Research Specialist in Image Analysis

Your position

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.

Your profile

• 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.