Research Specialist in Image Analysis (80-100%)

The 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; Image Analysis Specialist (this position); 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 develop and apply computational pipelines to align, segment, and interpret large multimodal imaging datasets, including functional imaging, histology, and spatial transcriptomics. The specialist will enable accurate registration of single cells across modalities over time and development, referencing public brain atlases where applicable.

Your responsibilities

• Build and maintain multimodal registration pipelines to align calcium imaging, histological, volumetric, and transcriptomic data.
• Establish single-cell correspondence across datasets, accounting for tissue deformation and using fluorescent landmarks or anatomical features.
• Perform advanced segmentation of complex tissues, including dense or heterogeneous molecular labeling.
• Align datasets to common coordinate frameworks (e.g., Allen Brain Atlas) and integrate public reference volumes.
• Support segmentation and registration of spatial transcriptomics datasets, incorporating immunostaining channels.
• Process and visualize large 3D volumes generated by facility instruments.
• Develop tools for multimodal integration (imaging, transcriptomics, proteomics).
• Train researchers in computational workflows and best practices.
• Collaborate closely with microscopy and data-analysis specialists in the Biozentrum and broader Basel community.

• PhD in computational biology, computer science, biomedical engineering, neuroscience, or related field.
• Expertise in image registration, segmentation, and large-scale 3D imaging analysis.
• Proficiency with tools such as Python, MATLAB, ITK/VTK, Napari, Fiji, ANTs, Elastix and emerging AI-assisted methods.
• Experience with atlas alignment, multimodal registration, and dense tissue segmentation.
• Familiarity with integrating functional, anatomical, and molecular datasets desirable.
• 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.
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