Educational activities

The MiFoBio thematic school is a place for scientific exchange and experimentation through a wide range of educational activities. It offers a rich and diversified range of content. This page provides a description and links to the various educational activities taking place during the week, often in parallel with each other (except for courses and seminars).

Courses and Seminars

The core of the school’s teaching is organized around 6 thematic modules and an initial module giving the fundamental concepts. These modules bring together 4 to 6 courses and are complemented by seminars and cross-disciplinary courses (see schedule).

This year, we are celebrating the 20th anniversary of the community’s structuring into GDRs. To mark the occasion, special seminars will highlight the major developments of the last 20 years.

Thematic tracks

The courses combine modules, workshops and roundtables on a common theme, and conclude with a debriefing roundtable. This enables participants to identify more effectively the workshops that correspond to their interests, and to follow the desired course in part or in full. There are 8 courses:

This track aims to bring together courses and workshops driven by the same strategy: improving resolution. Because of the diffraction barrier, various strategies have been developed to improve resolution. Super-resolution techniques (SIM, STED, STORM) can improve resolution through optical or data processing developments. These methods require expertise and expensive machines. More recently, expansion microscopy techniques, which involve “inflating” the sample so that it can be observed using traditional methods (confocal or other), are enjoying considerable growth. This tour brings together these different strategies, so that you can form your own opinion on the various alternatives available. The tour is accompanied by a round-table discussion led by members of the RTmfm working groups: GT expansion, GT STED, GT STORM, who meet throughout the year to improve their results. The “super-resolutionists” advocate non-distortion of samples, the expansionists advocate ease of technique and accessibility of confocals. Don’t hesitate to come and debate all this to liven up this exciting match!”

Related module: Module 2, Nanoscale quantification and studies of supramolecular assemblies.

Workshops and roundtables of this track  :

This track aims to bring together courses and workshops concerned with the imaging of thick samples: this includes very large organoids, organotypic slices, tissues, right down to the small animal. A whole panoply of strategies is available for this purpose: optical strategies (tomography, fast light-sheet imaging, wavefront management using adaptive optics), sample preparation strategies (new contrasts, transparentization, fabrication of supports to avoid crushing the sample, etc.), and sample preparation strategies (new imaging techniques). The course is associated with a round-table discussion led by the organizers of the GDR’s wave, multicellular and nanoscopy modules, and the culture/sample preparation room. The aim is to bring together physicists, biologists and chemists to identify problems and solutions. Don’t hesitate to come and do your shopping at this round table.

Related modules: Module 4, Waves on living organisms: New imaging techniques for organisms, Module 5, Imaging self-organizing biological systems, from cell to organ.

Workshops and roundtables in this track:

The aim of this track is to bring together courses and workshops on “ooids” in the broadest sense, i.e. organoids (with the ability to perform an integrated function in the same way as an organ), but also spheroids (cellular aggregates not necessarily displaying the functions of an organ).

Combined with a little challenge: standardized samples will be available during Mifobio week in culture rooms. They will be distributed to participants wishing to take up the challenge of imaging them on the system(s) of their choice. The best strategies and images generated (depth, speed, etc.) will be discussed during the round table. Don’t hesitate to come and take up this challenge!

Other topics include: problems encountered in 3D culture in the culture room (A043), microfluidic TP for bio-manufacturing (A056), organotypic slices, embryos, etc.”

Related module: Module 5, Imaging self-organizing biological systems, from cell to organ

Workshops and roundtables in this track:

Contact sites between different organelles (e.g. between the reticulum and the plasma membrane, or the reticulum and mitochondria, or the reticulum and endosomes, etc.) are sites of multiple molecular and signaling exchanges. Contact sites are functional platforms made up of two membranes separating 3 compartments. They fine-tune the transport of metabolites, ions and lipids, giving rise to signals between cells, organelles, extracellular matrix and organelles. The combination of electron and photonic microscopy, chemical and biological probes opens up a new understanding of contact sites.

