Job Advertisement HKI-Cluster of Excellence "Balance of the Microverse”

The Cluster of Excellence "Balance of the Microverse” studies the fundamental principles underlying microbial community interactions and functions in diverse habitats, ranging from oceans and groundwater to plants and human hosts. We integrate insights across ecological and medical fields to enhance our understanding of microbial balance from the molecular to the ecosystem level. We develop tools and detection technologies to shape microbiome dynamics for environmental and human health benefits. The affiliated early career program of the Jena School for Microbial Communication offers an ambitious, structured and interdisciplinary post-graduate training based on top-level fundamental research.

Doctoral Researcher in Automated Image Processing of Immune Interactions in Organ-on-Chip Models (m/f/div)

commencing on January 1, 2026 or upon agreement. We offer a part-time position (65%, fixed-term position for 3.5 years) at the Leibniz Institute for Natural Product Research and Infection Biology. The doctoral project is part of the collaborative project MIRAGE – Microbiome Interactions in the Respiratory and Gut Epithelium. MIRAGE focuses on advanced organ-on-chip models to investigate how host epithelial and immune cells interact with the gut microbiota during infection and inflammation. Given that these models are highly amenable to imaging, we are seeking a highly motivated candidate interested in working on automated image processing using and adapting the Java Image Processing Pipeline (JIPipe: www.jipipe.org). This research aims to provide novel mechanistic insights into how microbial metabolites influence inflammation and infection dynamics and may identify new strategies to restore microbiome balance in human disease.

Your responsibilities:

• Perform computational image analysis using the Java Image Processing Pipeline (JIPipe: www.jipipe.org) and work independently towards your doctoral research project

• Analyse project results, generate figures for publications, and write scientific manuscripts for publication

• Present your results at local, national, and international meetings and conferences

• Work closely together with other experimental and computational researchers in the research group and within the Cluster

• Assist with training and supervising other researchers (e.g. student assistants, BSc students)

• Contribute to the friendly, welcoming, and collaborative environment in our team

Your profile:

• A MSc in bioimage analysis / bioinformatics / computer vision / computer science / physics / or closely related disciplines (candidates close to completion may also apply)

• Desired methodological skills include experience in automated image processing

• We expect very good programming skills

• A high level of curiosity, self-motivation, enthusiasm and attention to detail

• A cooperative personality actively seeking to contribute to our interdisciplinary and inclusive Microverse community

• Very good written and spoken English communication skills Are you unsure because you don't meet one or some of our requirements? Please do not hesitate to apply and give us a chance to get to know you.

We offer:

• A highly communicative atmosphere within an energetic and interdisciplinary scientific network

• The Jena School for Microbial Communication offers a structured and interdisciplinary doctoral training program based on top-level fundamental research and provides comprehensive mentoring programs and soft skills courses

• Jena – City of Science, a young and lively city with a vibrant local cultural agenda

• A dedicated management team, providing support and information on non-scientific subjects, such as onboarding and family life, and organizing individualized career development programs, and events on topics like diversity and collaboration

• Remuneration based on the provisions of the Collective Agreement for the Public Sector of the Federal States (TV-L) at salary scale E13 — depending on the candidate’s personal qualifications—, including a special annual payment in accordance with the collective agreement

  The 3.5 year doctoral researcher position (TV-L E13, 65%) is funded through the Excellence Strategy of the German federal and state governments. The employment contract will be with the Leibniz Institute for Natural Product Research and Infection Biology. To promote gender equality in science, applications by women are particularly welcome. Candidates with severe disabilities will be given preference in the case of equal qualifications and suitability. Are you eager to join us? Then apply by October 20, 2025 using our online portal.