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 :
- A008 : Automated reconstruction of massive amount of super-resolution single particle trajectories
- A010 : Lifetime STED microscopy to resolve the organization of the Golgi apparatus at super-resolution in plant samples
- A018 : 3D Single Molecule Localization Microscopy on reconstituted systems: purified proteins and model membranes
- A020 : Whole workflow for plant expansion microscopy: from sample preparation to image analysis
- A024 : Obtenir la PSF d’un système de microscopie de fluorescence
- A029 : 3D STED microscopy for nanoscopic imaging of virus-host cell interactions.
- A038 : Event-based Single-Molecule Localization Microscopy for fast and dense high resolution imaging
- A044 : Structured illumination microscopy with a chip based light source
- A059 : Expansion microscopy on mouse brain tissue slices: gain of resolution allowing deciphering of synapse substructure
- A064 : DNA-PAINT imaging of intact Drosophila muscles
- A068 : Microscopie à expansion sur différents échantillons infectieux (Autophagie norovirus / toxoplasme)
- A072 : La microscopie par dSTORM pour cartographier les crêtes mitochondriales
- A078 : STED-FLIM, apport du temps de vie de fluorescence dans les techniques de STED au niveau multi-couleur, 3D et vivant
- A082 : How to reach mitochondrial inner membrane remodeling by super resolution live imaging
- A085 : Super-resolved Imaging based on RIM technology
- A086 : Eternity-Plus buffer for 3 color Nanoscale imaging in depth.
- A092 : Single Molecule Localization Microscopy and use of calibration tools to unravel EVs composition and 3D morphology at a single-vesicle level
- A095 : Contribution of expansion microscopy for studying organs: Example of lymph node
- A098 : Optimizing fluorophores and data acquisition parameters in SMLM and sptPALM in silico using the SMIS simulator
- A100 : Optimizing imaging schemes for PALM and single particle tracking in bacteria
- A109 : Microscopie d’expansion: Trucs et astuces pour l’analyse des compartiments cellulaires dans les cellules de mammifères et dans la levure
- A120 : Nanoscale imaging of the Toxoplasma gondii microtubules network using Expansion microscopy and 3D-STED
- A122 : COLORME/FLUOGAN : Super-resolution in fluorescence microscopy with standard setup.
- A135 : Single Molecule Orientation and Localization Microscopy (SMOLM) using polarized super resolution imaging and PSF engineering
- A143 : Coupling Expansion to STED microscopy for centriole protein imaging
- A144 : Imaging contact sites in neuronal and epithelial cells by multicolor STED microscopy
- A147 : Multi-target imaging in 3D single molecule localization microscopy with a single laser : Spectral vs Flux demixing
- A154 : Adaptable excitation field for enhanced single-molecule regime in dSTORM
- A159 : Metal-Induced Energy Transfer Single-Molecule Localization Microscopy (MIET-SMLM)
- TR171-A challenge in super-resolution: choosing the best technique for your biological question. Inter-WG organized debate.
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:
- A002 : Home-made wavefront microscopy: working principle and application to dry mass measurements of bacteria and neurons in culture, with a sub-picogram sensitivity.
- A007 : Label-free correlative microscopy of 3D samples: from light sheet to confocal microscopy
- A012 : Imaging transcription at the single cell level during zebrafish development
- A016 : Parallel long-term live imaging of developing C. elegans larvae with microfluidics
- A020 : Whole workflow for plant expansion microscopy: from sample preparation to image analysis
- A031 : Fast 2D and 3D imaging of cells and spheroids for quantitative analysis on high-speed fluorescent light-Sheet microplate cytometer.
- A036 : High content 3D imaging of small specimens and automatic analysis in the context of screening applications
- A037 : Whole brain single cell resolution study of the mouse brain using iDISCO, light sheet microscopy and the ClearMap2 software.
