PhD in Deep learning for Electron Microscopy pipelines (1.0 fte)

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

PhD in Deep learning for Electron Microscopy pipelines (1.0 fte)

As a PhD student, you will be embedded in the research groups Computational Imaging and Deep Learning (CIDL) and Applied Quantum Algorithms (aQa), part of the Leiden Institute of Advanced Computer Science (LIACS). The CIDL group develops cutting-edge techniques for advanced computational imaging systems, combining expertise from Mathematics, Computer Science, and Physics. The aQa group studies quantum algorithms and their applications to problems in natural sciences (physics, chemistry) and practical computing (machine learning, AI, optimization), and methods to make them compatible with near-term quantum devices.

Your project, “Deep learning for Electron Microscopy pipelines (DEEM), focuses on the application of deep learning methodologies to enhance electron microscopy (EM). The research addresses existing challenges within EM, such as image noise, artifacts, the optimization of acquisition parameters, and the integration of information from various EM techniques. The overall goal is to improve the output of EM systems and potentially extend their experimental capabilities by integrating deep learning throughout the imaging workflow, from data acquisition to final analysis.

As a PhD student in this project, you will undertake several research activities. These include the development and implementation of algorithms for self-supervised denoising and artifact removal in EM images, which may involve modeling specific physical effects. The student will also investigate data-driven methods for the optimization of EM experimental settings and image processing workflows. A further area of research will be the development of techniques to leverage data from multiple EM modalities to improve image quality. All developed methodologies will be validated using appropriate EM datasets and experimental setups, in collaboration with Leiden Institute of Physics (LION), which houses several EM setups.

As a candidate, you must have a strong background in computational imaging and image processing, as well as excellent programming skills and experience with Deep Learning. In addition, you must have an understanding of or an interest in the physics of (EM) image formation.

Key responsibilities

• Conduct original and novel research in the field of Computational 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, Applied Mathematics, Physics, 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 Python);
• Excellent proficiency in English (oral and written).
• Flexibility regarding working on-site with the diverse project partners.

Research at our faculty and institute
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 https://www.universiteitleiden.nl/en/science.

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 https://www.cs.leiden.edu.

The city of Leiden
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. The salary will be in the range of € 2.901,= to € 3.707,= (PayScale P) gross per month, subject to national taxation and social contributions. 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.

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.

Diversity and work-life balance
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. Childcare is available at and near the Bio Science Park.

Information
Inquiries about the research area can be made to Dr. D.M. Pelt d.m.pelt@liacs.leidenuniv.nl. If you have any questions about the application procedure, please send an email to jobs@liacs.leidenuniv.nl

Applications
Please submit your application online via the blue button in the vacancy. Please ensure that you upload the following additional documents:

• your CV;
• Motivation letter;
• List of courses you took for your M.Sc. and corresponding grades;
• Names and contact details of at least two references who agreed to be contacted;

Only applications received no later than July 10, 2025 can be considered. The selection procedure will take place in July 2025, and selected candidates may be invited for an online and/or physical interview in this period, during which you are kindly requested to be available.