Related modules: Module 1: From molecule to microscope: Labeling strategies, probes and contrasts, Module 2: Nanoscale quantification and studies of supramolecular assemblies, Module 3: Molecular dynamics and interactions in cells and tissues: experimentation and modeling

Workshops and roundtables in this track:

This track aims to bring together courses and workshops concerned with image analysis. It includes strategies for conventional segmentation, artificial intelligence and multidimensional visualization.

Premodules: Basics of image analysis; Introduction to machine learning for image processing.

Workshops and round tables :

This course brings together lectures and workshops on approaches to bioimage analysis (using artificial intelligence, AI) with QuPath as the main software tool. The course is led by members of the RTmfm MAIIA working group and friends. 
The MAIIA (Méthodes d’Analyses d’Images par AI) group brings together users (biologists, microscopists & bio-image analysts) of “turnkey” AI tools, and aim to facilitate their deployement and adoption by the community. The proposed course presents the deployment and use of some of these AI tools (Cellpose, Stardist, etc.) for image analysis , and the best practices to be adopted by the community (standardisation of protocols, quality control, etc.). 
In addition to the workshops focusing on artificial intelligence tools, 3 workshops will present the poweful tool either embedded in QuPath or third party software for analyzing slide scanner images. These three workshops can be followed in this order from the basics of its use, to the use of AI tools (Machine Learning and Deep Learning) up to the analysis of multiplexed images with the help of CytoMap:

A058 : Beginners initiation of whole slide image 2D analysis. From tissue to cells with QuPath

A074 : Integrated machine learning for scanned slides analysis with Qupath

A110 : Analysis of multiplexed whole slide images with QuPath and Cytomap

Workshops of this track

Practical workshops

An essential part of Mifobio, workshops are proposed by participants with the aim of sharing know-how through practice, with other participants taking part in the workshop around a machine or in a computer room. Equipment is either provided by our industrial partners, or brought in by academics (home-made systems). Lasting 1 hour 45 minutes, workshops are limited to 20 participants, and registration is required in advance of MiFoBio via the Atelier website

Workshops take place throughout the week, in the afternoons and evenings, in parallel sessions.

You will find a list of all workshops in the following PDF file:

Listing of whole workshops [PDF]

Round Table (TA), Advanced Courses (CA) et Mini-Symposium (MS)

Another Mifobio staple, they provide a relaxed forum for discussion on a given topic. TRs are a less formalized space for discussion, while the CA format is more like an interactive course, with a more formal presentation but very open to discussion. As for MS, they are linked to modules and therefore organized around themes. They enable young researchers to present their work and discuss technical issues.

Round tables, advanced courses and mini-symposia take place at the same time as the workshop slots. There are 25 scheduled over the week. It is therefore advisable to register on the Ateliers website to integrate them into individual schedules

TR168-Intelligence Artificielle dans les métiers de l'imagerie
TR169-Fluorophores pour les plantes
TR170-Do we need really label free imaging? Can vibrational imaging techniques (CARS/SRS) help to progress in life sciences (cell, organoid, ?
TR171-A challenge in super-resolution: choosing the best technique for your biological question. Inter-WG organized debate.
TR172-Biosenseurs pour l'imagerie des organelles: développements et défis
TR173-IA KAFOKON :  IA pour l'analyse d'images  
TR174-Couplage entre microscopie à force atomique (AFM) et imagerie de fluorescence de super-résolution : état de l’art et défis à venir    
TR175-Career development perspectives for young scientists in Industry and in Academia
 TR176-Mifobio Home-made Workshop : expectation and feedback (for participants and workshopper)
TR177-Fixation des échantillons biologiques 
TR178-Suivi de qualité d’un microscope photonique dans le temps – dialogue avec les constructeurs
TR179-Imagerie environnementale
TR180-Imagerie multispectral , quelles approches, quels fluorochromes pour imager plus de 8 couleurs
TR181-Imaging-based spatial omics
TR182-Gestion des données de microscopie
TR183-Quand les physiciens rencontrent les biologistes: de nouvelles solutions d'imagerie  pour l'imagerie profondeur à haute résolution mais sans phototoxicité. ☺
TR184-Assemblages multicellulaires, -oïdes, tranches, tissus natifs et biofabriqués : où en est-on et où va-t-on ?

