PhD DoPredict project

PhD DoPredict project

Published Deadline Location
4 Jun yesterday Amsterdam

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We are looking for an enthusiastic PhD student for the DoPredict project in which we want to study new drugs and therapy response in fibrotic lung tissue using dynamic 3D imaging techniques.

Job description

The researchers will focus on pulmonary fibrosis and lung cancer, using HHG microscopy to track the tissue in 3D during culture, resulting in 4D data. They will develop analytical methods based on artificial intelligence (AI) to analyze the HHG images and use these to quantify the production and breakdown of connective tissue, the numbers of healthy and tumor cells over time, and the microstructure of the tissue, thus measuring the response to treatment. They will investigate and validate the predictive power of these characteristics with feedback from patients on the treatment they actually received from their clinicians.

The research group has already developed a system for culturing lung tissue from patients and microscopically imaging the cells and all parts of the tissue in 3D for five days. In this so-called precision-cut lung slice (PCLS) model, equipped with an innovative higher harmonic generation (HHG) microscope, lung tissue can be exposed to various therapeutic agents, and the therapy response can be directly assessed. Currently, the model is still in the experimental phase, but in DOPREDICT, the model will be further optimized for clinical application.

As a PhD candidate, you will be part of the DoPredict project at Amsterdam UMC, PUFFIN lab, responsible for further optimizing and improving tissue culture, testing various (experimental) drugs, and analyzing the tissue after experiments using immunohistochemistry, Western blot, and qPCR. These analyses, the 'gold standard,' will be compared with the HHG images to validate them.

You will closely collaborate with a PhD student at the VU LaserLab in developing the testbed where multiple tissue slices/biopsies can be cultured and imaged simultaneously with the HHG microscope and general HHG imaging.

Additionally, you will conduct experiments testing various experimental compounds on their effect on fibrotic processes and tumor tissue in lung tissue, potentially leading to new insights for therapeutic interventions for these conditions.


Amsterdam UMC


  • You have (upon beginning your appointment) a master's degree in Biomedical Sciences or another subject within the life sciences, with a strong emphasis on pathophysiological mechanisms, pathology and cell biology;
  • You have experience performing the following lab techniques: cell and/or tissue culture, immunohistochemistry, Western blot and qPCR. Affinity for lung disease research is a plus;
  • Experience with advanced microscopic techniques such as fluorescence microscopy and the analysis of these images is a plus;
  • Good written and oral communication skills in English are essential to communicate in our international team.

Conditions of employment

The start date is negotiable, but preferably in September or October to coincide with the VU Laser Lab PhD as much as possible.
  • A flying start to your career in research work in a metropolis with a diverse and open culture, and a multicultural society.
  • Working with motivated colleagues from all corners of the world.
  • You will start with a contract for one year (12 months) with the possibility of extension for another three years (36 months).
  • Salary scale: OIO: € 3.017,- in the first year and increases to € 3.824,- in the fourth year (based on a fulltime workweek), depending on qualifications and experience.
  • In addition to a good basic salary, you will receive, among other things, 8.3% year-end bonus and 8% vacation allowance. Calculate your net salary here.
  • Pension via BeFrank
  • Reimbursement of 75% of your public transport costs. Would you rather travel by bike? Then we have a good bicycle scheme.
  • An active staff association and the Young Amsterdam UMC association, both of which organize fun (sports) activities and events.


Amsterdam UMC

The DoPredict project consists of researchers from three different academic centers, each contributing their own expertise. From Amsterdam UMC, specifically the PUFFIN laboratory led by dr. Jan Willem Duitman, the contributions include (cell) biology, tissue culture, pathological and molecular techniques, and pathophysiological mechanisms of lung fibrosis. From the VU Amsterdam, prof. Marloes Groot of the LaserLab is involved with extensive expertise in innovative microscopic techniques, specifically HHG microscopy in this project. From Radboud UMC, dr. Francesco Ciompi is involved with expertise in AI analysis of 3D and 4D images.


  • PhD
  • Health
  • max. 36 hours per week
  • €3017—€3824 per month
  • Doctorate
  • 11891



Meibergdreef 9, 1105AZ, Amsterdam

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