Postdoc: Crop Health Simulation and Agricultural Modeling at University of Copenhagen

The IMAGE section at Department of Computer Science is offering a Post Doc position in in mechanistic co-simulation of Insects, Weeds and Plant Infestation in Agricultural Fields as a part of the One Crop Health project commencing 1 November 2025, or as soon as possible hereafter.

Our group and research
The IMAGE section hosts researchers in image analysis and processing, computer vision, computer simulation, numerical optimization, machine learning, computational modelling, geometry and geometric statistics. The work ranges from theoretical analyses, over algorithm development, to solving concrete problems for science, industry and society. We are part of the recently launched SCIENCE AI Centre at the University of Copenhagen.

Project summary:

The project involves continuous data collection from around 100 farmers in Denmark and the United Kingdom, integrating ecological, environmental, and agricultural data. Central to the project is the development of a mechanistic systems model that simulates complex interactions between crops, weeds, pests (including beneficial insects), plant diseases, and external conditions such as weather, soil, and field management practices.

A major component of the work involves the automated integration of data collected from pioneer farms, long term experiments, and other sources of data integrating those into mechanistic models and extending the models with appropriate integration to other models to build a more complete systems model. The goal is to first establish a base model and then extend the model through co-simulation principles to include additional model for pest weed and diseases. This will be based on informed decisions through e.g. statistical modelling or ML with proper validation. We will in the project take offset in the APSIM framework and therefore it is essential with knowledge of C++ and Python.

The challenges are integrations and domain understanding. To this end a close integration with domain experts is imperative and the postdoc will be jointly supervised by faculty from computer science (DIKU), plant and environmental science (PLEN) in collaboration with Rothamsted. Furthermore, it is required that the postdoc spend much of their time at PLEN in the group of the project leader Paul Neve. Furthermore, it is expected that any change of environment will be mainly at Rothamsted research Centre in the UK at location.

Role of the Postdoc:

The postdoc will play a central and bridging role in the project—serving as the key link between the computational modeling efforts from a PhD student and the plant science and agronomy teams at PLEN. This includes:

• Act as interface between computer science and crop modelling, ensuring coherence and relevance of the modelling activities at DIKU in relation to PLEN.
• Providing scientific and technical leadership in the development and extension of a mechanistic base model, with a focus on simulating interactions among pests, weeds, diseases, and crops.
• Supporting and mentoring the PhD student in model development and integration of empirical monitoring data.
• Facilitating collaboration and knowledge exchange between the computer science and plant science groups, ensuring that ecological and agronomic domain knowledge is meaningfully incorporated into the model.
• Participating in the design of field data collection protocols and ensuring data quality and relevance for modeling.
• Coordinating closely with researchers at Rothamsted Research in the UK, including short- to medium-term research stays.
• Contributing to publications and dissemination of results in high-impact journals and conferences.

Required Qualifications:

• A PhD in Computer Science, Mathematical Modeling, Systems Biology, Agricultural Engineering, or a related field.
• Strong programming skills, particularly in C++ and Python.
• Background in numerical modeling, simulation, or systems analysis.
• Excellent communication skills and experience working in interdisciplinary research environments.
• Demonstrated ability to publish in peer-reviewed journals.

Preferred Qualifications:

• Experience with ecological or agricultural systems modeling.
• Familiarity with integrating biological and environmental data into computational models.
• Familiarity with Statistics
• Experience with APSIM
• Proficiency with collaborative software development tools (e.g., Git, CI/CD workflows).
• Experience working with or supporting graduate students.

Interest

Principal supervisor is Professor Sune Darkner, Section for Image Analysis, Computational Modelling and Geometry (IMAGE) at Department of Computer Science, gibsonchadjenniferellisondarkner@di.ku.dkaustin-adams.dkgonzalez.dkcole-holmes.dk, Direct Phone: +45 21308584.

Start: 1 November 2025

Duration: 3 years as a postdoc

Job description
Your key tasks as a Post Doc Faculty of Science are:

• Carrying through an independent research project under supervision.
• Participating in active research environments including a stay at another research team.
• Obtaining experience with teaching or other types of dissemination related to your PostDoc project
• Teaching and disseminating your knowledge.

Key criteria for the assessment of applicants
Applicants must Ph.D. degree related to the subject area of the project as indicated below.

Required qualifications:

• A PhD degree in computer science, bioinformatics, mathematics, software engineering or a related field.
• Educational training or previous experience in programming for image analysis and computer vision.
• Educational training covering image analysis and computer vision.
• Educational training covering machine learning and in particular deep learning for image analysis and computer vision.
• Demonstrate good academic writing skills as proven in the motivated letter of application and in any previous publications.

Place of employment

The place of employment is at the Department of Computer Science, Faculty of Science, University of Copenhagen. We offer creative and stimulating working conditions in dynamic and international research environment. Our research facilities include modern computing facilities and laboratories.

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 starting date is the 1 November 2025 or soon thereafter.

Salary, pension and other conditions of employment are set in accordance with the Agreement between the Ministry of Taxation and AC (Danish Confederation of Professional Associations) or other relevant organisation. Currently, the monthly salary starts at 38,700 DKK/approx. 5,100 EUR (April 2025 level). Depending on qualifications, a supplement may be negotiated. The employer will pay an additional 18,07% to your pension fund

Questions
For specific information about the Post Doc fellowship, please contact the principal supervisor.

Application procedure
Your application must be submitted electronically by clicking ‘Apply now’ below. The application 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 all relevant diplomas and transcript of records in the original language, including an authorized English translation if issued in other language than English or Danish

4. Publication list

Application deadline: 1 September 2025, 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.

You find information about the recruitment process at: http://employment.ku.dk/faculty/recruitment-process/

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

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