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PhD student, on the subject of Ultra-Fast 3D Reconstruction

Centrum Wiskunde & Informatica (CWI) and the Mathematical Institute of Leiden University seek a dedicated candidate for a PhD position in the …

ongeveer een jaar geleden


Science Park, Amsterdam, Noord-Holland
Tijdelijk contract / Tijdelijke opdracht
Uren per week:
40 uur


Centrum Wiskunde & Informatica (CWI) and the Mathematical Institute of Leiden University seek a dedicated candidate for a PhD position in the interdisciplinary field of Mathematical Analysis, Algorithms and Computation for Tomography.
As a PhD student, you will be part-time embedded in the Computational Imaging group at CWI, and part-time in the Analysis and Dynamical Systems group of the Mathematical Institute of Leiden University. As a team, we develop cutting-edge techniques for advanced tomographic reconstruction, combining expertise from Mathematics (Inverse Problems and Dynamical Systems), Computer Science (Efficient Algorithms and High Performance Computing), and Physics (Image Formation Modelling). Our goal is to develop novel computational methods for 3D and 4D imaging.
We work closely with research colleagues both inside the hosting institutes as well as externally, with industrial partners and with international X-ray and electron imaging groups.
Your PhD project will be part of the Marie Skłodowska-Curie Innovative Training Network, “Multiscale, Multimodal, Multidimensional imaging for EngineeRING” or in short MUMMERING. The network is concerned with interdisciplinary R&D and training in 3D imaging and its application in materials- and information science. The network offers totally 15 PhD positions. You can find information about all 15 PhD positions at https://euraxess.ec.europa.eu/jobs/256053 .

Scientifically, the network addresses the challenges 3D imaging has to overcome for being a workable tool in materials science and engineering. This means filling the gap between the capacities by which experimental data can be captured and by which the data can be processed. Today the data processing lags behind.

The main goal of your PhD project will be to develop novel algorithms for fast reconstruction in 3D and 4D tomography. The term “4D” refers to the case where a series of 3D images corresponding to the evolution of the scanned object needs to be computed from a large number of noisy 2D projection images. Your focus will be on electron imaging, but your methods will also be applicable for large-scale synchrotron X-ray data. Your techniques will incorporate concepts from dynamical systems theory to effectively model the evolution of the scanned object during the measurement process. Such evolution includes morphological changes in the sample, but can also capture sampling errors and object motion during the scan, leading to image alignment problems. Due to the fast image acquisition, high noise levels are inevitable, requiring robust algorithms.


Responsibilities and tasks
As PhD student, we expect that you take full responsibility for your PhD project and your learning under the guidance of your experienced supervisors. Moreover, we expect that you actively involve with and seek benefit from:

  • The training provided by the MUMMERING network
  • Secondments to the industry partner, and other network partners
  • CWIs excellent computational imaging research infrastructure, including a state-of-the-art X-ray CT lab.
  • Your embedding in the dynamical systems group at the Mathematical Institute of Leiden University, which offers many opportunities for advanced courses and research collaborations.

Via the mandatory network training provided by MUMMERING, you will participate in summer schools, workshops, and scientific meetings together with top scientists and your 14 fellow PhD students in the MUMMERING network. During your secondments, you will be involved with data acquisition at electron microscopes and at a large-scale synchrotron facility. You will also gain experience with industrial software implementation.

Your task will be to handle all aspects of your PhD project and training. This means that you will:

  • Work out and update your study plan and a personal career development plan
  • Plan, conduct and report your experiments
  • Seek the learning you need for conducting your research
  • Publish your results

We expect you to master the balance between working independently and taking initiative on the one hand, and seeking advice from your supervisors, your fellow PhD students and colleagues on the other hand.


Candidates should have a master's degree in mathematics, or a similar degree with an equivalent academic level and a strong mathematical background.

Candidates shall moreover comply with H2020 definition of an Early-Stage Researcher, i.e. be in the first four years of the research career, and have not yet been awarded a doctoral degree.

