Staff Scientist – Tissue Clearing and Image Analysis; m​/w​/d

Staff Scientist – Tissue Clearing and Image Analysis

(m/f/d)

The Hospital of the University of Munich, Germany, is one of the largest and most competitive university hospitals in Germany and Europe. 48 specialized hospitals, departments and institutions harbouring excellent research and education provide patient care at the highest medical level with around 11.000 employees.

The Institute for Stroke and Dementia Research (ISD) at LMU, Munich is mostly financed by foundation funds. Its activities range from basic research to the conduct of clinical trials. The ISD employs around 150 staff, doctoral students, scholarship holders and visiting scientists from abroad.

This is a scientist role at the Mesoscale Hub of the DFG-funded Excellence cluster for Systems Neurology (SyNergy) with a strong “science enabler” and project-driver focus. You will run and evolve our tissue clearing and light‑sheet imaging pipeline, support and manage collaborations across SyNergy, and help translate data into robust, quantitative insight.
The primary responsibility is to support and drive collaborative SyNergy projects; in addition, the role includes scientific contributions to a defined research topic aligned with the Mesoscale Hub, with co‑authorship on resulting publications.

• Implementation of tissue‑clearing projects in collaborative projects with the SyNergy Excellence Cluster
• Help with data analysis and data visualization
• Development of new analysis pipelines in collaboration with our AI team
• Lab support:
  Maintenance of cutting‑edge light‑sheet microscopes
• (Optionally) support with writing new animal experiment licenses
• Troubleshoot data acquisition and integration with LIMS, cloud and on‑prem systems

Strong background in tissue clearing and/or fluorescence microscopy.

• Hands‑on experience with light‑sheet systems and 3D imaging workflows
• Proficiency with 3D visualization tools such as Imaris and/or arivis Vision4D; experience with Big Stitcher or similar for large volumes
• Practical knowledge of atlas registration and quantitative analysis in cleared tissues
• Working knowledge of image analysis and automation is welcome (examples: Fiji Image
  
  J, Python for batch processing, napari, basic ML or deep learning tool chains)
• Advantageous but not required: FELASA B and experience coordinating animal experiments
• Experience with VR‑based annotation tools and 3D proofreading
• MSc or PhD in life sciences, biomedical engineering, optical physics, or a related field
• Excellent communication skills in scientific English
• Service mindset, strong organization, and the ability to keep multiple collaborations moving

We are a highly collaborative team at the interface between LMU and Helmholtz Munich.

Our mission is to understand complex biology in 3D by combining tissue clearing, light‑sheet and advanced microscopy, high‑throughput analysis, and AI. The Mesoscale Hub serves SyNergy investigators with end‑to‑end support: experimental design, clearing and staining, 3D imaging, atlas registration, quantitative analysis, secure data handling, and training.

Our culture is team‑driven, international, and interdisciplinary, with biologists, engineers, physicists, and computer scientists working side by side on ambitious projects.

To learn more about our ground‑breaking work, visit our website at

Remuneration is based on the Collective Agreement for the Public Sector of the Länder (TV‑L) including all allowances customary in the public sector.

Please send a single PDF including your short cover letter, CV, two to three referees, and earliest start date.

Disabled persons will be preferentially considered in case of equal qualification. Presentation costs cannot be refunded.

Please note that we cannot reimburse travel expenses incurred through interviews.

We ask you for your understanding that postal applications will not be returned, but will be destroyed in accordance with data protection regulations. The data usage information also applies to postal applications.