PhD fellow in Medical Image Analysis

Department of Computer Science, Faculty of Science at University of Copenhagen is offering a PhD scholarship in Medical Image Analysis commencing 1 December 2019 or as soon as possible thereafter.

Description of the scientific environment 

The research time will conducted partly in the Machine Learning Section at the Department of Computer Science, University of Copenhagen and in the group of Ivan Richter Vogelius at the Radiation Oncology Department at Rigshospitalet, Copenhagen, Denmark.

The Machine Learning Section provides a strong, international environment for research within Machine Learning, Medical Image Analysis, Natural Language Processing and Information Retrieval. The section currently holds about 20 PhD students and 12 postdocs. It is housed within the main Science Campus which is located centrally in Copenhagen. For details, see

The group of Ivan Richter Vogelius works on developing predictive models to individualize and improve radiation treatment in cancer patients. The Department of Oncology currently includes about 20 PhD students with backgrounds within various technical fields and medicine. In addition we employ 3 postdocs. See for a brief presentation of Ivan Vogelius’ previous work.

Project description 

Injury of organs due to radiation exposure is an important risk of radiation treatment. Knowing the consequences of radiation dosage to particular body part is crucial in radiation treatment planning to mitigate these risks. Some organs, such as the oesophagus are considered in daily planning, but delineation is manual and time consuming. Other such as the network of blood vessels supplying critical organs are largely not considered, partly because there is a lack of studies quantifying effects of radiation dose to specific vessels and partly because of the enormous amount of work it is to delineate them. 

The aim of the PhD project is to develop deep learning based methods to automatically segment radiation critical organs in the head, neck and chest regions, and specifically the blood vessels and the oesophagus in routine treatment planning scans in clinical databases. The automatic segmentations will then be used to quantify radiation dose exposure to these structures in large numbers of patients treated in the period 2009-2019.

The resulting data will be combined with Danish registries of hospital records for assessment of the risk of side-effects. Also, we will monitor changes in time series of 3D scans acquired during treatment (daily 6 weeks) and subsequent follow-up scans. It is a focus of the project to help accelerate the development in the field by the creation of open datasets and challenges around the problems at hand. The results of the PhD project will be used in larger projects and collaborations with clinicians and medical physicists to develop risk models and longer term new treatment plans using the unique registry data available in Denmark as well as retrospectively collected data from Hospital databases.

Principal supervisor is Associate Professor, Sune Darkner, Department of Computer Science,, Direct Phone: +45 21308584.

Job description 

The position is available for a 3-year period and your key tasks as a PhD student at SCIENCE are:

  • To manage and carry through your research project
  • Attend PhD courses
  • Write scientific articles and your PhD thesis
  • Teach and disseminate your research
  • To stay at an external research institution for a few months, preferably abroad
  • Work for the department

Formal requirements 

The applicant should either have a background in (Medical) Image Analysis or Machine Learning, and is expected to have significant prior experience with programming. Applicants should hold a MSc degree in computer science, bioinformatics, physics, chemistry, statistics or a closely related field, or be in the final stages of acquiring such a degree. Candidates must have good interpersonal and communication skills. The group is international and fluency in spoken and written English is a requirement. As criteria for the assessment of your qualifications emphasis will also be laid on previous publications (if any) and relevant work experience.

Terms of employment 

The position is covered by the Memorandum on Job Structure for Academic Staff. Terms of appointment and payment accord to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State.

The starting salary is currently at a minimum DKK 325.625 (approx. €43,400) including annual supplement (+ pension up to DKK 44,980). Negotiation for salary supplement is possible.

Application Procedure 

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

Please include

  • Cover Letter
  • CV
  • Diploma and transcripts of records (BSc and MSc)
  • Acceptance Letter for the relevant MSc Programme at SCIENCE, if any
  • Other information for consideration, e.g. list of publications (if any),
  • Full contact details (Name, address, telephone & email) of 1-3 professional referees

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

The deadline for applications is 15 September 2019 GMT +2.

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

For specific information about the PhD scholarship, please contact the principal supervisor Associate Professor, Sune Darkner, Department of Computer Science,, +45 21308584 or one of the co-supervisors Jens Petersen, Department of Computer Science,, +45 60687733, or Ivan Richter Vogelius, Department of Clinical Oncology,, +45 35459885‎.

General information about PhD programmes at SCIENCE is available at


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