Staff Scientist – Tissue Clearing and Image Analysis

LMU Klinikum; München; Vor Ort; EUR 60.000 - 80.000; Vollzeit

Zusammenfassung

A leading research institute in Munich seeks a Scientist to support and drive innovative neuroscience projects. The ideal candidate has a strong background in tissue clearing and fluorescence microscopy, oversees tissue clearing projects, and works collaboratively on advanced imaging techniques. A MSc or PhD in life sciences is required. The role emphasizes data analysis, development of new pipelines, and contributions to significant research publications. The team offers a collaborative and interdisciplinary environment with an international focus.

Leistungen

Collaborative team environment

Research opportunities in neuroscience

Qualifikationen

• Strong background in tissue clearing and fluorescence microscopy.
• Hands-on experience with light-sheet systems and 3D imaging workflows.
• Practical knowledge of atlas registration and quantitative analysis.

Aufgaben

• Run and evolve tissue clearing and light-sheet imaging pipeline.
• Support and drive collaborative SyNergy projects.
• Develop new analysis pipelines in collaboration with the AI team.

Kenntnisse

Tissue clearing expertise

Fluorescence microscopy

Light-sheet imaging

3D visualisation tools (Imaris, arivis Vision4D)

Data analysis and visualisation

Image analysis (Fiji ImageJ, Python)

Team collaboration

Communication skills in scientific English

Ausbildung

MSc or PhD in life sciences or related field

Tools

Light-sheet microscopes

Data integration tools (LIMS)

Jobbeschreibung

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.

Scope of duties

This is a scientist role at the Mesoscale Hub of the DFG-funded Excellence cluster for Systems Neurology 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 visualisation
• Methods development
• 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 licences
• Troubleshoot data acquisition and integration with LIMS, cloud and on‑prem systems

Our requirements

• Strong background in tissue clearing and or fluorescence microscopy
• Hands‑on experience with light‑sheet systems and 3D imaging workflows
• Proficiency with 3D visualisation tools such as Imaris and or arivis Vision4D; experience with BigStitcher 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 ImageJ, Python for batch processing, napari, basic ML or deep learning toolchains)
• 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 organisation, and the ability to keep multiple collaborations moving

Our offer

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.

Our pioneering work has been recognised by high‑profile scientific journals including Nature Neuroscience, Cai…Ertürk 2018, Cell, Pan…Ertürk 2019, Cell, Zhao…Ertürk 2020, Cell, Bhatia…Ertürk 2022, Cell, Kolabas…Ertürk (2023), Nature Biotechnology, Mai…Ertürk (2024), Nature Biotechnology, Luo…Ertürk (2025), and has been featured in prominent media outlets like the New York Times, Wall Street Journal, BBC, and Süddeutsche Zeitung.

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

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

How to apply

• Primary contact: Prof. Ali Maximilian Ertürk
• Please send a single PDF including your short cover letter, CV, two to three referees, and earliest start date