The Van de Plas Lab is currently offering PhD positions in signal analysis and machine learning for multi-modal imaging, with a focus on spectral imaging modalities such as imaging mass spectrometry and multiplexed immunofluorescence microscopy, as well as a focus on exceptionally large and high-dimensional data.

Our lab is located at the Delft University of Technology (TU Delft) in the Netherlands and is part of the Delft Center for Systems and Control. Our research activities lie at the interface between (i) mathematical engineering and machine learning; (ii) analytical chemistry and instrumentation; and (iii) life sciences and medicine. We explore new ways of acquiring, processing, and mining the massive (multi-terabyte) datasets that imaging mass spectrometry and other molecular imaging modalities can produce. Research topics include:

• Signal processing (e.g. noise removal, automated feature detection);
• Dimensionality reduction and transformations (e.g. Fourier/wavelet transforms);
• Pattern recognition and factorization in large datasets (e.g. non-negative matrix/tensor factorization);
• Supervised, semi-supervised, and unsupervised machine learning (e.g. multivariate regression, tumor/abscess classification, manifold learning);
• Mathematical optimization & casting problems in biology into computer-solvable form (e.g. convex optimization, automated anatomical interpretation);
• Data mining across different imaging sensors and technologies (e.g. data-driven multi-modal image fusion).

Our lab has a strong international network of academic and industry collaborators. These include chemistry and instrument partners, such as the Mass Spectrometry Research Center and Caprioli lab at Vanderbilt University (U.S.A.), as well as medicine and biology partners, such as the Swinnen lab at the Dept. of Oncology of KU Leuven University Hospital (Belgium).

The positions will be part of several ongoing multi-disciplinary research projects. These include:

• Two projects within the Human BioMolecular Atlas Program (HuBMAP) of the United States’ National Institutes of Health, which aims to build a 3-D molecular atlas of the human body at single-cell resolution. Both projects are in close collaboration with Vanderbilt University (U.S.A.), one focusing on human kidney and the other on human eye and pancreas;
• Two National Institutes of Health projects on molecular imaging of microbial communities and infectious disease, in collaboration with Vanderbilt University Medical Center (U.S.A.);
• SMART BRAIN, a FLAG-ERA JTC project in collaboration with University of Modena and Reggio Emilia (Italy) through which our lab is an associated member of Europe’s Human Brain Project Flagship.

Relevant lab publications:

• Van de Plas R. et al., Image fusion of mass spectrometry and microscopy: a multimodality paradigm for molecular tissue mapping, Nature Methods, vol. 12, no. 4, 2015, pp. 366–372.
• Verbeeck N. et al., Automated Anatomical Interpretation of Ion Distributions in Tissue: Linking Imaging Mass Spectrometry to Curated Atlases, Analytical Chemistry, vol. 86, no. 18, 2014, pp. 8974–8982.
• Verbeeck, N. et al., Unsupervised Machine Learning for Exploratory Data Analysis in Imaging Mass Spectrometry., Mass Spectrometry Reviews, 2019.
• Cassat, J. E. et al., Integrated molecular imaging reveals tissue heterogeneity driving host-pathogen interactions., Science Translational Medicine, vol. 10, no. 432, 2018.
• HuBMAP Consortium, The human body at cellular resolution: the NIH Human Biomolecular Atlas Program., Nature, vol. 574, no. 7777, 2019, pp.187.

Applicants should have:

• A Master degree in Engineering, Computer Science, Systems & Control, Statistics, Computational Physics, or any field related to the lab’s research topics.
• A background in image & signal processing, machine learning, numerical analysis, or statistics.
• Strong motivation to work in a multidisciplinary environment and interact with collaborators in medicine, biology, chemistry, and physics is essential.
• Good command of English is required.

Candidates with experience in mass spectrometry, imaging, pattern recognition, or biotechnology are especially encouraged to apply.

Fixed-term contract: 4 years.

TU Delft offers PhD-candidates a 4-year contract, with an official go/no go progress assessment after one year. Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities, increasing from € 2395 per month in the first year to € 3061 in the fourth year. As a PhD candidate you will be enrolled in the TU Delft Graduate School. The TU Delft Graduate School provides an inspiring research environment with an excellent team of supervisors, academic staff and a mentor. The Doctoral Education Programme is aimed at developing your transferable, discipline-related and research skills.

The TU Delft offers a customisable compensation package, discounts on health insurance and sport memberships, and a monthly work costs contribution. Flexible work schedules can be arranged. For international applicants we offer the Coming to Delft Service and Partner Career Advice to assist you with your relocation.

Delft University of Technology

Delft University of Technology is built on strong foundations. As creators of the world-famous Dutch waterworks and pioneers in biotech, TU Delft is a top international university combining science, engineering and design. It delivers world class results in education, research and innovation to address challenges in the areas of energy, climate, mobility, health and digital society. For generations, our engineers have proven to be entrepreneurial problem-solvers, both in business and in a social context. At TU Delft we embrace diversity and aim to be as inclusive as possible (see our Code of Conduct). Together, we imagine, invent and create solutions using technology to have a positive impact on a global scale.

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Faculty Mechanical, Maritime and Materials Engineering

The Faculty of 3mE carries out pioneering research, leading to new fundamental insights and challenging applications in the field of mechanical engineering. From large-scale energy storage, medical instruments, control technology and robotics to smart materials, nanoscale structures and autonomous ships. The foundations and results of this research are reflected in outstanding, contemporary education, inspiring students and PhD candidates to become socially engaged and responsible engineers and scientists. The faculty of 3mE is a dynamic and innovative faculty with an international scope and high-tech lab facilities. Research and education focus on the design, manufacture, application and modification of products, materials, processes and mechanical devices, contributing to the development and growth of a sustainable society, as well as prosperity and welfare.

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The department Delft Center for Systems and Control (DCSC) of the faculty Mechanical, Maritime and Materials Engineering, coordinates the education and research activities in systems and control at Delft University of Technology. The Centers' research mission is to conduct fundamental research in systems dynamics and control, involving dynamic modelling, advanced control theory, optimisation and signal analysis. The research is motivated by advanced technology development in physical imaging systems, renewable energy, robotics and transportation systems.