We are seeking a highly motivated Computational Scientist or Research Software Engineer to join a collaborative international team working at the intersection of cell biology, advanced imaging, and software development. This position is a joint initiative between the Allen Institute for Cell Science (Seattle, USA) and the at the Friedrich Miescher Institute for Biomedical Research and ETH Zurich (Basel, Switzerland).
The successful candidate will play a key role in developing and integrating advanced image analysis workflows for complex biological datasets, including lightsheet microscopy images. This work will help shape the future of interactive visualization and analysis tools for multidimensional biological imaging. It is an exceptional opportunity to contribute to open-source scientific infrastructure while working within a diverse, interdisciplinary team.
This position is primarily based in Basel, Switzerland and involves active collaboration and travel to Seattle, USA.
In this role, you will
1. Develop robust, scalable image analysis workflows for lightsheet microscopy using OME-Zarr and related technologies.
2. Integrate workflows into platforms such as Fractal and tools for 3D+t interactive visualization and quantitative feature space exploration.
3. Contribute to the design and development of the OME-NGFF specification.
4. Collaborate across international teams to ensure seamless integration with existing tools and frameworks.
5. Engage regularly with biologists, engineers, and developers to support effective cross-disciplinary research and tool development.
About you
Required
6. You hold a MSc or PhD degree in computer science, data science, computational biology, or a related field.
7. You have 2+ years of relevant experience.
8. You are proficient in Python or similar programming languages.
9. You have demonstrated track record in open-source scientific software development for image analysis.
10. You are familiar with software engineering best practices, including version control, testing, and continuous integration.
11. You possess strong interpersonal communication skills with experience working across teams and disciplines.
12. You are independent, proactive, and goal-oriented and have a passion for scientific discovery and tool building.
Preferred
13. You have experience in processing lightsheet microscopy images or other large-scale multidimensional image datasets.
14. You are familiar with cloud-native applications and the OME-Zarr file format.
15. You have contributions to community-driven software infrastructure projects.
What we offer
16. The opportunity to develop cutting-edge tools at the frontier of quantitative cell biology.
17. Access to state-of-the-art facilities and international collaborations across Basel and Seattle.
18. A creative and inclusive research environment that values innovation, openness, and mentorship.
19. The chance to contribute to globally used open-source software platforms.
How to apply
Please submit your application online at www.fmi.ch/opening. Applications will be reviewed on a rolling basis until the position is filled. Your application should include:
20. A cover letter outlining your experience and motivation for this role.
21. A CV, including links to relevant software contributions open-source projects.
22. The names and contact details of 3 referees.
For further information, please contact Prof. Prisca Liberali (prisca.liberali@fmi.ch), Dr. Gustavo Quintas Glasner de Medeiros (gustavo.medeiros@fmi.ch), or Dr. Koen Oost (koen.oost@fmi.ch).
About the FMI
The FMI is a world-class biomedical research institute affiliated with the University of Basel and Novartis Biomedical Research. With an international staff of about 330 people, including more than 150 postdoctoral fellows and graduate students, the FMI conducts cutting-edge research in genome regulation, multicellular systems and neurobiology. We are located in the vibrant city of Basel, Switzerland’s third-largest city and Europe’s leading hub for the life sciences.
At the FMI, diversity is the cornerstone of innovation and collaboration. We foster an inclusive environment where everyone can thrive and contribute meaningfully. We welcome applicants of all genders, cultures, ethnicities, and demographics who can complement our existing team. Join us in building a scientific community that represents and benefits the world we study.