PhD position: “Developing automated image analysis to examine an overlooked link in the North Sea: Zooplankton”

This vacancy is the result of the collaboration between Utrecht University and NIOZ. The department of Estuarine & Delta Systems (EDS) of the Royal Netherlands Institute for Sea Research (Royal NIOZ) and the department of Information and Computing Sciences of the Utrecht University are looking for an enthusiastic PhD-student with a degree in marine ecology or computer sciences and expertise/affinity for the other.

2020-12-16 14:38:44

VACANCY ID:             2020-78
CLOSING DATE:       February 10th, 2021


Zooplankton, the animal component of the planktonic community in the ocean, has a key role in marine ecosystems by transferring energy and nutrients from autotrophs to organisms higher up the food web. However, zooplankton is not monitored in the Dutch North Sea, which is a major omission for ecosystem-based policy. NIOZ recently purchased an underwater microscope which is designed to take images of zooplankton and marine snow at very high temporal frequency. This interdisciplinary PhD-project combines in situ imaging and machine learning to build an automated observation-monitoring platform for zooplankton to better understand the role of zooplankton in the North Sea. We foresee that the methodology will be applied during monitoring cruises of the governmental Rijkswaterstaat to provide data for future ecosystem studies.


This PhD-project is uniquely situated at the interface of marine ecology and computer science. On the one hand, you will prepare and join research cruises, sample zooplankton with traditional zooplankton nets, sort zooplankton specimens behind the microscope and interpret results in the context of food web dynamics. On the other hand, you will ensure proper storage of large volume of images and develop machine learning techniques, such as classifiers using artificial neural networks, to automatically classify the hundreds of thousands of images that are captured by the imaging instruments. Results from the traditional net samples will be confronted with the results from the imaging instruments. Initially, images and net samples will be collected in the accessible Oosterschelde estuary during day trips. Subsequently, cruises to various North Sea regions will be held to further develop, validate and apply the imaging technique for ecosystem studies.


We are looking for an enthusiastic candidate that is challenged by this interdisciplinary project. Hence, we look for a candidate with a MSc. degree in marine ecology and expertise in computer science or a MSc. degree in computer science and expertise in marine ecology. The candidate enjoys working with scientific equipment, going on fieldwork, working in the laboratory, but also enjoys data analysis, programming and developing machine learning techniques. Given the interdisciplinary nature of the work, it is important that the candidate is open and communicative to facilitate interactions with other members of the group. Excellent English oral and writing skills are essential. We highly encourage applicants from all members of our research community and of diverse background to join us. The candidate will be based at NIOZ in Yerseke which is at commuting distance of cities like Antwerpen, Breda, Middelburg and Vlissingen and will benefit from a close cooperation between the departments from NIOZ and Utrecht University.


Employment of this position at Royal NIOZ is by NWO (The Netherlands Organization of Scientific Research). We offer a position for a period of 4 years (fulltime). We offer a position for a period of 1 year (fulltime). At the end of this first year, the employment will be extended for a fixed-term of a maximum of 4 years, if the first year evaluation held with the employee is positive. The salary is compliant to the CAO-OI (Collective Labour Agreement for Dutch Research Institutes), a pension scheme, a holiday allowance of 8% of the gross annual salary, a year-end bonus of 8,3%, flexible work arrangements and 42 days of holiday leave (fulltime position).

You may expect attractive secondary employment conditions. We offer generous relocation expenses for employees coming from abroad and support with finding accommodation..


For additional information about this vacancy, please contact Dr. Dick van Oevelen (sr. scientist at NIOZ), Prof. dr. Frank van der Stappen (Professor of Robotics and Automation at UU) or Prof. dr. Karline Soetaert (Research leader at NIOZ) . For additional information about the procedure, please contact  Sigrid Moerbeek (senior HR advisor).

Please visit the Department of Estuarine & Delta Systems (EDS) here. Learn more about the department Department of Information and Computing Sciences at the University of Utrecht here.

Find more information about the UU-NIOZ projects here.

Please note: The first round of job interviews is foreseen for early February and will take place online. When feasible, a visit to the NIOZ-EDS department in Yerseke and second interview will take place in February.




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