE%20REGIONALE%20IdF/Programme%202017.aspx