Formations
Histology: from sample preparation to validation of markings by image analysis
From Monday 17/11/2025 to Friday 21/11/2025
The training programme
Aims:
- Acquire a theoretical and practical grounding in the preparation of samples for photonic microscopy (visible light and fluorescence) and signal quantification
- Know how to prepare a histology sample (staining - immunolabelling)
- Know the different types of preparation depending on the biological question asked
- Know how to adapt sample preparation for robust and reproducible signal analysis
- Recognise the most common preparation artefacts and check the quality of markings using image analysis software.
Contacts inscription : CNRS formation entreprises - Tél. : +33 (0)1 69 82 44 55 - cfe.contact@cnrs.fr
2025 demo café cycle
The MicroPICell facility is organising a series of image analysis demo-cafés. Come and discover analysis software while enjoying a cup of tea or coffee! Registration is required for these events.
Icy, Thursday 13 March 1 to 2 pm Room 4 https://forms.gle/muk4EBj7XEnFzksQ7
Imaris, Tuesday 6 May from 1pm to 2pm Room 4 https://forms.gle/naHf5Fd4no6tKZb36
Napari, Thursday 12 June from 1pm to 2pm Salle 4 https://forms.gle/59wFPsJ85Hb4iZfy5
Arivis, Tuesday 9 September from 1pm to 2pm Room 4 https://forms.gle/g8KfmhXFdwjTbJoc8
CellProfiler, Tuesday 7 October from 1pm to 2pm Room 635 https://forms.gle/UAXTYyJLi8zZFRbt8
NIS module GA3, Thursday 13 November 1 pm 2 pm Room 4 https://forms.gle/8RRdeX91mYd34YiD6
Jupyter Notebook, Tuesday 9 December 1 - 2 pm Room 4 https://forms.gle/1UFzFSjRiFLxf6Sy9
Image analysis training cycle 2025
The MicroPICell platform is organising a series of training courses in image analysis. Places are limited on a first-come, first-served basis (please contact us by email (melodie.ambroset@univ-nantes.fr) to be put on the complementary list).
You must bring a laptop for these courses. If you register for the course, please make a note of the dates in your diaries and let us know if you will be absent.
Introduction to image analysis with QuPath ( Tuesday 25 February 2025)
Prerequisites: A laptop computer with a sufficiently comfortable screen and administrator privileges.
Objectives: Acquire the basics of digital image processing and analysis in biology; Learn how to apply them in QuPath.
Program: Introduction to digital image analysis in biology (basic concepts); Introduction to QuPath: general concepts (notion of project, loading images, interface); Colour deconvolution; Object and tissue detection, segmentation and classification; Density maps and spatial measurements; Exporting measurements; Introduction to automation (workflow recorder, batch automation).
Duration/dates: 1 day Tuesday 25 February from 9am to 12.30pm and from 2pm to 5.30pm
Google form link: https://forms.gle/L3RHXrJrPDoVPTat8
Creating scientific figures and image ethics (Thursday 13 March 2025)
Prerequisites : A laptop computer with a sufficiently comfortable screen and administrator privileges; You must have completed the introduction to ImageJ/Fiji or have mastered the basics of the software.
Objectives : Learn how to present your microscopy images in scientific publications
Program : Image ethics and best practice for creating microscopy image figures; Presentation of the EZFig plugin in ImageJ
Duration/dates: 1 half-day Thursday 13 March 2pm to 5.30pm
Google form: https://forms.gle/AcrcucKzPgFNm7sv8
Introduction to image analysis with Fiji/ImageJ (Tuesday 29 April 2025)
Prerequisites: A laptop with a sufficiently comfortable screen and administrator privileges
Objectives: Acquire the basics of digital image processing and analysis in biology; learn how to put them into practice on ImageJ/Fiji
Programme Introduction to digital image analysis in biology (basic concepts); Image pre-processing; Segmentation: thresholding, watershed, starDist; Performing measurements; Ethics and reproducibility; Recording and modifying simple macros
Duration/date : 1 day Tuesday 29 April from 9am to 12.30pm and from 2pm to 5.30pm
Google form: https://forms.gle/qRkEk8xR7bLQKV6d6
Introduction to writing macros in ImageJ: IJ1 scripting (Thursday 22 May 2025)
Prerequisites : A laptop computer with a sufficiently comfortable screen and administrator privileges; Have taken an introductory course to ImageJ or be familiar with the software.