- A043 : A practical review of several 3D-culture methods for the generation of hollow or solid organoids/spheroids with a unique cell-type, how environment matters
- A051 : Upcycling 3D Printers for bioimaging
- A052 : Two photon imaging of plant tissues with photo switchable Dronpa
- A056 : Beginner’s guide to the fabrication and use of microfluidic organ-on-chip systems
- A059 : Expansion microscopy on mouse brain tissue slices: gain of resolution allowing deciphering of synapse substructure
- A069 : In Resin Fluorescence (IRF) Correlative Light and Electron Microscopy (CLEM) for plant tissues
- A080 : Photoacoustic and fluorescence imaging through a single multimode fiber using wavefront shaping
- A081 : Fast imaging of 3D models for Hight Content Screening quantitative analysis in 3D
- A082 : How to reach mitochondrial inner membrane remodeling by super resolution live imaging
- A083 : Optimization of 3D High Content Screening (HCS) acquisitions on thick samples
- A085 : Super-resolved Imaging based on RIM technology
- A095 : Contribution of expansion microscopy for studying organs: Example of lymph node
- A103 : Single-shot polarimetric and quantitative phase imaging
- A106 : Quantitative phase imaging with a diffuser
- A108 : Simultaneous multiplexed staining of the infarcted area and Connexin-43 on wide thick heart sections
- A114 : Exploring the Impact of Laser Power and Pulse Duration on Two-Photon Microscopy
- A118 : Clearing and 3D imaging of mesenteric adipose tissue of rat
- A120 : Nanoscale imaging of the Toxoplasma gondii microtubules network using Expansion microscopy and 3D-STED
- A126 : Cell and tissue manipulation with ultrashort infrared pulses in multi-view light sheet microscopy
- A144 : Imaging contact sites in neuronal and epithelial cells by multicolor STED microscopy
- A145 : Label-free imaging of entire organisms using a mobile optical coherence microscopy platform
- A146 : Label-free imaging of tissues and collagen with high-definition quantitative phase imaging
- A148 : Identification de nanoparticules et de virus-like-particles avec la microscopie de phase quantitative
- A149 : Label-free highly multimodal nonlinear micro-endoscopy: demonstration and practice
- A150 : Adaptive optics two-photon fluorescence microscopy for in depth bioimaging
- A151 : Hands-on light sheet microscopy with Flamingo, the shareable custom research microscope
- A153 : Customized Mounting of Cleared Organs (Brain, Ovary and Placenta) and organoids using CUBIC and Lighsheet imaging
- A155 : Compact, simple and versatile light-sheet fluorescence microscopy module for long-term 1P/2P functional imaging.
- TR183 : Quand les physiciens rencontrent les biologistes: de nouvelles solutions d’imagerie pour l’imagerie profondeur à haute résolution mais sans phototoxicité.
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:
- A003 : Automated acquisition of organoids in high-throughput assays for cancer research
- A007 : Label-free correlative microscopy of 3D samples: from light sheet to confocal microscopy
- A012 : Imaging transcription at the single cell level during zebrafish development
- A013 : ZERO CODE MACHINE & DEEP LEARNING
- A016 : Parallel long-term live imaging of developing C. elegans larvae with microfluidics
- A020 : Whole workflow for plant expansion microscopy: from sample preparation to image analysis
- A031 : Fast 2D and 3D imaging of cells and spheroids for quantitative analysis on high-speed fluorescent light-Sheet microplate cytometer.
