Image Analysis and Data Management Expert / Image Analysis and Data Management Expertess
ETH Zurich - April 28, 2025
Image Analysis and Data Management Expert
100%, Basel, permanent
ETH Zurich is a prestigious university committed to advancing science, engineering, and technology. The Single Cell Facility (SCF) is a vital research and service platform within the Department of Biosystems Science and Engineering (D-BSSE) located in Basel. This central facility provides access to an advanced instrument portfolio for optical single-cell analysis, including light microscopy and flow cytometry technology. The SCF is dedicated to uncovering the design principles of cells in stochastic environments and applying these insights for network design. The SCF team collaborates closely with the Lab Automation Facility (LAF), which develops and maintains complex robotic systems integrated with readout technologies, such as high-content imaging, for experimental workflows in biology and biochemistry.
Project Background
The SCF's centralized instrument pool is complemented by expert support from staff who provide training, maintenance, 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 other IT-related projects for SCF users and staff, working on a diverse range of biology and biotechnology projects. Starting date: June 1, 2025.
Job Description
Your responsibilities will include:
Providing first-line support for image analysis requests (from optical microscopy).
Offering expert input for microscopy imaging projects, working closely with SCF microscopy specialists to align analysis strategies with image acquisition parameters.
Training users on existing analysis software (Imaris, Huygens, Fiji, ImageJ, CellProfiler, MATLAB, etc.) and staying updated on developments in commercial and open-source tools.
Developing tailored solutions for specific user projects (MATLAB scripts, ImageJ macros/plug-ins, CellProfiler pipelines, Python coding, etc.).
Organizing and teaching an image analysis module in a laboratory course for biotechnology master's students.
Contributing to the creation and maintenance of facility infrastructure (hardware and software), including:
Content creation and management of the facility's website and wiki.
Maintenance of the facility's resource and booking management tool (openIRIS).
Development of tools for machine maintenance (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 sense of teamwork who can effectively collaborate on projects within a scientific core facility:
PhD in natural sciences, preferably with a strong focus on 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 advanced image processing and analysis tools with a proven track record in developing innovative image analysis and data science solutions.
Proficient in software engineering with expertise in programming languages such as MATLAB, C++, C#, Java, Python (Napari, Stardist, Scikit-image), PHP, SQL, Tcl/Tk.
Experience in training and/or applying deep learning models.
Background in data pipelines following FAIR principles, with expertise in compressed sensing, image noise reduction, big data management, cloud computing, and high-performance computing.
Experience in using and administering various operating systems.
Self-motivated, able to work independently and collaboratively in a team environment.
Demonstrated ability to manage multiple projects simultaneously with a high level of technical autonomy.
Excellent communication skills in both written and spoken English.
Workplace
Join us in a stimulating work environment equipped with state-of-the-art facilities, situated at one of the world's leading universities.
We Offer
A dynamic work environment with cutting-edge technology at a globally recognized institution.
A chance to work within an international and multidisciplinary team that is part of a vibrant research community.
Competitive salary and excellent benefits in line with ETH Zurich guidelines.
We Value Diversity
ETH Zurich strives to foster an inclusive culture. We promote equal opportunity, value diversity, and nurture an environment where the rights and dignity of all staff and students are respected. For more information about our commitment to diversity, please visit our Equal Opportunities and Diversity website.
Curious? So Are We!
We invite you to apply online using the form below. Please ensure that your submission includes the following documents:
Cover letter detailing your motivation for applying.
Detailed curriculum vitae with references and their contact information.
Links to your software samples (e.g., GitHub), clearly indicating your contributions.
Only applications matching the job profile will be considered.
For inquiries regarding the position, please contact Dr. Thomas Horn at Show e-mail.ch"> (no applications).
For recruitment services, the GTC of ETH Zurich apply.
About ETH Zurich
ETH Zurich stands as a leading university specializing in science and technology. Renowned for delivering excellent education and cutting-edge research, we strive to transfer new knowledge directly to society. With over 30,000 individuals from more than 120 countries, our university encourages independent thinking in an environment that inspires excellence. Situated in the heart of Europe, we connect globally to develop solutions for both current and future challenges.