ILRS_04/2017 // From single-cell to whole-organ monitoring: Morphokinetic characterisation of infection via quantitative image analysis


Infectious diseases affect the function and morphology of single cells, as well as of whole organs. The wide range of spatial dimensions require the application of various imaging techniques, e.g. laser-scanning fluorescence microscopy (LSM) to study the single-cell level, and lightsheet microscopy (LiSM) to characterise the whole-organ level. An objective characterization of the infection processes demands the development of new mathematical algorithms that are able to analyse and quantify the image data automatically and without bias. We are looking for a motivated candidate, who would develop new image analysis algorithms for LSM and LiSM data, as well as extend and optimize already established image analysis pipelines. This will involve automatic detection and quantification of various regions of interest (ROI), such as cells and tissue areas, in 2D and 3D microscopy data of infected tissues and organs. For instance, one of the tasks will be to develop novel segmentation algorithms that identify individual ROI without applying fluorescence labelling. Another challenging aspect is handling the large amounts of 3D image data produced by LiSM, where effective algorithms need to be developed in order to find a balance between accurate data quantification and the utilization of computational resources in terms of time and memory. All developed algorithms will be applied to experimental data obtained from our collaboration partners in order to investigate actual biological questions from the field of infection biology.

 We expect that the candidate has:

  • a Master’s degree (or equivalent allowing her/him to pursue a PhD degree) in Natural or Computer Sciences. Candidates about to earn their degree are welcome to apply.
  • strong programming skills, including the knowledge or deep interest in learning C/C++; experience in image analysis is an advantage
  • a keen interest in understanding the biological processes behind the image data
  • high motivation to join one of the research areas of ILRS
  • very good communication skills in English

We offer:

  • a top-level research environment
  • efficient supervision by a team of advisors
  • a comprehensive mentoring programme
  • courses in state-of-the-art technologies and soft skills
  • strong communication and interaction between the involved institutions
  • Jena – City of Science: innovative business activities, successful scientific centres and a vibrant cultural scene around the famous Friedrich Schiller University

The three-year Doctoral Researcher position is available starting from January 2018. The position will be financially supported according to TV-L (salary agreement for public service employees). HKI is an equal opportunity employer.

Further information:

Prof. Dr. Marc Thilo Figge, PI:

Dr. Christine Vogler, ILRS Coordinator:

The application process is handled exclusively online. Please acquaint yourself with the scientific projects offered on our website. Please note that you can choose up to 3 projects of interest in your application. It is only necessary to fill in the application form for your first preference of projects; the other two projects can be selected in the application form. In order to apply via the online application portal, go to

Deadline for application: Oct 22, 2017.

Successful applicants will be invited to attend a recruitment meeting in Jena (envisaged date: Dec 14-15, 2017).

Project details

Work plan


Marc Thilo Figge

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