Postdoc / Research Software Engineer – Real-Time Live-Cell Image Analytics and Experimental Control Full-time

Microorganisms in the Gut Microbiome

Microorganisms in the gut microbiome play a key role in health and disease, but their behavior in complex, dynamic microenvironments is still poorly understood. Within a Helmholtz collaboration, we are building a high-throughput single-cell analysis platform that combines microfluidics, advanced imaging and AI-based analysis to study gut microbial consortia. You will drive the development of the next-generation image analysis and control framework for microfluidic live-cell analytics in close collaboration with partners at HZI, Helmholtz Munich and HHU.

Your tasks in detail:

• Establish deep-learning–based segmentation, species classification and lineage tracking workflows for multi-species time-lapse data
• Optimise models and pipelines for real-time performance, enabling adaptive imaging and feedback
• Develop active learning and retraining pipelines to adapt to new consortia
• Implement event-triggered, autonomous experiment control to steer imaging in space and time
• Provide FAIR analytics workflows and contribute open source tools for use in data analysis
• Present your results at international conferences, publish in peer-reviewed journals, and contribute to training activities within the consortium

Your profile:

• Excellent Master and subsequent PhD in computer science, engineering, biophysics, applied mathematics, computational biology or a related field
• Proven programming expertise in Python (PyTorch, scientific Python) with solid experience in scientific computing and software development; familiarity with C++ and Linux environments is an advantage
• Strong background in deep learning for image analysis / computer vision, ideally on microscopy or time-lapse data
• Experience in at least one of: tracking / time-series analysis, probabilistic modelling / uncertainty, real-time or streaming pipelines
• Strong mathematical / statistical background, with pronounced analytical and problem-solving skills
• No prior wet-lab experience is required; curiosity for biological questions and willingness to collaborate with experimentalists is sufficient
• Excellent collaboration and communication skills, and enjoyment of working in an international, interdisciplinary research team
• Prior research experience (e.g. internships, thesis projects, open-source software contributions, or publications) is highly desirable
• Excellent English skills; German is a plus but not required

Our offer:

• INTERDISCIPLINARY WORK: An exciting, interdisciplinary research environment at the interface of AI, imaging and microbiome research in an Helmholtz-wide collaboration
• CUTTING-EDGE INFRASTRUCTURE: Access to state-of-the-art imaging, microfluidics and computing infrastructure
• INNOVATION & TRANSLATION: Opportunities to engage in technology translation and spin-off preparation within FZJ's innovation ecosystem
• KNOWLEDGE & FURTHER TRAINING: Comprehensive training and development opportunities for personal and professional development with support from experienced PIs.
• FLEXIBILITY: Flexible working time models, including options close to full-time, allow you to tailor your working hours to suit your individual needs
• VACATION: You will receive 30 days of vacation plus additional days off (e.g. between Christmas and New Year`s)
• FAIR REMUNERATION: Depending on your existing qualifications and the tasks assigned to you, you will be classified in pay grade 13 of the TVöD-Bund (Collective Agreement for the Public Service). All information on the TVöD-Bund collective agreement can be found on the BMI website: https://go.fzj.de/bmi.tvoed. The monthly salaries in euros can be found on page 69 of the PDF download
• FIXED-TERM: The position is limited to 3 years
• SUPPORT FOR INTERNATIONAL EMPLOYEES: Our International Advisory Service makes it easier for international employees to get started

In addition to exciting tasks and a collegial working environment, we offer you much more: https://go.fzj.de/benefits We welcome applications from people with diverse backgrounds, e.g. in terms of age, gender, disability, sexual orientation / identity, and social, ethnic and religious origin. A diverse and inclusive working environment with equal opportunities in which everyone can realize their potential is important to us. The following links provide further information on diversity and equal opportunities: https://go.fzj.de/equality and on specific support options for women: https://go.fzj.de/womens-job-journey

We look forward to receiving your application. The job will be advertised until the position has been successfully filled. You should therefore submit your application as soon as possible.