OMERO embedding and Optimisation of Biom3d, an image analysis tool using deep-learning networks

Organisation/Company Université Clermont Auvergne Research Field Computer science » Informatics Biological sciences » Biology Researcher Profile Recognised Researcher (R2) Leading Researcher (R4) First Stage Researcher (R1) Established Researcher (R3) Application Deadline 31 Mar 2026 - 22:00 (UTC) Country France Type of Contract Temporary Job Status Full-time Offer Starting Date 1 Sep 2026 Is the job funded through the EU Research Framework Programme? Not funded by a EU programme Is the Job related to staff position within a Research Infrastructure? No

Offer Description

Neural networks, employing deep learning (DL), have become essential for high-throughput image analysis. However, DL tools should be made accessible to a broader scientific community, including plant biologists.

In line with the FAIR (Findable, Accessible, Interoperable, Reusable) principles, we aim:

• (Obj1) to implement new image analysis functionalities into Biom3d, a modular framework based on DL networks initially designed to quantify nuclear shape and chromatin organization.
• (Obj2) to facilitate the use of Biom3D for end users’, we will improve its interoperability with OMERO, a popular image data management system created by the University of Dundee, with Imaris, a proprietary software from Oxford Scientific, and with the FRACTAL web-platform developed by the bioimaging center in Zürich in order
• (Obj3) to contribute to the design of new set of workflows called ChromTrack3D adapted to microscopists’ needs in image analysis. Finally, we will explore connecting OMERO servers within the AGILE consortium to promote the accessibility and sharing of image datasets in collaboration with the University of Dundee.

You will learn how to implement and train new deep-learning models in the Biom3d framework, develop OMERO interface scripts, run jobs on High Performance Computing (HPC) clusters and develop new functionalities in Biom3d like preprocessing OME-Zarr images.

Significant experience in Python (and Java) scripting, and knowledge in (plant) molecular biology and image analysis.

A Master in the bioinformatics or image analysis. A desire to succeed in science.

Applicants must

not have resided OR worked in France during the last three years (or less than 12 months)hold a master’s degree (obtained no later than September 2026)