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3 PhD students Simulated MRI data to develop MRI segmentation methods

Eindhoven University of Technology (TU/e) has the following vacancy for 3 PhD students “Simulated MRI data to develop MRI segmentation methods that are as much as possible independent of the specific MR image ...

10 maanden geleden


Eindhoven, Noord-Brabant
Tijdelijk contract / Tijdelijke opdracht
Uren per week:
38 uur


The 'Open Ground Truth Training Network' (openGTN) research project aims to use simulated MRI data to develop MRI segmentation methods that are as much as possible independent of the specific MR image contrast (T1-weighted, T2-weighthed, etc.).

It therefore seeks to develop methods for the generation of large quantities of simulated magnetic resonance image (MRI) data, needed for the training and validation of image analysis algorithms (registration, segmentation, quantification), especially for machine learning approaches such as deep learning using convolutional neural networks.

The project also aims to make the simulated MRI data available in public databases, which can be used for optimizing and benchmarking image analysis algorithms (often called 'algorithm challenges').

The research in openGTN will be performed within a network of 7 R&D institutes spread over Europe; the Eindhoven University of Technology will host 3 Early Stage Researchers (ERSs), supported by the highly prestigious and competitive Marie Curie Innovative Training Networks (ITN) fellowship program (https://ec.europa.eu/research/mariecurieactions/about/innovative-training-networks_en).

The team

You will become part of the Medical Image Analysis group at the Department of Biomedical Engineering, Eindhoven University of Technology. The group consists of around 20 researchers, all working on the development of image analysis methodology as well as clinical applications. Collaborations with various hospitals and with industry ensure involvement of clinical experts, and hence a focus on clinically relevant topics. Through various (formal and less formal) meetings, the members of the group share ideas and work together in an enthusiastic and encouraging atmosphere. More information on the group can be found at www.tue.nl/image.

For this Marie Curie ITN project, you will spend 50% of your time at Philips Research Hamburg, Germany (in the first three years), and you will work for extended secondments (short externships) at one or more of the following institutes: the University Medical Center Utrecht, The Netherlands, Philips Healthcare, Best, The Netherlands, King's College London, United Kingdom, Deutsches Zentrum für Neurodegeneratieve Erkrankungen, Bonn, Germany, and Klinikum Rechts der Isar / Technical University, München, Germany. You will be academically supervised by prof. dr. Marcel Breeuwer (professor at TU/e and Principal Scientist at Philips Healthcare, project leader of openGTN) and prof. dr. Josien Pluim (head of the Medical Image Analysis department).

The openGTN project will provide high quality network-wide scientific training courses and complementary skills training.

Your role and responsibilities

Your research will focus on methods for generating realistic simulated MRI data of the brain and spine (ESR1) and the heart (ESR2), including pathology, and the application of these simulated data to develop and validate image analysis algorithms that are as much as possible independent of the applied specific MRI acquisition method (ESR3). Your will publish your results at scientific conferences and in peer-reviewed scientific journals.


Applicants should have a Master's degree in Electrical Engineering, Computer Science, Applied Physics, Applied Mathematics or Biomedical Engineering. Applicants with prior experience in MRI and medical image analysis will be given highest preference, as will candidates with ample experience in software design and implementation. Candidates should be able to work independently as well as in a team and be highly skilled in written and spoken English.

Candidates will be required to meet the Marie Curie Early Stage Researcher eligibility criteria. In particular, at the time of recruitment by the host organisation, candidates must be in the first four years (full-time equivalent research experience) of their research careers and not yet have been awarded a doctoral degree. This is measured from the date when they obtained the degree that would formally entitle them to embark on a doctorate. They are required to undertake trans-national mobility (i.e. move from one country to another) when taking up their appointment. At the time of recruitment by the host organisation, researchers must not have resided or carried out their main activity (work, studies, etc.) in The Netherlands for more than 12 months in the 3 years immediately prior to the start date. Short stays such as holidays and/or compulsory national service are not taken into account.


This post is available from 1st June 2018 or as soon as possible thereafter, but not later than 1 August 2018, and will be offered a full-time appointment for four years at Eindhoven University of Technology.

We offer you:
  • An exciting job in a dynamic work environment
  • The possibility to present your work at international conferences.
  • A full time appointment for four years at Eindhoven University of Technology (www.tue.nl/en)
  • The salary is in accordance with the Collective Labour Agreement of the Dutch Universities, increasing from € 2,222 per month initially, to € 2,840 in the fourth year.
  • An attractive package of fringe benefits, including end-of-year bonus (8,3% in December), an extra holiday allowance (8% in May), moving expenses and excellent sports facilities.

  • Additionele informatie

    The application contains, at least:
  • a brief letter motivating your interest in the position,
  • a detailed curriculum vitae,
  • transcripts of academic records indicating courses taken (including grades),
  • half-page summary of your MSc thesis,
  • contact details of two relevant references (email, phone number).
  • Screening of applications will start as soon as applications are received and will continue until the position has been filled.
  • Questions regarding the academic content of the position can be directed to prof. Marcel Breeuwer (m.breeuwer@tue.nl).
  • Other information can be obtained from the HR department, email: HRServices.Gemini@tue.nl.