Introduction
Antimicrobial resistance (AMR) is one of the most urgent global health threats projected to cause up to 10 million deaths per year by 2050. The AI4AMR project brings together teams from Institut Pasteur (France), Helmholtz Centre for Infection Research (Germany), and University of Würzburg (Germany) to revolutionize antibiotic discovery.
Using advanced microscopy, mass spectrometry, and deep learning, our goal is to identify new antibiotics and their modes of action. To make these methods accessible to the scientific community, we are developing an open-source platform that will allow biologists with no coding or AI background to upload and analyze bacterial images through a user-friendly interface.
We are looking for a postdoctoral researcher with experience in developing open-source bioimage analysis tools and a strong interest in deep learning and drug discovery. The position is based at Institut Pasteur (Paris).
Your Mission
- Develop a robust, scalable user interface (using Python-based frameworks or a web application) enabling image upload, AI-based analysis, and visualization of bacterial phenotypes.
- Perform image analysis using existing deep learning algorithms developed within the AI4AMR consortium, adapt them when necessary, and contribute to improving their performance.
- Work closely with microbiologists, data scientists, and AI researchers.
- Implement pipelines for deep learning inference on HPC or cloud clusters.
- Contribute to developing an open-source platform that supports FAIR data management and reproducible research.
Your Profile
- Strong experience in Python, software development, and prior experience with implementing and deploying user-friendly open-source tools as plug-ins for platforms like napari or ImageJ and/or as web applications.
- Knowledge of deep learning frameworks (PyTorch or TensorFlow) and experience with data pipelines or image analysis.
- Familiarity with HPC environments, or cloud services (AWS, GCP, Azure, etc.) is a plus.
- Interest in next-generation bioimaging file formats such as OME-ZARR / OME-NGFF is a strong plus.
- Experience contributing to open-source projects and a genuine interest in biological research.
Why Join Us?
You will join a cross-disciplinary team at Institut Pasteur (Paris) working at the interface of AI, microbiology, metabolomics, and image analysis.
The Zimmer Lab, which has developed widely used open-source platforms such as Shareloc and ImJoy (Ouyang et al., Nat. Methods 2022; Ouyang et al., Nat. Methods 2019), offers an ideal environment for creating tools that unite cutting-edge computation and biology.
As part of the ERC Synergy project AI4AMR, your work will directly contribute to accelerating the discovery of life-saving antibiotics and ensuring that this technology remains freely available to the research community.
How to apply
Send a single PDF containing your CV along with a brief motivation letter (max 3 pages total) to alessandro.torri@pasteur.fr with benoit.lelandais@pasteur.fr and christophe.zimmer@pasteur.fr in CC.