AMBER Postdoctoral Fellowship: Development of AI-assisted sample optimisation workflows for cryo-EM

Benefits

Additional Information

EMBL is Europe's life sciences laboratory - an intergovernmental organisation with more than 110 independent research groups and service teams covering the spectrum of molecular biology. It operates across six sites in Heidelberg (headquarters), Barcelona, Cambridge, Grenoble, Hamburg and Rome. Our mission is to perform basic research in molecular biology; train scientists, students and visitors at all levels; offer vital services to scientists in the public and private sectors within the member states; develop new instruments and methods; and engage actively in technology transfer. This post-doctoral position is part of the EU cofund research project AMBER, Advanced Multiscale Biological imaging using European Research infrastructures, will address scientific and sectoral gaps in biological imaging ranging from molecular, through cellular, to tissue, organ and organism levels of organisation, and is coordinated by LINXS Institute of advanced Neutron and X-ray Science. AMBER is funded by the EU Marie Skłodowska-Curie (MSCA) COFUND scheme. Around 8 postdocs will be recruited in the Final call with each fellowship lasting 36 months. AMBER has six core partners: Lund University/MAX IV, Sweden, the European Spallation Source (ESS), Sweden, the European Molecular Biology Laboratory (EMBL), Institut Laue-Langevin (ILL), France, the International Institute of Molecular Mechanisms and Machines, (IMOL), Poland, and the Leicester Institute of Structural and Chemical Biology, United Kingdom. Your work may include clinical and biomedical projects. It may also include technique development work aimed at combining imaging techniques and data analysis to provide a more integrated picture of life processes in the context of health and disease. To be a postdoc fellow at the AMBER programme you will get unprecedented medical, biological, and methodological capabilities, with a profound potential impact for Europe's next generation of research and researchers. When you have completed the AMBER programme you will be extraordinarily well equipped to further your career in academia, at infrastructures, in the health and MedTech sectors, and beyond. For more information about the total announced post-doctoral positions within in the AMBER co-fund project please visit https://www.euraxess.se/jobs/437869 The interviews will start in October/November 2026. For more information about AMBER, application and evaluation process etc please visit: ambercofund.eu. Your role Recent developments in cryo-EM workflows have highlighted how machine learning approaches can be successfully applied at several stages of the pipeline. While these tools are relatively easy to implement at the image processing level (e.g., particle picking or reconstruction), their application to sample preparation and vitrification remains challenging. This is largely due to the lack of automated and reproducible workflows, which are a necessary prerequisite for generating consistent experiments and enabling comprehensive data logging. The EasyGrid instrument developed at EMBL is currently one of the most advanced and versatile automated sample preparation systems in the field. It enables fully automated preparation of cryo-EM samples, covering all steps from plasma treatment of sample supports, through sample dispensing and spreading, to jet vitrification and storage in cryo-EM boxes. The workflow is complemented by a quality control instrument (EasyGrid Control) capable of generating nanometer-scale thickness maps of the prepared specimens. Together, the sample preparation and quality control instruments can be integrated into a closed-loop workflow, enabling optimization of cryo-EM sample preparation parameters without requiring immediate access to a cryo-EM microscope. In parallel, a database is being developed to automatically store all metadata associated with each prepared sample, including chemical composition, preparation and vitrification parameters, pre-screening atlases, storage conditions, and cryo-EM screening data. Mining this comprehensive dataset will enable the training of specialized AI models, ultimately allowing automated and data-driven optimization of cryo-EM sample preparation. The EasyGrid database will be integrated with EBI's structural biology resources, including EMPIAR, EMDB, PDB. This will cover alignment of the EasyGrid sample preparation metadata with EMPIAR's deposition schema (building on REMBI and related community standards), and cross-resource linking so that sample records can be related to related sequence, model, and structure entries. The AMBER postdoc will act as the primary point of contact between Grenoble and EBI, supported by the EMPIAR and EMDB teams. You have a maximum 8 years after a doctoral degree (PhD), as required by the project Grant Agreement signed with the European Commission, at least one original publication in a peer-reviewed journal, a background in the relevant methods, a complete application p

Your Match

How well this role fits your profile.

Company Intel

What employees say

Worked at embl? Share your experience