The University of Zurich is the largest university in Switzerland and one of the most prominent in Europe. For research purposes the Biovision Center and Flow Cytometry Facility offer services to support high ranking publications in the field of life sciences.
The BioVisionCenter and the Flow Cytometry Facility at the University of Zurich are seeking a Bioimage Analyst to join a unique joint project at the intersection of advanced spectral flow cytometry and modern AI-driven bioimage analysis.
Modern flow cytometers capture not only high-parameter spectral fluorescence signatures but also imaging data for each cell at remarkable throughput. While this opens up the exciting possibility of extracting rich morphological readouts, the analytical tools shipped with such instruments are usually limited to rudimentary image processing, leaving most of this potential untapped. This project aims to close that gap by bringing flow cytometry data into the world of modern, scalable, AI-powered image analysis using the OME-Zarr community standard and the Fractal bioimage analysis platform. The developments will be validated in close collaboration with various UZH research groups, with the longer-term ambition of assessing the potential for image-activated cell sorting.
The successful candidate will be embedded in the BioVisionCenter and the Flow Cytometry Facility and should have a valid work permit for Switzerland or the EU.
The successful candidate will:
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develop OME-Zarr conversion workflows tailored to flow cytometry imaging data
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design and implement novel components for Fractal addressing common use-cases identified together with the Flow Cytometry Facility, including AI-based segmentation and morphological feature extraction
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validate the pipeline on biological applications, in close collaboration with UZH researchers
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produce high-quality documentation, tutorials, and training materials to ensure the uptake of these tools by the UZH research community
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contribute to the scientific dissemination of the work through publications, presentations, and community engagement within the Fractal and OME-Zarr ecosystems
We are looking for a motivated scientist with strong computational skills and a genuine interest in bridging advanced image analysis and biology.
Furthermore, you should bring the following qualifications:
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a master's degree or PhD in computational biology, bioinformatics, computer science, biomedical engineering, physics, or a related field
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strong programming skills in Python, including experience with scientific libraries for image analysis (e.g. scikit-image, numpy, dask) and familiarity with version control (Git)
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experience with bioimage analysis, ideally including AI-based segmentation methods
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familiarity with modern image data standards such as OME-Zarr, or a clear willingness to learn them
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experience in having mastered a biological project involving microscopy/flow cytometry data is an advantage but not required
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the ability to work independently as well as collaboratively across interdisciplinary teams (computational and experimental)
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excellent communication skills in English (German is not required)
Please submit your application until 31 July 2026 as a single PDF. The PDF should include a CV, a short motivation letter outlining your fit for the position and academic background, as well as the names and contact details of two persons of reference. Applications will be reviewed on a rolling basis until the application deadline.
We offer a stimulating, interdisciplinary working environment at the interface of computational and experimental life sciences, close collaboration with leading core facilities and research groups at UZH, and the opportunity to contribute to an open-source ecosystem used by the international bioimaging community.
An extension beyond the initial 12‑month temporary contract may be considered subject to performance, project developments, and available funding, but cannot be guaranteed at this stage.
