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Data Science Lab & Microscopy Imaging Center Employment for 3 years starting from January 2025, with prolongation relying on project success

The Microscopy Imaging Center (MIC) and the Data Science Lab (DSL) are core facilities of the University of Bern providing scientific support for researchers across all faculties. The two units have long-standing collaboration to help researchers access advanced image analysis methods through custom software development and support for existing bioimage analysis tools.

Job Description
Running bioimage analysis workflows requires increasingly complex setups posing challenges to researchers (large computational resources, software installation complexity, large data sizes). To alleviate some of these constraints for researchers, the MIC and DSL are joining forces to create a state-of-the-art bioimage analysis platform. The latter will serve as a critical resource for researchers, by giving them access to advanced bioimage analysis tools running on high performance computing resources. As an application specialist for the platform, we are seeking a bioimage analyst to join our team. As a successful candidate you will setup and maintain multiple tools and workflows made available to researchers. For this task you will be in close contact with researchers from various areas of imaging, helping them process their data on the platform. You will also work in close collaboration with an IT specialist who will take care of the platform infrastructure.

Key Responsibilities

• Install popular bioimage tools on the platform (in collaboration with IT expert).
• Test and document tools by creating example workflows on the platform.
• Keep tools up-to-date and ensure the researchers’ needs are fulfilled.
• Explore cutting edge methods for the platform and advertise them to researchers.
• Help organize trainings for tools using the platform.
• Write workflows specifically for the platform (e.g. porting computational notebooks).
• Maintain comprehensive documentation for users and maintainers.

Qualifications

• Proven experience in the bioimage analysis area as a researcher or imaging facility expert (PhD or equivalent research experience).
• Proven experience with Fiji and Python scripting.
• Experience with additional open-source tools such as QuPath, napari, CellProfiler, Ilastik, Chimera, RELION is highly desirable.
• Experience with ML/AI methods is highly desirable.
• Experience with microscopy is highly desirable.
• Efficient communication skills in English; knowledge of German is a plus.

What We Offer

• A stimulating interdisciplinary team working with cutting edge methods in AI/ML.
• An opportunity to help shaping an important new platform from zero.
• The potential for a long-term position based on the platform success.
• Work conditions according to cantonal regulations and flexible working hours.
• Easily reachable offices at the main railway station in Bern.

Application Process
Interested candidates should submit their CV, a cover letter detailing their relevant experience and motivation for the position and contact information for at least two references as one pdf file to
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. Please do not use the "Apply now" button. For technical questions regarding the position, please contact
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. The position is open until filled.

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