Job Advertisement HKI-58/2025

At the Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), we investigate the pathobiology of microorganisms and develop new natural product-based active compounds for the treatment of infectious diseases. As part of the structured doctoral program International Leibniz Research School ILRS 2.0 we invite talented candidates to apply for a position as

Doctoral Researcher (m/f/div)

for four years.

Project title: Advancing image quantification of organ-on-chip-based experiments within JIPipe

Research Area:

During recent years, the research unit Applied Systems Biology (ASB) at the Leibniz-HKI has developed an entirely new approach towards automated image analysis based on the Java Image Processing Pipeline (JIPipe: www.jipipe.org). JIPipe is a fully graphical image analysis language that is freely available to the scientific community and has been successfully employed to characterize both single- and multi-layer cell-based biological samples, as well as organ-on-chip (OoC) models. JIPipe offers a programming-free, entirely graphical environment for conducting both basic and advanced image analysis, enabling fully documented quantification workflows that are easy to share among collaborators. JIPipe is well-received in the scientific community and currently comprises a library of over 2,000 existing JIPipe building blocks that enable us to pursue the following two objectives in this project:
  1. Development of location-linked deconvolution and implementation in JIPipe and
  2. Implementation of goal-oriented learning of JIPipe through artificial intelligence in terms of large language models.

Required Qualifications:

  • Master’s degree (or equivalent) in bioimage analysis / bioinformatics / computer vision / physics / or related disciplines. Candidates about to obtain their degree are welcome to apply.

  • Desired methodological skills include experience in automated image processing and in artificial intelligence approaches.

  • We expect very good programming skills, preferentially in Java and/or C++ and/or Python.

  • The candidate should be willing and able to work in an international, interdisciplinary research team.

  • Very good communication skills in English.

We offer:

  • Cutting edge research facilities and world-renowned faculty

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

  • Integration into the structured and interdisciplinary doctoral training program ILRS 2.0

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

  • Salary is paid according to German TV-L (salary agreement for public service employees).

The successful candidate will be hosted in the Research Group Applied Systems Biology (Prof. Marc Thilo Figge) and jointly supervised by Junior Research Group Adaptive Pathogenicity Strategies (Dr. Mark Gresnigt). The Leibniz-HKI is embedded in the outstanding scientific environment of the Beutenberg Campus providing state-of-art research facilities and a highly integrative network of life science groups.

Further information:

For more information about ILRS2.0, please click here.

Christine Vogler | christine.vogler@leibniz-hki.de

Applications:

Leibniz-HKI is proud to be an equal-opportunity employer and promote diversity and inclusion in the workplace. It aims to increase the proportion of underrepresented groups in case of equal suitability. All qualified persons, regardless of color, religion, age, sex, sexual orientation, gender identity, national origin, disability, veteran status, or other classification protected by law, will receive consideration for employment.

Complete applications in English should include a cover letter, a CV, a certificate of study/transcript of records, the addresses of three possible referees, and should be submitted via the Leibniz-HKI online application system. The deadline for applications is December 13, 2025. Selected candidates will be invited to a recruitment meeting in Jena in early 2026 for personal interviews.
 


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