Image Analysis and Data Management Expert

ETH Zurich is a world-leading university dedicated to advancing science, engineering, and technology. The Single Cell Facility (SCF) is a central research and service platform at the Department of Biosystems Science and Engineering (D-BSSE) of the ETH with location in Basel. It is a departmental core facility providing access to a high-end instrument portfolio for optical single cell analysis such with light microscopy and flow cytometry technology. The SCF is part of the D-BSSE's commitment to elucidate the design principles of cells in stochastic environments and their exploitation for network design. The SCF staff works closely with the Lab Automation Facility (LAF) team, which develops and maintains complex robotic setups integrated with readout technologies such as high content imaging for experimental workflows in biology and biochemistry.

The SCF's centralized instrument pool is accompanied by expert service provided by staff who offer instrument training, hardware and software maintenance, and advice on sample preparation, assay design, image analysis, and data management.

As a member of the SCF, you will perform image analysis, data management, and other IT-related projects for SCF users and staff related to a wide variety of biology and biotechnology projects. Starting date: 1. June 2025.

As a member of the SCF, you will perform image analysis on microscopy data, data management for various applications and pipelines of the facility, and other IT-related projects for SCF users and staff related to a wide variety of biology and biotechnology projects.

Your resposibilities:

• First line support for image analysis requests (from optical microscopy).
• Providing expert input to microscopy imaging projects to help design experimental protocols in close collaboration with SCF microscopy experts to align analysis strategies with image acquisition parameters.
• Train users in the use of existing analysis software (Imaris, Huygens, Fiji, ImageJ, CellProfiler, MATLAB, etc.). Keep abreast of developments in such commercial and open-source image analysis tools.
• Develop ad-hoc solutions for specific user projects (MATLAB scripts, ImageJ macros/plug-ins, CellProfiler pipelines, Python coding, etc.).
• Organization and teaching of an image analysis module in a laboratory course for biotechnology master students.
• Development of analysis software tools for proprietary image formats (super-resolution data, plug-ins).
• Contribute to the creation and maintenance of the infrastructure (hardware and software) of the facility:
  • Content creation and maintenance of the facility's website and wiki management.
  • Maintenance of the facility's resource and booking management tool (openIRIS).
  • Development of tools for the maintenance of the analysis and acquisition machines (data movers, data pipelines, storage management).
  • Scouting for new commercial and open-source software tools.
  • Develop image analysis-based quality control tools for microscopes.

We are looking for an enthusiastic, service-oriented, proactive personality with great team spirit and drive to collaborate with others on their projects within a scientific core facility.

• PhD in natural sciences, preferably with a strong background in life sciences (cell and molecular biology, biotechnology).
• Familiarity with microscopy experimental workflows and data from different types of instruments (automated/smart, confocal, super-resolution, light sheet microscopy).
• Knowledge of state-of-the-art image processing and analysis tools and a track record in developing innovative image analysis and data science tools.
• Adept in software engineering with fluency in programming languages such as MATLAB, C++, C#, Java, Python (Napari, Stardist, Scikit-image), PHP, SQL, Tcl/Tk.).
• Knowledge of training and/or application of deep learning models.
• Experience with data pipelines following FAIR principles, with skills in compressed sensing, image noise reduction and big data management, cloud computing, high performance computing, virtual machine infrastructure.
• Use and administration of various operating systems.
• Self-motivated and able to work both independently and in a team.
• Experience of working in a multidisciplinary environment and ability to manage several projects simultaneously with a high degree of technical autonomy.
• Superior communication skills in written and spoken English.

• A stimulating work environment with state-of-the-art facilities and technology portfolio at one of the world’s top universities
• Work in an international and multidisciplinary team embedded in a vibrant research community
• Benefits. competitive salary and excellent benefits in accordance with ETH Zurich guidelines