- A043 : A practical review of several 3D-culture methods for the generation of hollow or solid organoids/spheroids with a unique cell-type, how environment matters
- A051 : Upcycling 3D Printers for bioimaging
- A056 : Beginner’s guide to the fabrication and use of microfluidic organ-on-chip systems
- A059 : Expansion microscopy on mouse brain tissue slices: gain of resolution allowing deciphering of synapse substructure
- A069 : In Resin Fluorescence (IRF) Correlative Light and Electron Microscopy (CLEM) for plant tissues
- A081 : Fast imaging of 3D models for High Content Screening quantitative analysis in 3D
- A082 : How to reach mitochondrial inner membrane remodeling by super resolution live imaging
- A083 : Optimization of 3D High Content Screening (HCS) acquisitions on thick samples
- A085 : Super-resolved Imaging based on RIM technology
- A095 : Contribution of expansion microscopy for studying organs: Example of lymph node
- A108 : Simultaneous multiplexed staining of the infarcted area and Connexin-43 on wide thick heart sections
- A120 : Nanoscale imaging of the Toxoplasma gondii microtubules network using Expansion microscopy and 3D-STED
- A145 : Label-free imaging of entire organisms using a mobile optical coherence microscopy platform
- A149 : Label-free highly multimodal nonlinear micro-endoscopy: demonstration and practice
- A151 : Hands-on light sheet microscopy with Flamingo, the shareable custom research microscope
- A153 : Customized Mounting of Cleared Organs (Brain, Ovary and Placenta) and organoids using CUBIC and Light-sheet imaging
- TR184-Assemblages multicellulaires, -oïdes, tranches, tissus natifs et biofabriqués : où en est-on et où va-t-on ?
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:
- A015 : Fluorescence-based techniques to study ER–mitochondria contact sites
- A025 : AFM and FluidFM to probe the hydrophobic properties of living cell surfaces
- A027 : Single-cell force spectroscopy to probe cell-cell interactions using AFM and AFM combined with microfluidics
- A032 : Force spectroscopy on virus-like particle producing cells using atomic force microscopy
- A068 : Microscopie à expansion sur différents échantillons infectieux (Autophagie norovirus / toxoplasme)
- A072 : La microscopie par dSTORM pour cartographier les crêtes mitochondriales
- A082 : How to reach mitochondrial inner membrane remodeling by super resolution live imaging
- A105 : FRET SRRF: where super-resolution meets protein activation
- A113 : Multiplexed biosensor imaging to visualize and quantify signaling pathways in 2D and 3D cellular models.
- A115 : Monitoring calcium responses of moving T cells in fresh tissue slices by multiphoton microscopy
- A123 : A simple way to enhance TIRF microscopy using dedicated coverslips
- A144 : Imaging contact sites in neuronal and epithelial cells by multicolor STED microscopy
As its name suggests, this track is dedicated to the specificities of plant imaging: labeling strategies, how to manage autofluorescence, …
Related module: Module 1, From molecule to microscope: Labeling strategies, probes and contrasts.
Workshops and roundtables in this track:
- A020 : Whole workflow for plant expansion microscopy: from sample preparation to image analysis
- A028 : Microfluidics and microscopy for plant biology
- A052 : Two photon imaging of plant tissues with photo switchable Dronpa
- A069 : In Resin Fluorescence (IRF) Correlative Light and Electron Microscopy (CLEM) for plant tissues
- A091 : Fluorescence to measure light intensity
- A145 : Label-free imaging of entire organisms using a mobile optical coherence microscopy platform
- TR169-Fluorophores pour les plantes
This track brings together courses and workshops concerned with phase imaging, which allows access to physiological parameters without necessarily using fluorescence, thus avoiding any phototoxicity.
Related module: Module 4, Waves on living organisms: New imaging techniques for organisms.
Workshops and roundtables in this track:
- A002 : Home-made wavefront microscopy: working principle and application to dry mass measurements of bacteria and neurons in culture, with a sub-picogram sensitivity.