The candidate can be of any nationality but is required to undertake physical transnational mobility meaning that you have to move to The Netherlands from another country when taking up the appointment.

The scholarship for the PhD degree is subject to academic approval, and the candidates will be enrolled in the Graduate School of Leiden University. For information about the general requirements for enrolment and the general planning of the scholarship studies, please see: https://www.universiteitleiden.nl/en/science/graduate-school-of-science.

The assessment of the applicants will be made by Prof. Joost Batenburg (CWI) and Dr. Hermen Jan Hupkes (Leiden University).


We offer a fulltime employment as a PhD student for four years. The appointment is initially for 18 months. After the first year, we will evaluate whether we expect that a PhD thesis can be completed successfully. If this is the case, the contract will be extended to 3 years. If the progress towards the PhD degree after 3 years is satisfactory, you will be offered a 4th year at Leiden University to finalize your project and finish your thesis.

The terms of employment are in accordance with the Dutch Collective Labour Agreement for Research Centres ("CAO-onderzoeksinstellingen"). The fellows to be recruited by CWI will be employed with full social security coverage and all benefits in accordance with the Marie Sklodowska-Curie ITN fellowship regulations of the European Union (highly competitive salary plus allowances for living and mobility expenses).

CWI offers attractive working conditions, including flexible working times and help with housing for expat employees.

Please visit our website for more information about our terms of employment: www.cwi.nl/terms-of-employment

Additional information

Additional information
You will use the ASTRA Toolbox to create high-performance, parallel implementations of your algorithms, using either Python or C++. The ASTRA toolbox is a powerful, open-source platform for tomography algorithm development that provides many of the building blocks required by your algorithms.

As a candidate, you must have a strong background in the (computational) mathematics of inverse problems and/or dynamical systems. In addition, you must have an understanding of or an interest in the physics (X-ray and/or electron) of the image formation. Programming skills will also help your application.

Please note that there is no fixed deadline for submitting your application. We will evaluate the applications on a running basis. We therefore advise you to submit your application as soon as possible. We expect that you start between 1 January and 1 May 2018.

Candidates may apply prior to obtaining their master's degree, but cannot begin before having received it.

All interested candidates irrespective of age, gender, race, sexual orientation, disability, religion, ethnic background etcetera, are encouraged to apply.

Further information may be obtained from Professor Joost Batenburg (joost.batenburg@cwi.nl) and Dr. Hermen Jan Hupkes (hhupkes@math.leidenuniv.nl).


Centrum Wiskunde & Informatica (CWI) is the Dutch national research institute for mathematics and computer science and linked to the Netherlands Organisation for Scientific Research (NWO). The mission of CWI is to conduct pioneering research in mathematics and computer science, generating new knowledge in these fields and conveying it to trade, industry, and society at large.

CWI is an internationally oriented institute, with 160 scientists from approximately 27 countries. The facilities are first-rate and include excellent IT support, career planning, training, and courses. CWI is located at Science Park Amsterdam that is presently developing into a major location of research in the natural sciences in The Netherlands, housing the sciences of the University of Amsterdam and of the Vrije Universiteit as well as several other national research institutes next to CWI.

Mathematical Institute of Leiden University

The Mathematical Institute performs high quality research at the frontiers of mathematical knowledge, and educates future generations of mathematicians and statisticians in a friendly but challenging environment.

The expertise of the members of the institute covers a broad range of topics, with a focus on Algebra, Geometry and Number Theory; Analysis and Dynamical Systems; Probability Theory; and Statistics. Research is focused both on fundamental mathematics and statistics and on applications in other sciences, society and industry. The institute offers educational programmes in pure and applied mathematics and statistics.

Additional information about the Mathematical Institute of Leiden University can be found on https://www.universiteitleiden.nl/en/science/mathematics.

For more information about the Analysis and Dynamical Systems Group of Leiden University, visit: https://www.universiteitleiden.nl/en/science/mathematics/analysis-and-dynamical-systems