Objectives: To learn how to generalise a workflow and apply it to image batches.
Program: Preparing an automation: definition of elementary tasks and notion of algorithmics; Notion of variable, loops and conditional execution; Using ImageJ's own functions in macros: filtering, regions of interest manager, morphometry, etc.; Using functions added to ImageJ in macros: plugins; Simplifying repeated actions and clarifying code: notions of functions; Interacting with the user: input/output and graphical interface.
Duration/dates : 1 journée Jeudi 22 Mai de 9h à 12h30 et de 14h à 17h30
Google Form : https://forms.gle/MVz3P5YoCWRpp5F66
Sensibilization to Deep Learning + Cellpose human-in-the-loop (Tuesday September 30, 2025)
Prerequisites : A laptop with a sufficiently comfortable screen, administrator privileges and at least 8GB of RAM
Objectives : Familiarise yourself with the basic principles and vocabulary of artificial intelligence for image analysis; learn how to use the Cellpose tool for segmentation
Program : Understanding the theoretical principle of Deep Learning and the differences with Machine Learning; Learning the vocabulary of Deep Learning; Installing Cellpose; Annotating with Cellpose and re-training a model
Duration/dates : 1 day Tuesday 30 September from 9am to 12.30pm and from 2pm to 5.30pm
Google Form : https://forms.gle/oRGA7JKm2pqg6TmBA
Introduction to image analysis with QuPath (Thursday 23 October 2025)
Prerequisites : Un ordinateur portable avec écran suffisamment confortable et privilèges administrateur
Aims: Acquérir les bases du traitement et de l’analyse des images numériques en biologie ; Apprendre à les mettre en pratique sur QuPath
Program : Introduction à l’analyse d’images digitales en biologie (notions de base); Introduction à QuPath: concepts généraux (notion de projet, charger des images, interface); Déconvolution couleur; Détection d’objets, de tissu, segmentation et classification; Cartes de densité et mesures spatiales; Exporter des mesures; Introduction à l’automatisation (workflow recorder, automatisation en lots)
Duration/dates : 1 journée Mardi 25 Février de 9h à 12h30 et de 14h à 17h30
Lien Google Form : https://forms.gle/RWYNTpMcVvsPkxzV8
Individual training on request
These courses are designed for users with a short-term need for MicroPICell platform services.
Requests for training are made following a initial contact with platform staff
HISTOLOGY TRAINING
Microtome
Practical training session, duration 1 hour.
Cryostat
Practical training session, duration 1 hour.
PHOTONIC IMAGING TRAINING
-Confocal :
An initial 4-hour theoretical part, followed by a 4-hour applied practical part.
Thereafter, each user using a system will be accompanied by the facility managers.
-Super resolution SIM :
This training will be given after the user is fully autonomous on a confocal system. Duration: 2 hours.
-Slide scanner :
The training consists of a 1 to 1.5 hour training session. Users must specify whether or not they require fluorescence mode.
Simple video microscope or intracellular ion measurement (ex : Fura-2) :
Training will be by osmosis. The platform managers will operate the system in the presence of the user, who will be asked to note down the various stages.
Depending on the complexity of the request, this "hands-on" training may last several sessions.
On request
3D printer
A practical training session lasting 1 hour.
IMAGE PROCESSING TRAINING
Imagej / Fiji / icy/QuPath/Imaris
Individual training will be provided to answer a specific question.
For more general training, please refer to the platform's training plan.