- A106 : Quantitative phase imaging with a diffuser
- A146 : Label-free imaging of tissues and collagen with high-definition quantitative phase imaging
- A148 : Identification de nanoparticules et de virus-like-particles avec la microscopie de phase quantitative
- TR183 : Quand les physiciens rencontrent les biologistes: de nouvelles solutions d’imagerie pour l’imagerie profondeur à haute résolution mais sans phototoxicité
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 :
- A001 : Segmentation and classification under Napari
- A003 : Automated acquisition of organoids in high-throughput assays for cancer research
- A004 : Unmixing of spectrally identical fluorescent proteins by lifetime imaging
- A008 : Automated reconstruction of massive amount of super-resolution single particle trajectories
- A013 : ZERO CODE MACHINE & DEEP LEARNING
- A014 : DEEP NAPARI
- A034 : 3D Deconvolution
- A035 : Cellpose 2.0 and TrackMate: A powerful combination for effortless and accurate analysis of live cells in phase microscopy
- A036 : High content 3D imaging of small specimens and automatic analysis in the context of screening applications
- A040 : Segmentation with machine learning solution Cellpose for absolute beginners
- A042 : Deep Learning for Bioimage Analysis: Concepts and Hands-on Neural Networks Training with a Critical Approach
- A045 : Coordinate-based quantification of multidimensional and multicolor single-molecule localization microscopy data
- A046 : An easy-to-use deep learning method for 3D semantic segmentation
- A049 : Deep Learning Bootcamp Desk
- A054 : Virtual reality for multidimensional data visualization and analysis
- A058 : Beginners initiation of whole slide image 2D analysis. From tissue to cells with QuPath
- A060 : Deep learning annotations for 2D model creation : Tips / Tricks and Model’s Quality Control
- A067 : Nuclei segmentation with StarDist, a user-friendly deep-learning tool for the biologist
- A074 : Integrated machine learning for scanned slides analysis with QuPath
- A087 : DeepIcy: A user-friendly plugin to use latest Deep Learning methods in Icy
- A089 : Deep Learning for fluorescence lifetime imaging microscopy (FLIM)
- A090 : Batch processing images from OMERO in Fiji
- A093 : MorphoNet : How to segment a 3D dataset in just a few clicks?
- A101 : Slide scanner use case: from the acquisition to the analysis of a stack of 2D slices registered onto a 3D reference brain atlas
- A107 : Roboscope prototype for smart automated microscopy
- A110 : Analysis of multiplexed whole slide images with QuPath and Cytomap
- A116 : Analysis of the 3D spatial organization of cells and molecules with FIJI and Napari
- A117 : Orchestrating complex bioimage workflows- leading up to smart microscopy
- A121 : Phasor analysis of Fluorescence Lifetime Microscopy (FLIM)
- A128 : 3D Image Analysis Flash Tutorials: 3D reconstruction, visualization tools and movie creation
- A129 : 3D Image Analysis Flash Tutorials: Machine learning and object classification in routine
- A130 : 3D Image Analysis Flash Tutorials: Cells quantification: model cells as mesh objects to obtain their counts, volumes and morphologies
- A131 : 3D Image Analysis Flash Tutorials: 3D co-distribution analysis for Neurobiology
- A132 : 3D Image Analysis Flash Tutorials: Deciphering immune cell shape over time
- A133 : 3D Image Analysis Flash Tutorials: Neuron tracing using Machine Learning
- TR168 – Intelligence Artificielle dans les métiers de l’imagerie métiers de l’imagerie
- TR173 – IA KAFOKON : IA pour l’analyse d’images
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
- A014 : DEEP NAPARI
- A040 : Segmentation with machine learning solution Cellpose for absolute beginners
- A042 : Deep Learning for Bioimage Analysis: Concepts and Hands-on Neural Networks Training with a Critical Approach
- A058 : Beginners initiation of whole slide image 2D analysis. From tissue to cells with QuPath
- A060 : Deep learning annotations for 2D model creation : Tips / Tricks and Model’s Quality Control
- A067 : Nuclei segmentation with StarDist, a user-friendly deep-learning tool for the biologist
- A074 : Integrated machine learning for scanned slides analysis with Qupath
- A110 : Analysis of multiplexed whole slide images with QuPath and Cytomap
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 http://ateliers-mifobio.fr.
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:
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 http://ateliers-mifobio.fr
| CA187-Temps de vie de fluorescence |
| CA188-Microscopie de fluorescence polarisée, quelle utilité? |
CA189-Imagerie de phase et tomographique |
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)
Fab-Lab
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)
Optic-Lab
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
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 http://ateliers-mifobio.fr.
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: https://filesender.renater.fr/?s=download&token=6efe0042-72db-43c0-b7ff-ae2529137405
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.
Planktoscope
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.