Research Engineer Position for Photonic Imaging Data Management and Structuring

Context:

La Timone Institute of Neuroscience (INT UMR7289 CNRS – amU), located on the Timone campus in Marseille, is a joint research unit specializing in neuroscience. The INT brings together approximately 200 people, organized into 13 scientific teams and 7 technological platforms, working to study the nervous system across scales (from molecular to cognitive functions) and animal models.

For several years, INT has been developing photonics imaging approaches (INPHIM Platform) to support research projects. These studies are essential in modern neuroscience, as they enable the anatomical characterization of neural networks underlying the functions under investigation. These anatomical studies generate large volumes of data in various formats, requiring optimized structuring and management procedures.

Since 2012, the laboratory has built a robust IT infrastructure covering networks, systems, centralized computing, and storage resources. This strategy has partially addressed data management challenges. However, with the growing needs of the INT, it is now necessary to develop and optimize new methods for managing and processing complex scientific data while adhering to the principles of open science.

 

Position:

The engineer will be integrated into the Neuroinformatics and Information Technology (NIT) platform of the INT, a team of 9 people, and will work in close collaboration with the INPHIM photonics imaging platform (scientific manager: Ivo Vanzetta; operational manager: Alberto Lombardini). They will be directly supervised by Arnaud Le Troter (project leader and coordinator of the FAIR2Lense project, funded by the Amidex Foundation for this position) and overseen by Nicolas Wanaverbecq, the project leader.

Mission:

In collaboration with the researchers and technicians from the NIT and INPHIM platforms, the research engineer will implement the structuring, standardization, and securitization of photonics imaging data produced at the Institute. They will be responsible for deploying and maintaining FAIR-compliant tools (OMERO, BIDS, eLabFTW) and will serve as the technical interface with regional and national platforms (amU Datacenter, 4Domics, FBI.data).

Main Responsibilities:

• Deploy, configure, and maintain the OMERO database for anatomical and functional data.
• Integrate metadata into processing pipelines according to BIDS/eLabFTW standards.
• Ensure traceability and reproducibility of data from acquisition onward.
• Collaborate with platform teams to facilitate user adoption of tools.
• Manage data transfers and archiving on INT’s local servers and national platforms (4Domics, FBI.data).
• Develop automated pipelines for data organization and processing.
• Participate in user training and support for imaging platforms.
• Contribute to documentation and best practices to ensure system sustainability.

Duration: Fixed-term contract (24 months, renewable)

With the objective of permanent position

Start Date: Between June and October 2026

Workload: Full-time (100%)

We are looking for a candidate with an engineering degree or a Master’s degree (MSc, or higher) in computer science, with a strong interest in imaging, data science, neuroinformatics, and open-source approaches. A PhD, or previous experience as a research engineer, would be considered a strong asset. Experience with collaborative software development practices (contributions to open-source projects) will be highly appreciated. The position may also offer opportunities for continuation or recruitment following the contract.

Required Skills:

·         Knowledge

• Scientific database management tools and FAIR standards (OMERO, BIDS, eLabFTW).
• Photonics image formats.
• Programming languages: Python, Fiji plugins, Napari.
• Distributed storage infrastructures and iRODS systems.

·         Operational Skills

• IT tools, programming, and algorithmics.
• Methods for analyzing large-scale data: managing and processing complex, heterogeneous biological imaging data.
• English language: Level B2 to C1 (Common European Framework).
• Ability to configure, administer, and maintain scientific databases.
• Aptitude for structuring and standardizing heterogeneous data formats.

·         Soft Skills

• Rigor and method for documentation and traceability.
• Pedagogyand ability to train and support users.
• Ability to work at the interface of multidisciplinary teams.
• Proactive mindset to anticipate and solve technical issues.

To be specified according to the amU regulatory grid and experience

Employer:

At the forefront of French and Francophone universities, Aix-Marseille Université (amU) brings together 78,000 students, 8,000 staff members, and 122 research structures in partnership with the leading organizations in the field. Its five major campuses host students across all academic disciplines available in France. The diversity of its sites offers unique career opportunities today.

Join us to build a future where diversity is our greatest strength.