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Tasks : As part of the HR support provided by the A*Midex Foundation of Excellence to the CEREGE's MICROAUTOMATE platform (automated recognition of microorganisms using Artificial Intelligence), the tasks of this post are to maintaining and developing the production environments used in the platform.
These are made up of software chains made up of a succession of segments, such as: . automation of digital image capture (microscope and digital camera drivers) . image segmentation in certain cases . morphometric analysis of digitised images . neural network training . prediction by deploying neural networks in . the production environment (inference).

Unit: Centre de Recherche et d'Enseignement en Géosciences de l'Environnement CEREGE, Aix en Provence, France Teams : Climats Analytical platforms: MicroAutomate Contact: [Luc Beaufort](mailto: beaufort@cerege.fr "Luc Beaufort"), [Thibault de Garidel-Thoron](mailto: garidel@cerege.fr "Thibault de Garidel-Thoron )

Job description

• A Research Engineer (M/F) - Expert in scientific computing

Place of work CEREGE - Aix-en-Provence
Type of contract : Scientific CDD
Contract duration 24 months, renewable for 24 months
Planned date of hire September 2024
Number of hours worked : Full-time Level of education required: BAC+5
Desired experience 3 years

Background:
CEREGE is coordinating the national IMAGINE2 platform (Plateforme nationale d'IMagerie et d'Analyse pour Guider l'INnovation face à la transition Environnementale et Énergétique - €7m 2021-2029 (project structured on the basis of the IR RéGEF)) funded by the France 2030 national investment plan.
The aim of IMAGINE2 is to create an open technology platform, distributed across the region, to characterise a wide range of complex, heterogeneous and generally fragile materials and samples, in connection with the environmental and energy transition. The strength of this platform lies in its ability to carry out analyses on several spatial and temporal scales, under static and dynamic conditions and subject to chemical, physical, biological and mechanical constraints.
By developing correlative imaging and multimodal analysis, IMAGINE2 will bring together a chain of 2D-3D X-ray, electronic and spectroscopic imaging equipment.

Tasks :
In collaboration with the heads of the Equipex+ IMAGINE2 instruments, the research engineer will be responsible for the processing and analysis of 2D and 3D images and the implementation of correlative imaging. He/she will use mathematical and computational methods to develop original and innovative software tools for image analysis and will contribute his/her expertise, particularly in the use of artificial intelligence methods and technologies.

Main activities:
Developing specific and innovative algorithms for the quantitative analysis of 2D and 3D images and the correlation of images between the various Equipex+ instruments.

Develop codes to obtain quantitative data from X-ray (fluorescence and tomography) and electronic imaging techniques

Advising researchers on the choice of software and mathematical methods to be used depending on the problem to be addressed

Working with scientists to write/implement algorithms to solve electron microscopy, fluorescence and X-ray tomography image processing problems.

Documenting, maintaining and publishing the methods and tools developed

Manage the lifecycle of input and output data for calculations

Deliver presentations and training to ensure the transfer of knowledge and skills

Skills :
Knowledge
. Mathematics
. Algorithms
. Scientific calculation methods and tools
. Programming language (Python, C++, etc.)
. English language: B1 to B2 (Common European Framework of Reference for Languages)

Operational skills

. Experience in designing and developing mathematical and computer methods to solve a theoretical problem in a scientific project.
. Experience in image analysis and processing required.
. Experience in the use and/or development of image analysis tools using ImageJ, MATLAB, Java or an equivalent programming language (C++, Python, etc.).
. Working as part of a team
. Drafting user documentation

To apply
Please send your CV, covering letter and two letters of reference to rose@cerege.fr and borschneck@cerege.fr.
Deadline for applications: 28 June 2024