TR190-Rencontre : Impact environnemental de nos activités de recherche

TR191-Rencontre : Art et science
CA187-Temps de vie de fluorescence
CA188-Microscopie de fluorescence polarisée, quelle utilité?

CA189-Imagerie de phase et tomographique

MS186-Imagerie et mesures physiques, mécanobiologie

MS193-Dynamique moléculaire : mesure et modélisation

Other educational actions

Bar à Image

The Bar à Image (BAI) is a meeting place for participants with image processing and analysis problems, and experts on hand to solve them.

The Bar à Image takes place from 2 to 4 pm on November 11, 12, 13, 15 and 16. Access is free and no registration is required (Lounge Mer area).

DeepLearning Boot Camp

The DeepLearning Boot Camp (DBC) helps participants gain access to advanced deep learning tools. On-site experts will help participants install the necessary tools (CUDA library, GPU installation).

The DeepLearning Boot Camp takes place in parallel with the 2 poster sessions (Thursday November 9 and Friday November 10 at 9:30pm) and from 2pm to 4pm, on November 11, 12, 13, 15 and 16, in parallel with the BAI. Access is free and no registration is required. (Earth Lounge area)

3D Image Analysis Flash Tutorials

These are short (30 min) tutorials on how to process and analyze your 3D images with Imaris.

The program can be viewed below:

3D Flash Tutorials take place on November 11, 12, 13, 14, 15 and 16, from 1:30 to 2:00 pm. Access is free and without registration, subject to availability. (Bergerie room)


From computer-aided design to Arduino programming and 3D printing, the Fab-Lab brings together a whole range of techniques and skills through dedicated experts, to support everyone’s projects and ideas.ès libre, en plus des créneaux Ateliers. (espace Business Center)


The aim of the OpticLab is to enable participants, whether beginners or more experienced microscopists, to learn how to carry out performance measurements on optical systems and, above all, to understand the underlying physical principles through practical work that can be carried out independently (with little or no supervision).

The Optic-Lab is freely accessible, in addition to the workshop slots. (Ayguade room)


Chem-Lab is offering a 4-slot workshop where participants can make their own fluorescent probe, then test it on cells and visualize the result under the microscope. This chemlab is limited to 6 people and you must register for all 4 sessions on the Atelier website

The Chem-Lab takes place on November 12, 13 and 15 from 4pm to 6pm, then on November 15 from 9:30pm to 11pm. (Salle Capte and Les Salins)

Technical Focus

Technical Focus are meetings where industry experts offer to deepen participants’ knowledge in their areas of expertise (lasers, detectors, etc.).

Technical Focus sessions take place on November 11, 12, 13, 15 and 16, from 1:30 to 2:00 pm, with free access and no prior registration required. (Porquerolles room)

Practical Setup Focus

Dedicated to the discovery of new technologies present at Mifobio, Practical Setup Focus are a time for exchanges and discussions between manufacturers and participants around the systems brought to the event.

Link to the Mifobio 2023 industry book [PDF]

The Practical Setup Focus will take place on Friday November 10, from 2 pm to 3:45 pm, as participants stroll through the various industrial rooms.

Scanning Party

The Scanning Party is an opportunity to discover slide scanners in an original way, as participants are invited to bring their own slides and image them on the 3 slide scanners present at Mifobio. The images thus generated can be analyzed directly during workshops (notably the Qupath workshops). The presentation flyer, sample description form and descriptions of the 3 systems can be found here:

Slides will be collected at the start of Mifobio on Thursday November 9 and Friday November 10, so that images can be made available as soon as possible.


Plankton Planet is an international initiative based in France, bringing together academics and the general public to study marine plankton and assess ocean health. Participants will be able to discover the imaging tools created and used by this consortium, accompanied by the Banyuls Observatory Biodiversarium and its team of scientific mediators around the marine environment. The Planktoscope will be accessible throughout Mifobio.