Research
EMBL Heidelberg

The European Molecular Biology Laboratory (EMBL) is a world leader in scientific research and at the forefront in the development of cutting-edge technologies. We are seeking a highly motivated colleague to join the research group of Anna Kreshuk as a Research Software Engineer for a project concerned with novel technology development in electron microscopy.

The project is funded by the Chan Zuckerberg Initiative and will be carried out in close collaboration with the groups of Simone Mattei (EMBL Imaging Center) and Julia Mahamid (EMBL MSB Unit). Together, we will develop segmentation, registration and analysis methods along the cryogenic imaging pipeline, from cryoLM to cryoFIB to cryoET. The ultimate goal is to make the developed methods accessible as user-friendly tools for imaging scientists and users of microscopy facilities.

Your role

The successful candidate will work in the Kreshuk Group at EMBL Heidelberg, interacting closely with colleagues at the Imaging Center, at the EMBL Electron Microscopy Facility and in the Mahamid Group at the MSB Unit. The work will entail designing, developing and applying methods for multimodal volume registration and segmentation, including the development of methods for on-the-fly finding of best acquisition targets. While the methods will be tested on concrete biological use cases, the goal is to develop a modular framework that can easily be reused for a large diversity of samples and questions. Many of the modules will include AI components, with human-in-the-loop finetuning and adaptation UIs.

Closing date: 31 December 2024

Contract duration: 3 years

Grading: 5 or 6, depending on qualifications and experience (monthly salary starting from 3,9k EUR after tax + other paid benefits)

Reference number: HD02756

You have

Candidates should have a university degree in life or computational sciences, physics or engineering, preferably with a PhD or equivalent experience. Familiarity with image analysis and machine learning methodology (in Python) using modern software development practices (Git, TDD, CI) is essential. You have curiosity and motivation to work in interdisciplinary projects, and are eager to get to grips with relevant areas of biology and the technologies used in biological research. You are aware of potential domain gaps between developers and your targeted users and are motivated to find a common language both in communication, and user-facing software components. You are skilled in planning and execution of R&D projects, and you have the ability to work effectively both independently and as part of a multidisciplinary team. Fluency in English is compulsory.

You might also have

A background in microscopy and image analysis technologies, experience with developing computer vision methods for microscopy, experience with end-user tool development and deployment for non-computational users.

Why join us

Our team

The group of Anna Kreshuk develops new machine learning methods for image analysis problems in microscopy. On the research side, they are especially interested in large-volume segmentation, multi-modal registration and representation learning for characterization of phenotypes. In addition to these research endeavours, the group maintains and develops the popular machine learning tool ilastik and, collaboratively, develops the cell segmentation tool PlantSeg. The team is also part of the consortium behind the BioImage Model Zoo initiative.

Our institute

EMBL is curiosity-driven, community-oriented and international. As an inclusive, equal opportunity employer, we believe that diversity enables us to collaborate more effectively and be innovative in our approaches. We are, therefore, committed to creating an inclusive and flexible culture - one where everyone can realise their full potential and make a positive contribution to our organisation.

We encourage applications from individuals who can complement our existing team – we believe that success is built on having teams whose backgrounds and personal experiences reflect the diversity of the populations that our science serves. We actively encourage applications from all genders and cultures, ethnic groups and all demographics to help us avoid perpetuating biases and oversights at this transformational point in our people strategy.

EMBL offers attractive conditions and benefits appropriate to an international research organisation with a very collegial and family-friendly working environment. Competitive salary and social security benefits, financial support for relocation, a relaxed culture, professional development, an on-site nursery, canteen and other staff facilities make EMBL a great place to work.

** Don’t meet every single requirement? We are dedicated to building a diverse, inclusive and authentic workplace, so if you’re excited about this role but your past experience doesn’t align perfectly with every qualification in the job description, we encourage you to apply nevertheless.

What else you need to know

We are Europe’s research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with more than 1900 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome.

Our mission is to offer vital services in training scientists, students and visitors at all levels; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research. The working language of the institute is English.

Please note that appointments on fixed term contracts can be renewed up to 9 years in total, depending on circumstances at the time of the review.

EMBL is a signatory of DORA. Find out how we implement best practices in research assessment in our recruitment processes here.

Please apply online through: www.embl.org/jobs