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

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.

The fellow will join the Papp Team & Djinovic Group at EMBL Grenoble. The selected candidate will work in close collaboration with the conceptors and super users of the  EasyGrid system. EMBL EBI collaboration will be established with Hartley (EMPIAR) and Morris (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 package submitted through the AMBER portal (including CV and detailed research plan), and finally, 
• strict compliance with the MSCA mobility rule that the researcher must not have resided or carried out his/her main activity (work, studies, etc.) in the host organisation's country for more than twelve months in the three years immediately prior to the call deadline.

Contract length: 3 years

Instructions on how to apply

For more information and documents/templates/europass link, please visit https://www.ambercofund.eu/for-applicants 
Incomplete applications will not be considered. Please make sure that you upload all the required documents specified below i-ix.
If you are interested in applying for more than one position (maximum 3) you must be prepared to make a full application for each individual position.
Applications shall be written in English and all documents shall be in pdf format.

i) A Curriculum Vitae (europass format). Your CV shall be exported to a PDF file that you use in your application.
ii) A detailed research plan including any foreseen secondments (candidates can suggest more than the mandated one, they can also suggest their own secondments), schools and conferences as well as a templated budget plan. The research plan should be as concise as possible, 3 pages, including one-third page of summary/abstract. 

Additional texts to include in the PDF are:
iii) Letter of Commitment from any additional secondment partners the candidate wishes to bring
onboard.
iv) Evidence of English proficiency (minimum CEFR B22, also checked at interview).
v) A draft Individual Career Development Plan (ICDP).
vi) Two reference letters.
vii) Any additional documents to support the application, for example PhD certificate/diploma, PhD upcoming defense date
viii) Ethical questionnaire (HE ethics checklist + research ethics commitment) 

In addition, the application will require:
ix) Any candidate can apply for maximum of 3 positions. You must apply for each individual position. A list with order of preference of positions should be sent to the AMBER management. amber@linxs.se 

Professional development support

The EMBL Fellows’ Career Service provides support and guidance to predoctoral and postdoctoral fellows across all six EMBL’s sites.

Working with a dedicated Careers Advisor, this invaluable service will help you to take informed decisions about your career planning both in the short and longer term. Whether your main interest is pursuing a career path in academia, exploring opportunities in industry or exploring an independent venture, the EMBL Fellows’ Career Service with provide you with a portfolio of activities and resources to help you.

To find out more please visit - EMBL-fellows-career-service

Why join us

Enjoy lots of employee benefits:

• Financial incentives: Monthly family and child allowances, generous stipend reviewed yearly, pension scheme, death benefit and unemployment insurances

• Flexible working arrangements including hybrid working patterns 

• Private medical insurance for you and your immediate family 

• Generous time off: 30 days annual leave per year in addition to public holidays

• Campus life: Free shuttle bus (Heidelberg), on-site library, subsidised on-site cafeteria, casual dress code, extensive sports and social club activities (on campus and remotely)

• Family benefits: Kindergarten (Heidelberg), 10 days of child sick leave, paid maternity & parental leave, holiday clubs on campus and monthly family and child allowances
   

What else you need to know

• International applicants: We recruit internationally and successful candidates are offered visa exemptions. Read more on our page for international applicants. 

• Diversity and inclusion: At EMBL, we believe that diverse teams drive innovation and scientific excellence. We encourage applications from candidates of all genders, identities, nationalities and/or any other diverse backgrounds.

• Job location: All our fellowships are based on-site (for at least part of each week). If you are living overseas, you will receive a generous relocation package to support you. 

• EMBL is a signatory of DORA. Find out how we apply DORA principles to our recruitment and performance assessment processes here

• How to apply: To apply please submit a cover letter and a CV through our online system. Applications will close at 23:59 CET on the date shown below. We aim to provide a response within two weeks after the closing date.

Closing Date