Postdoctoral fellow (project leader) Computational image science in infection biology
The Department of Biomedicine is a joint effort between the University of Basel and the University Hospitals Basel. It unites basic and clinical scientists to advance our understanding of health and disease and to develop pioneering therapies benefiting the lives of patients in areas of unmet need.
With more than 70 research groups and 800 employees, the Department of Biomedicine is the largest department at the University. We are located in the heart of Basel at 6 different locations. Be part of our future!
Antibiotic testing is still defined by bulk growth inhibition measurements. We aim to replace this paradigm by
quantifying antibiotic action at single-cell resolution.
The scientific aim
Our laboratory has established a large-scale live-cell imaging platform that tracks hundreds of millions of individual bacteria during antibiotic exposure (Nature Microbiology, 2026). This platform enables systematic assessments of tens of thousands of experimental conditions across bacterial species, clinical strains and diverse drug treatments. These xperiments capture antibiotic activity in real-time at the level of individual cells. Yet much of the biological information embedded in these data remains unexplored. The next step is to convert these time-lapse images into accurate single-cell trajectories and subsequently into models of antibiotic responses, with direct relevance for drug development and patient treatment. We (boecklab.com) are looking for a scientist who will define the computational backbone of this programme.
Your position
The successful candidate will lead the computational single-cell imaging platform. This includes designing robust segmentation and tracking pipelines, developing classifiers of growth and viability, and establishing scalable frameworks across diverse bacterial species. The role also involves identification of dynamic phenotypes, defining descriptors of antibiotic response, and integration of these measurements into models. The candidate will co-supervise doctoral researchers, contribute to grant proposals, and provide technical leadership of the computational part within a highly interdisciplinary research environment.
Your profile
- PhD in computer vision, computational biology, physics or a related discipline
- Demonstrated expertise in image analysis and working with large-scale imaging datasets
- Strong expertise in deep learning (segmentation and foundation-model architectures)
- Demonstrated ability to design and execute technical projects
- Scientific independence with clear interest in biological mechanisms and clinical translation
- Collaborative mindset with enthusiasm for mentoring and teaching junior researchers
- Fluency in English
We offer you
- Access to several hundred terabytes of imaging data and strong computational infrastructure
- Intellectual ownership of the computational pipeline with to opportunity to shape its scientific direction
- Co-supervision of doctoral students and co-corresponding authorship where appropriate
- Direct translational integration through drug development and clinical research collaborations
- Active support for the project, grant applications, and development of an independent scientific profile
- An international, English-speaking cutting-edge research environment
- Competitive salary and high quality of life in Switzerland
Please use the link below to apply and submit the following documents:
- CV (with publication list)
- Cover letter summarising past achievements and research interests (1 page max.)
- Contact details for at least two referees
