The University of Basel's Biozentrum is internationally recognized for its pioneering research in life sciences, hosting 32 research groups and over 500 staff. The newly established Dietschy Facility for Tissue Science is a cutting-edge core unit designed to enable systematic investigation of individual cells within intact tissues, integrating advanced methods such as spatial transcriptomics, microscopy, volumetric imaging, neuronal activity mapping, and multimodal data analysis. The facility's initial focus is on neuroscience, and it aims to support a broad user base across the Biozentrum.

This fully funded PhD-level position as Research Specialist in Image Analysis is central to the facility's interdisciplinary platform. The successful candidate will develop and apply computational pipelines for aligning, segmenting, and interpreting large multimodal imaging datasets, including functional imaging, histology, and spatial transcriptomics. Responsibilities include building and maintaining registration pipelines for calcium imaging, histological, volumetric, and transcriptomic data; establishing single-cell correspondence across datasets; performing advanced segmentation of complex tissues; aligning datasets to common coordinate frameworks such as the Allen Brain Atlas; and integrating public reference volumes. The role also involves supporting segmentation and registration of spatial transcriptomics datasets, processing and visualizing large 3D volumes, developing tools for multimodal integration, and training researchers in computational workflows.

Applicants should hold a PhD in computational biology, computer science, biomedical engineering, neuroscience, or a related field. Essential skills include expertise in image registration, segmentation, and large-scale 3D imaging analysis, with proficiency in Python, MATLAB, ITK/VTK, Napari, Fiji, ANTs, Elastix, and emerging AI-assisted methods. Experience with atlas alignment, multimodal registration, and dense tissue segmentation is required, and familiarity with integrating functional, anatomical, and molecular datasets is desirable. Strong communication skills, an interest in interdisciplinary collaboration, and the ability to train students and postdocs are also important.

The Biozentrum offers a highly stimulating collaborative research environment, world-class infrastructure in a brand-new building, and state-of-the-art technology platforms. The position is fully funded, with salary according to institutional guidelines, and is initially for two years with the possibility of extension following a positive evaluation. Basel is a vibrant, cosmopolitan city at the intersection of Switzerland, Germany, and France, renowned as Europe's leading life sciences hub and offering a high standard of living and rich cultural opportunities.

To apply, candidates should submit an online application including a cover letter, CV, contact information for three referees, and examples of relevant work such as publications, software, pipelines, or imaging datasets. The application deadline is March 1, 2026. For informal enquiries, contact Professor Alex Schier at [email protected].