Image Analysis and Data Management Expert / Image Analysis and Data Management Expertess
ETH Zurich - April 24, 2025
Image Analysis and Data Management Expert
100%, Basel, permanent
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) located in Basel. This core facility provides access to a high-end instrument portfolio for optical single cell analysis, including 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 collaborates closely with the Lab Automation Facility (LAF) team, which develops and maintains complex robotic setups integrated with readout technologies for experimental workflows in biology and biochemistry.
Project Background
The SCF's centralized instrument pool is supported by expert services from staff who provide instrument training, hardware and software maintenance, as well as advice on sample preparation, assay design, image analysis, and data management.
As a member of the SCF, you will engage in image analysis, data management, and other IT-related projects related to a diverse range of biology and biotechnology initiatives. Starting date: June 1, 2025.
Job Description
As a member of the SCF, you will perform the following:
First line support for image analysis requests from optical microscopy.
Provide expert input to microscopy imaging projects, designing 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.), staying current with developments in 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.).
Organize and teach an image analysis module in a laboratory course for biotechnology master’s students.
Contribute to the creation and maintenance of the facility's infrastructure (hardware and software) by:
Creating and maintaining the facility's website and wiki management.
Maintaining the facility's resource and booking management tool (openIRIS).
Developing tools for the maintenance of analysis and acquisition machines (data movers, data pipelines, storage management).
Scouting for new commercial and open-source software tools.
Developing image analysis-based quality control tools for microscopes.
Profile
We are seeking an enthusiastic, service-oriented, proactive individual with strong teamwork skills to collaborate with others on research 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 various instruments (automated/smart, confocal, super-resolution, light sheet microscopy).
Knowledge of state-of-the-art image processing and analysis tools, with a proven track record in developing innovative image analysis and data science tools.
Adept in software engineering; fluent 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 adhering to FAIR principles, along with skills in compressed sensing, image noise reduction, big data management, cloud computing, high-performance computing, and virtual machine infrastructure.
Proficient in using and administering various operating systems.
Self-motivated, capable of working independently and collaboratively in a team environment.
Experience working in a multidisciplinary setting and effectively managing multiple projects with a high degree of technical autonomy.
Superior communication skills in written and spoken English.
Workplace
ETH Zurich offers a stimulating work environment equipped with cutting-edge facilities and technology at one of the world's top universities. You will work within an international and multidisciplinary team, embedded in a vibrant research community.
We Offer
A stimulating work environment with state-of-the-art facilities and technology at one of the world's top universities.
An international and multidisciplinary team experience within a vibrant research community.
A competitive salary and excellent benefits in accordance with ETH Zurich guidelines.
We Value Diversity
In alignment with our values, ETH Zurich promotes an inclusive culture. We support equal opportunities, value diversity, and nurture a working and learning environment where the rights and dignity of all our staff and students are respected. Visit our Equal Opportunities and Diversity website to learn more about our commitment to fostering a fair and open environment that allows everyone to thrive.
Curious? So Are We.
We look forward to receiving your online application using the form below, which should include:
Cover letter describing your motivation to apply for this position.
Detailed curriculum vitae with references and their contact details.
Links to your software samples (e.g., GitHub) with clear indications of your contributions.
Please note that only applications matching the job profile will be considered.
Further information about the SCF and LAF can be found on our websites. Questions regarding the position can be directed to Dr. Thomas Horn at Show e-mail.ch"> (no applications).
About ETH Zürich
ETH Zurich is one of the world’s leading universities specializing in science and technology. We are renowned for our excellent education, cutting-edge fundamental research, and efficient transfer of new knowledge into society. Over 30,000 individuals from more than 120 countries find our university to be a place that encourages independent thinking and fosters excellence. Situated in the heart of Europe, we forge connections across the globe, working collaboratively to develop solutions for the global challenges of today and tomorrow.