Research Specialist in Microscopy and Spatial Transcriptomics

The Biozentrum of the University of Basel is one of the world's leading life sciences institutes. With 32 groups and 500 employees, we are a dynamic and international research community that has spawned many fundamental discoveries in biology and medicine as well as several Nobel Laureates.

The Biozentrum is establishing the Dietschy Facility for Tissue Science, a new core unit enabling systematic investigation of individual cells within intact tissues. The facility will integrate state-of-the-art methods for spatial transcriptomics, advanced microscopy, volumetric imaging, neuronal activity mapping, and multimodal data analysis, with an initial focus on neuroscience. To build this interdisciplinary platform, we invite applications for three PhD-level Research Specialists: Microscopy and Spatial Transcriptomics Specialist (this position); Image Analysis Specialist; Computational Neuroscience and Data Analysis Specialist. These positions will work closely together and will support a broad user base across the Biozentrum. Become part of our community

This position will establish and operate advanced imaging and spatial transcriptomics pipelines for high-resolution molecular profiling in intact tissues. The specialist will develop and apply methods enabling large-volume processing-such as whole brain spatial transcriptomics-and integrate techniques including expansion microscopy and multiplexed FISH.

Your responsibilities

• Operate, maintain, and expand commercial and custom-built systems for spatial transcriptomics and microfluidic tissue processing.
• Develop protocols for volumetric molecular imaging, including expansion microscopy and multiplexed in situ hybridization workflows.
• Establish whole-mount and thick-section spatial transcriptomics pipelines, ensuring tissue integrity, reproducible labeling, and high-content imaging compatibility.
• Build or adapt instrumentation required for large-volume sample processing and imaging.
• Coordinate with researchers, image analysts and data specialists to generate robust, standardized whole-brain datasets.
• Train and support researchers in applying facility methods to their own samples.
• Contribute to development of facility infrastructure for long-term whole-tissue profiling.

• PhD in neuroscience, bioengineering, biophysics, molecular biology, or related discipline.
• Expertise in advanced microscopy (light-sheet, confocal, multiphoton).
• Experience with spatial transcriptomics, expansion microscopy, or multiplexed FISH.
• Skills in instrumentation, microfluidics, or custom optical systems.
• Experience with tissue clearing or large fixed tissue preparations advantageous.
• Strong communication skills, interest in interdisciplinary work, and ability to train students and postdocs.

The Biozentrum provides a highly stimulating collaborative research environment with a world-class infrastructure in a brand-new building, as well as state-of-the-art technology platforms for cutting-edge interdisciplinary research. The position is fully funded and salary is according to institutional guidelines. The position is initially for two years, with an option for extension after positive evaluation.

Basel is a cosmopolitan city with people from 150 nations. Located on the border where three countries meet – Switzerland, Germany and France – it is Europe's most important life sciences hub. Basel provides a high standard of living and a rich cultural atmosphere.

Application / Contact

Please apply online:

Your application should include:

• a cover letter describing relevant experience and interests
• a CV
• contact information for three referees
• examples of relevant work (e.g., publications, software, pipelines, imaging datasets)

Application deadline: March 1, 2026

For any informal enquiries, please contact:

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