Institut de Neurosciences Cognitives et Intégratives d'Aquitaine (UMR5287)

Aquitaine Institute for Cognitive and Integrative Neuroscience

Université de Bordeaux

Zone nord Bat 2 2ème étage
146, rue Léo Saignat
33076 Bordeaux cedex


Supervisory authorities

CNRS Ecole Pratique des Hautes Etudes Université de Bordeaux

Our partners

Neurocampus Unitéde Formation de Biologie


GDR Robotique GDR Mémoire GDR Multi-électrodes


Home > Facilities > Imagys : Microscopy & Image Analysis

IMAGYS : The Imaging Core Facility

by courtand - published on , updated on

Principal Engineer : Gilles Courtand

The Imaging Core Facility aims to assist users with all their microscopic or behavior imaging needs, from the conception of an idea, to final image analysis and presentation.
Under the responsibility of Gilles Courtand, Imagys supports you to solve image analysis problems whatever they are.
Our specific offerings are listed below:


Imagys offers a variety of microscopes to our users, which are all available for independent, as well as limited assisted use. These include regular widefield microscopes for fluorescence and brightfield imaging, laser scanning microscopes and macroscope.

Image analysis

We use state of the art in image analysis methods to investigate and solve image computing problems in basic and applied neuroscience as well as to design tools for subject-specific image analysis.
We provide access to several image analysis software packages (classical image processing, 3d reconstruction, deep learning...), and image analysis workstations that are optimized for handling large amounts of imaging data. We favor the use of free and open-source software (Fiji/ImageJ, Icy, Cell Profiler, neuTube, Kinovea, MedInria, 3dSlicer, paraview, DeepLabCut) but we also use commercial tool (Neurolucida).
We currently have three workstations with several different image analysis programs.

We are available to train users in the use of the software packages, help design most suitable analysis protocols, write macro or plugins, or develop own made software for a specific analysis (python).
Our ingeneer and programmer can tailor a solution to meet the needs of individual investigators.

We provide processing capabilities in collaboration with the Mesocentre de Calcul Intensif Aquitain (MCIA) to enable high computing task.

Training & Consulting

Our Education program consists of didactic lectures, image analysis workshops, as well as training users individually and in small groups. In addition, we offer free consultation of experiment design - including suggesting the best microscope for specific applications, optimal dyes or filter to use, we can advise you about cameras, specific lighting etc.
We also provide and training courses and focused software development consulting services on a short-term basis.