PhD fellowship in image analysis using deep learning at Department of Drug Design and Pharmacology

Faculty of Health and Medical Sciences

University of Copenhagen

We are offering a three-year PhD fellowship in image analysis using deep learning commencing 1 September 2023 or as soon as possible thereafter.

Project description

We are seeking a highly motivated PhD student to work on this joint project between the Eye Translational Research Unit at The University of Copenhagen and the Section for Visual Computing at DTU Compute. The project, called "Finding Ophthalmic Risk and Evaluating the Value of Eye exams and their Predictive Reliability - Optical Coherence Tomography" (FOREVER-OCT), is a subset of the ongoing FOREVER project (forever.ku.dk). The PhD project is focused on identifying risk factors for eye diseases based on fundus photographs and optical coherence tomography (OCT) scans of the participants in the FOREVER project.

In the FOREVER project, 30,000 fundus photographs and 10,000 OCT scans are collected for the FOREVER cohort. Fundus photographs are widely used in Denmark, but OCT is a relatively new imaging examination and not as widely incorporated in an optometric setting. During this PhD project, the research will be focused on:

• Investigate the diagnostic value of the OCT imaging modality in the diagnosis of ophthalmic diseases, compared to fundus images.
• Investigate the possibilities of a combined diagnostic model based on both fundus and OCT scans, and possibly other clinical data.
• Evaluate potential associations between OCT parameters and risk factors for glaucoma.

As a PhD student on this project, you will have the opportunity to work with a team of experienced researchers, clinicians, and data scientists on tasks including data collection and analysis. Your role will involve discussing and applying state-of-the-art deep learning methods to the FOREVER dataset. You will also be responsible for carrying out the analyses and assessing the results in a clinical context. As this is a joint project, it is expected that you will divide your time between the two different research environments at DTU Compute and the University of Copenhagen. You will publish your findings in academic journals and present your work at international conferences.

Supervisors
Professor Miriam Kolko, Department of Drug Design and Pharmacology, University of Copenhagen
Professor Anders Bjorholm Dahl, Technical University of Denmark

Start
1 September 2023

Duration
3 years as a PhD student

Our department

Department of Drug Design and Pharmacology is committed to research-based teaching and interdisciplinary research that supports the development and understanding of chemical and pharmacological properties of drugs and drug targets. We work as part of a dynamic academic community of research, education and innovation within the Pharmaceutical Sciences bridging Health Sciences and Life Sciences.

Information about the Department can be found at https://drug.ku.dk/

Job description
Your key tasks as a PhD student at the Faculty of Health and Medical Sciences are:

• Carrying through an independent research project under supervision
• Completing PhD courses or other equivalent education corresponding to approximately 30 ECTS points
• Participating in active research environments including a stay at another research team, preferably abroad
• Obtaining experience with teaching or other types of dissemination related to your PhD project
• Teaching of undergraduate students in pharmaceutical sciences
• Writing a PhD thesis on the grounds of your project

Key criteria for the assessment of applicants

Applicants must have qualifications corresponding to a master’s degree related to the subject area of the project, e.g. computer science, biomedical engineering, data science, mathematics, or a related field. Please note that your master’s degree must be equivalent to a Danish master’s degree (two years).

The ideal candidate will also have the following skills:

• Programming experience in Python
• Hands-on experience with deep learning frameworks such as keras, tensorflow, or pytorch, and libraries such as scikit-learn
• High level of motivation and innovation
• Experience with image analysis is a plus
• Excellent written and communication skills in English
• Motivated to work in cross-disciplinary teams
• A team player who values sharing knowledge with colleagues and collaborators.

Other important criteria are:

• Professional qualifications relevant to the PhD project
• Relevant work experience
• Previous publications
• The grade point average achieved
• Other professional activities
• A curious mind-set with a strong interest in medical image analysis and the development of advanced analytical algorithms with clear clinical goals
• Language skills

Place of employment

The place of employment is at the at Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen. We offer creative and stimulating working conditions in dynamic and international research environment. Our research facilities include modern laboratories, state-of-the-art equipment and technology.

Terms of employment

The average weekly working hours are 37 hours per week.

The position is a fixed-term position limited to a period of 3 years.

The employment is conditioned upon the applicant’s successful enrolment as a PhD student at the Graduate School at the Faculty of Health and Medical Sciences, University of Copenhagen. This requires submission and acceptance of an application for the specific project to the Graduate School of Health and Medical Sciences.

The PhD study must be completed in accordance with The Ministerial Order on the PhD programme (2013) and the Faculty’s rules on achieving the degree.

The PhD student is expected to be affiliated to the graduate programme in pharmaceutical sciences, Drug Research Academy .

Salary, pension, and terms of employment are in accordance with the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary starts at approximately 28,400 DKK/roughly 3,780 EUR (October 2022 level) plus pension.

Application procedure

Your application, in English, must be submitted electronically by clicking “Apply now” below and must include the following documents in PDF format:

1. Motivated letter of application (max. one page)

2. CV incl. education, experience, language skills and other skills relevant for the position

3. Certified copy of original Master of Science diploma and transcript of records in the original language, including an authorized English translation if issued in other language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted. As a prerequisite for a PhD fellowship employment, your master’s degree must be equivalent to a Danish master’s degree. We encourage you to read more in the assessment database: https://ufm.dk/en/education/recognition-and-transparency/find-assessments/assessment-database . Please note that we might ask you to obtain an assessment of your education performed by the Ministry of Higher Education and Science. Applicants with a Master´s degree from abroad should also enclose a short description of the grading scale used

4. Publication list (if possible)

5. Other information to consider: References and recommendations (if possible)

The deadline for applications is 1 April 2023, 23.59pm CET

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process

After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor.

The assessor makes a non-prioritized assessment of the academic qualifications and experience with respect to the above-mentioned area of research, techniques, skills, and other requirements listed in the advertisement.

Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.

The applicant will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.

Interviews are expected to be held in Mid-April.

You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/

Questions

For further information, applicants may contact the principal supervisor Miriam Kolko, e-mail:  [email protected] , phone: +45 2980 7667 or PhD coordinator Marianne W. Jørgensen, e-mail: [email protected] , phone: +45 3533 6449.

General information about PhD studies at the Faculty of Health and Medical Sciences is available at the Graduate School’s website: https://healthsciences.ku.dk/phd/guidelines/

For more information on working and living in Denmark visit http://ism.ku.dk (International staff mobility) and https://www.workindenmark.dk

The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background.

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.