PhD candidate in Machine Learning for Imaging


The Faculty of Science and Leiden Institute of Advanced Computer Science (LIACS) are looking for candidates

PhD candidate 
PhD Position in Machine Learning for Imaging

Project description
Using a variety of imaging techniques, it is now possible to create detailed 3D images of the surface and interior of objects ranging from large structures such as pyramids down to individual molecules and atoms using electron microscopy and acquire Terabytes of 3D voxel data within hours. To keep up with the rate of data being produced, the images must be segmented, annotated and analyzed at similar throughput rates, which has become the key bottleneck for large-scale scientific imaging. So far, the tasks of segmentation and annotation have been performed mainly by domain experts, as considerable domain knowledge is required. The broad diversity of task-specific imaging operations currently performed by the user depends strongly on the properties of the particular sample under investigation and the imaging procedure, hampering the use of one-fits-all postprocessing algorithms.

Convolutional neural networks form a strong foundation for postprocessing approaches that can learn to adapt to the particular task at hand. However, they typically require many training examples, which again is too costly to be created by human experts. In this project we will develop new approaches for semi-supervised segmentation of large 2D and 3D datasets by convolutional neural networks. We will focus on the interaction between the domain expert and the software, creating an efficient workflow for steering the training process and correcting errors on-the-fly.

We will apply the research to segmentation and annotation of biological electron tomography datasets and to the detection of archaeological points-of-interest in large-scale remote sensing data.

SAILS: The future of AI is human
Artificial Intelligence (AI) and related technologies are playing an increasingly important role in our society. At Leiden University we are convinced that the future of AI is human: to create AI for Good we need to combine the expertise from researchers in AI techniques with the human aspects of AI, involving law, language, psychology, and many other fields. To this end Leiden University has started a new, university wide initiative called SAILS (Social Sciences, Humanities, Law, Artificial Intelligence and Life Sciences) to enable collaboration on the development and application of AI. By building on and expanding the already existing expertise of AI, we advance science and improve the quality of life for all. All the disciplines of the University of Leiden are involved in the program: Archaeology, Humanities, Social Sciences, Law, Public Administration, Sciences, and also the Leiden University Medical Centre (LUMC), to collaborate and appoint new staff (full professors, assistant professors, postdocs, and PhD students to perform groundbreaking AI research across domain boundaries.

This PhD project is part of SAILS. You will actively engage in collaboration with the Leiden University Medical Centre (LUMC), the Netherlands Centre for Electron Nanoscopy (NeCEN), and the Faculty of Archaeology to jointly work towards novel AI systems and their applications. The broad project team will include experts from each of these domains.

Key responsibilities

  • Conduct original and novel research in the field of AI for imaging;
  • Publish and present scientific articles at international journals and conferences;
  • Contribute to educational activities;
  • Write a dissertation;
  • Engage in collaborations with colleagues across domains.

Selection criteria

  • A MSc degree in Computer science, AI, or a related field;
  • Good knowledge of and experienced with machine learning;
  • Good knowledge of and experienced with Image processing techniques;
  • Highly motivated to both perform foundational research and apply the developed methods to real-world problems;
  • Creative, ‘making things work’ mentality, independent, and communicative team player;
  • Experienced with writing scientific manuscripts and good academic writing skills;
  • Excellent programming skills (preferably C++ and/or Python);
  • Interested in participating in educational activities;
  • Excellent proficiency in English (oral and written).

Our organisation
The Leiden Faculty of Science is a world-class faculty where staff and students work together in a dynamic international environment. Our people are driven by curiosity to expand fundamental knowledge and to look beyond the borders of their own discipline.

The research carried out at the Faculty of Science is diverse, ranging from artificial intelligence, computer science, mathematics, astronomy, physics, chemistry and bio-pharmaceutical sciences to biology and environmental sciences. The faculty has grown strongly in recent years and now has more than 1,300 staff and almost 4,000 students. We are located at the heart of Leiden’s Bio Science Park, one of Europe’s biggest science parks, where university and business life come together. For more information, see the website.

The Leiden Institute of Advanced Computer Science (LIACS) is the Artificial Intelligence and Computer Science Institute of the Faculty of Science of Leiden University. We offer courses at the Bachelor and Master of Science level in the core areas of Artificial Intelligence, Computer Science, and Data Science, and also in the interdisciplinary areas of ICT in Business, Media Technology and Creative science, and Bioinformatics. According to an independent research visitation, we are one of the foremost computer science departments of the Netherlands. Our people and our focus on collaboration in a caring atmosphere are dear to us. We strive for excellence in a caring institute, where excellence, fun, and inclusiveness go hand in hand. We offer a clear and inviting career path to young and talented scientists with the ambition to grow. For more information about LIACS, see the website.

Leiden University is one of Europe’s foremost research universities. Leiden is a lively and beautiful city with a central location in Europe, at only 17 minutes from Schiphol International Airport. It is a very international city where almost everybody speaks English, candidates need not be afraid of the language barrier. Leiden is a typical historic university city, hosting the oldest university in the Netherlands (1575). The University permeates the local surroundings; University premises are scattered throughout the city, and the students who live and study in Leiden give the city its relaxed yet vibrant atmosphere. Today, with some 27,000 students, 5,500 staff, 16 Nobel prizes, more than 100 nationalities and a budget of more than 550 million Euros, it is one of the largest comprehensive universities in Europe. This prominent position gives our graduates a leading edge in applying for academic posts and for functions outside academia.

Terms and conditions
We offer a full-time appointment of initially one year. After a positive evaluation of the progress of the  research, teaching evaluations, personal capabilities and compatibility, the appointment will be extended for another three years. Salary range from € 2.395,-  to € 3.061,-  gross per month (pay scale P in accordance with the Collective Labour Agreement for Dutch Universities).

Leiden University offers an attractive benefits package with additional holiday (8%) and end-of-year bonuses (8.3%), training and career development. Our individual choices model gives you some freedom to assemble your own set of terms and conditions. Candidates from outside the Netherlands may be eligible for a substantial tax break.

All our PhD students are embedded in the Leiden University Graduate School of Science. Our graduate school offers several PhD training courses at three levels: professional courses, skills training and personal effectiveness. In addition, advanced courses to deepen scientific knowledge are offered by the research school.

Leiden University is strongly committed to diversity within its community and especially welcomes applications from members of underrepresented groups. LIACS is a highly diverse institute, in culture, background, and gender. We stand for excellence in a caring Institute. We wish to reflect society in all aspects, as we believe that this improves the dynamics in our organization. Therefore, we support and understand the need for a work/life/family balance and consequent varying working hours and places. We believe that doing good science is fun, and goes hand in hand with a friendly culture. In the Netherlands, a maternity allowance is standard for 16 weeks. Child care is available at and near the Bio Science Park.

Inquiries about the research area can be made to Joost Batenburg, email If you have any questions about the procedure, please contact Mischa Hautvast, email

To apply for this vacancy, please send an email to Applicants should submit their application letter, CV, and at least two references, quoting the vacancy number.

Vacancy number: 20-348

Closing date: 01 September 2020

Only applications received no later than September 1, 2020 can be considered. The selection procedure will take place in September 2020, and selected candidates may be invited for a Skype interview in this period, during which you are kindly requested to be available.

Leave a Reply