Research Specialist in Microscopy and Spatial Transcriptomics (80-100%)

Your position

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.

Your profile

• 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.

We offer you

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.