PhD Position in Life-time Imaging of the Chemical Microenvironment and Metabolic Activity in Biofilms and 3D Bioprinted Construc
University of Copenhagen Department of Biology

PhD Scholarship in Life-time Imaging of the Chemical Microenvironment and Metabolic Activity in Biofilms and 3D Bioprinted Constructs 

Department of Biology 
Faculty of Science 
University of Copenhagen 

PhD scholarship in Life-time imaging of the chemical microenvironment and metabolic activity in biofilms and 3D bioprinted constructs

Department of Biology, Faculty of Science at University of Copenhagen is offering 1 PhD scholarship in the Marie Sklodowska Curie Action Doctoral Network (MSCA-DN) FLIMagin3D

Scientific environment 

FLIMagin3D’s goal is to train a new generation of young researchers, based on an internationally competitive consortium of developers, users and industrial collaborators (see:
The scientific objective of FLIMagin3D is to synergistically evolve key aspects of Fluorescence Lifetime Imaging Microscopy (FLIM) across disciplines by i) advancing the acquisition of FLIM data and the analysis pipeline, ii) developing improved platforms that facilitate imaging for a wide range of (bio)medical, chemical and biophysical applications, and iii) advancing the state-of-the-art in FLIM biosensors. The project is a collaboration between 8 academic and 4 industrial partners from 7 European countries and brings together highly synergistic expertise on advanced bioimaging and image analysis.

The specific PhD project will be within the Microenvironmental Ecology &Symbiosis research group headed by Prof Michael Kühl at the Department of Biology, University of Copenhagen with the main workplace at the Marine Biological Section in Helsingør ( Besides in-house experiments on time- and frequency-domain lifetime imaging platforms, the studies will also involve work with microscopy platforms at the Center of Advanced Bioimaging ( in Copenhagen. The group has pioneered microenvironmental analyses and chemical imaging of natural aquatic systems and organisms, as well as chemical microenvironments in 3D bioprinted constructs. 

PhD Project outline:

3D mapping of the extracellular and intracellular chemical microenvironment in biofilms remains a major challenge to our understanding of this most common microbial lifestyle. In collaboration with our team and collaborators, the PhD student will develop new experimental platforms for i) the application in biofilms of O2 sensing probes compatible with phosphorescent lifetime (PLIM) and fluorescence lifetime (FLIM) imaging setups, ii) the incorporation of such sensing probes within functionalized bioinks, and iii) realizing 3D mapping of O2 and biomass in natural and bioprinted biofilms containing phototrophic and heterotrophic microbes. Together with collaborators, we will also explore imaging of NAD(P)H and develop computational models for O2 dynamics and distribution in such structures.  

Principal supervisor is Prof. Michael Kühl, Marine Biological Section ( , who can be contacted for further information via e-mail ( or phone (+45 4047 6304). The PhD student will also be co-supervised by Dr. Ruslan Dmitriev at Ghent University (

Who are we looking for? 

We are looking broadly across disciplines for a candidate with technical expertise and experience in live cell microscopy, bioimaging and image analysis. The MSCA Doctoral Network offer a unique opportunity to get cutting-edge training in advanced microscopy and image analysis in a multidisciplinary environment with a focus on academic and personal development of the PhD fellows. The supervisors in the network each provide specific competences and as part of the network you develop your skills and carry out research both independently and as part of a network of 12 PhD fellows. The consortium ensures exchange of ideas through network-wide training events, summer schools and secondments at academic and industrial partners in the network. As a PhD fellow in the FLIMagin3D network, you need to have good social skills, be innovative and goal-oriented and be willing to conduct the planned secondments and other network activities.  

Formal requirements  

Applicants should hold, or be very close to completing, a masters degree in physics, chemistry, biology, biomedicine or (bio)engineering. In particular, we require that candidates have prior experience with advanced microscopy and image analysis. Knowledge of optical sensors, microfluidics, 3D (bio)printing, or cell culture and sample preparation are considered great advantages.  Excellent command of spoken and written English is required. As criteria for the assessment of your qualifications, emphasis will also be laid on previous publications (if any) and relevant work experience.

Qualifications needed for the regular programme

To be eligible for the regular PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project. For information of eligibility of completed programmes, see General assessments for specific countries and Assessment database.

EU eligibility criteria for candidates 

The applicant may be of any nationality but in order to be eligible for the positions the following criteria applies to all applicants: 

  • The applicant shall at the time of recruitment be eligible as an Early Stage Researcher (ESR) by being in the first four years of his/her research career (after finishing a Masters degree) and must not have been awarded a doctoral degree.  
  • The applicant must not have resided or carried out his/her main activity in the country of the host institute for more than 12 months in the 3 years immediately prior to the recruitment. 

Job conditions 

The PhD student will be appointed under a 3-year employment contract at the host institution with a competitive salary and mobility allowance (+ a family allowance for candidates with a registered partnership). The fellow is expected to start between June 1 and at latest September 1, 2023. The PhD student will be enrolled in the PhD program of the Faculty of Science, University of Copenhagen, with the specific intent that it results in a PhD degree and scientific publications. 

Job description 

The position is available for a 3-year period. Your key tasks as a PhD student at SCIENCE and in the FLIMagin3D network are: 

  • To manage and carry through your research project 
  • Attend PhD courses both at within and outside the FLIMagin3D network 
  • Write scientific articles and your PhD thesis 
  • Participate in international congresses and FLIMagin3D network meetings 
  • Engage in several exchange visits and secondments with academic and industrial partners in FLIMagin3D 
  • Disseminate your research to a broad audience (students and the general public) 

Terms of employment in the regular programme

Employment as PhD fellow is full time and for maximum 3 years.

Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of SCIENCE, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

Terms of appointment and payment accord to the agreement between the Danish Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. The position is covered by the Protocol on Job Structure.

Application procedure 

The application, in English, must be submitted electronically by clicking APPLY NOW below.

Please include  

Cover Letter (max. 2 pages), detailing your motivation and background for applying for the PhD project 

CV (max. 2 pages) including a list of publications (if any) 

Summary of last degree thesis (1 page) 

Diploma and transcripts of records (BSc and MSc) 

Two references and full contact details (name, address, telephone & email) of professional referees 

IMPORTANT!  In addition to your application to University of Copenhagen outlined above, you also need to submit an application via the FLIMagin3D website:

The deadline for applications is 15 April 2023, 23:59 GMT +1.

Applications received after the deadline for applications will not be considered.  

After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Interview Committee. Afterwards an assessment committee will be appointed to evaluate the selected applications. The applicants will be notified of the composition of the committee and the final selection of a successful candidate will be made by the Head of Department, based on the recommendations of the assessment committee and the interview committee.  

The main criterion for selection will be the research potential of the applicant and the above mentioned skills. The successful candidate will then be requested to formally apply for enrolment as a PhD student at the PhD school of Science. You can read more about the recruitment process at General information about PhD programmes at SCIENCE is available at



Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.


Application deadline: 15-04-2023
Employment start: 01-06-2023
Working hours: Full time
Department/Location: Biologisk Institut

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