Internship OT-27689
Master's 2 internship: quantitative analysis of 3D image data
78350 Jouy en Josas
INRAE presentation
The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.
Work environment, missions and activities
Work environment, missions and activities
The Joint Research Unit for Reproductive Biology, Environment, Epigenetics and Development (UMR BREED), comprising approximately 80 people, aims to study the impact of the environment on embryonic and fetal development in mammals and the long-term consequences of early disturbances to this environment. The unit consists of three research teams and a research support team. You will be welcomed into the PROGENIE team.
The HAPPYSMELLING ANR project (https://anr.fr/Projet-ANR-22-CE20-0036) investigates the influence of the maternal context on in utero olfactory learning and its consequences on the socio-emotional behaviors of offspring from birth to juvenile age in male and female mice. To this end, pregnant mice were exposed or not to a synthetic odorant compound (anethole) during the last third of gestation. This compound was introduced into the drinking water, associated or not with a sugar reward, in order to induce (or not) a positive conditioning toward this odor throughout gestation. Four maternal groups were thus established (odorized/non-odorized, reinforced/non-reinforced), and feeding and social behaviors were monitored in their offspring from birth to the juvenile stage.
In parallel, at PND21, following exposure to anethole, the brains of these offspring were immunohistochemically labeled using an antibody against the c-Fos protein, allowing the identification of neurons activated by odor exposure (c-Fos belonging to the class of immediate early genes).
A lipophilic dye staining was also performed to serve as a reference for alignment with anatomical atlases.
The aim of the internship is to carry out quantitative analyses on the 3D images obtained from these brains, in order to highlight a possible modulation of neuronal plasticity induced by prenatal odor exposure in the offspring.
Activities the student will be in charge of:
- The student will implement an analysis pipeline developed on the local microscopy platform, involving Python scripts and steps carried out in the Fiji software, in order to: i) register an anatomical atlas onto the brain, ii) manually extract regions of interest, and iii) automatically quantify c-FOS+ neurons within these regions.
- Depending on their skills and interests, the student will also contribute to the development of improvements to all or part of the analysis pipeline. For example: adapting the atlas-sample registration tools from the BrainGlobe initiative (https://brainglobe.info/index.html); implementing machine learning methods to improve the automatic detection of c-FOS+ neurons; or further automating the analysis workflow by streamlining the different steps. This will involve writing Fiji macros and/or developing or refining Python programs.
Training and skills
Training and skills
Master's degree/Engineering degree in image science or data engineering
Strong fluency in the python programming language (SimpleITK, scikit-image, NumPy)
Knowledge of Java would be a plus
Theoretical knowledge in machine learning or deep learning
Knowledge in image registration would be a plus
INRAE's life quality
By joining our teams, you benefit from (depending on the type of contract and its duration):
- possibility of on-site accommodation
- collective catering.
How to apply
I send my CV and my motivation letter
All persons employed by or hosted at INRAE, a public research establishment, are subject to the Civil Service Code, particularly with regard to the obligation of neutrality and respect for the principle of secularism. In carrying out their functions, whether or not they are in contact with the public, they must not express their religious, philosophical or political convictions through their behaviour or by what they wear. > Find out more: fonction publique.gouv.fr website (in French)