Image Analysis and Data Management Expert / Image Analysis and Data Management Expertess
ETH Zurich - April 25, 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) of ETH Zurich, located in Basel. This facility provides access to a high-end instrument portfolio for optical single-cell analysis, utilizing cutting-edge light microscopy and flow cytometry technology. The SCF plays a key role in elucidating the design principles of cells in stochastic environments and their applications in network design. Our staff collaborates closely with the Lab Automation Facility (LAF) team, which develops and maintains complex robotic setups integrated with advanced readout technologies, such as high-content imaging, for innovative experimental workflows in biology and biochemistry.
Project Background
The SCF's centralized instrument pool is supported by expert services provided by our staff, who offer training on instruments, maintenance of hardware and software, and guidance 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 various IT-related projects for SCF users and staff, covering a diverse range of biology and biotechnology projects. Starting date: June 1, 2025.
Job Description
In this role, you will be responsible for performing image analysis on microscopy data, data management for multiple applications and pipelines within the facility, along with other IT-related projects to assist SCF users and staff.
Your Responsibilities:
Provide first-line support for image analysis requests related to optical microscopy.
Offer expert input for microscopy imaging projects, collaborating closely with SCF microscopy experts to align analysis strategies with image acquisition parameters.
Train users in the use of existing image analysis software (Imaris, Huygens, Fiji, ImageJ, CellProfiler, MATLAB, etc.) while staying updated on the latest developments in commercial and open-source image analysis tools.
Develop ad-hoc solutions for specific user projects, such as MATLAB scripts, ImageJ macros/plug-ins, CellProfiler pipelines, and Python coding.
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), including:
Maintaining the facility's website and managing its wiki.
Managing the facility's resource and booking tool (openIRIS).
Developing tools for maintaining analysis and acquisition machines (data movers, data pipelines, storage management).
Researching new commercial and open-source software tools.
Creating image analysis-based quality control tools for microscopes.
Profile
We are seeking an enthusiastic, service-oriented, and proactive individual with a strong team spirit who is eager to collaborate on various projects within a scientific core facility.
Qualifications:
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 (e.g., automated/smart, confocal, super-resolution, light sheet microscopy).
Knowledge of state-of-the-art image processing and analysis tools, along with a proven track record in developing innovative image analysis and data science solutions.
Adept in software engineering with proficiency in programming languages such as MATLAB, C++, C#, Java, Python (Napari, Stardist, Scikit-image), PHP, SQL, Tcl/Tk.
Experience with training and/or application of deep learning models.
Experience with data pipelines adhering to FAIR principles, including skills in compressed sensing, image noise reduction, big data management, cloud computing, and high-performance computing.
Proficiency in the use and administration of various operating systems.
Self-motivated, capable of working independently and collaboratively within a team.
Experience working in a multidisciplinary environment with the ability to manage multiple projects simultaneously while maintaining technical autonomy.
Excellent communication skills in written and spoken English.
Workplace
Join us in a stimulating work environment equipped with state-of-the-art facilities and a diverse technology portfolio at one of the world’s top universities. Be part of an international and multidisciplinary team immersed in a vibrant research community.
We Offer
A stimulating work environment with state-of-the-art facilities and technology portfolio at one of the world’s top universities.
Opportunity to work in an international and multidisciplinary team embedded in a vibrant research community.
Competitive salary and excellent benefits in accordance with ETH Zurich guidelines.
Apply online using the form below. Only applications matching the job profile will be considered.
We Value Diversity
ETH Zurich is committed to fostering an inclusive culture. We promote equality of opportunity, value diversity, and cultivate a working and learning environment that respects the rights and dignity of all our staff and students. Visit our Equal Opportunities and Diversity website to learn how we ensure a fair and open environment that allows everyone to thrive.
Curious? So Are We.
We look forward to receiving your online application along with the following documents:
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.
For any inquiries regarding the position, please contact Dr. Thomas Horn via email at (no applications).
About ETH Zurich
ETH Zurich is one of the world's leading universities specializing in science and technology. We are recognized for our excellent education, innovative fundamental research, and the effective transfer of knowledge into society. With over 30,000 people from more than 120 countries, ETH Zurich is a hub for independent thinking and an inspiring environment for excellence. Located in the heart of Europe, we forge connections worldwide to develop solutions for the global challenges of today and tomorrow.