PhD Positions in Signal Processing and Machine Learning for Multimodal Molecular Imaging

The Van de Plas lab is offering PhD positions in signal processing and machine learning for multimodal imaging, to build 3-D molecular atlases of human tissue. The positions have a special focus on spectral imaging modalities such as imaging mass spectrometry and multiplexed immunofluorescence microscopy, as well as 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 lies 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 commonly deliver.

Research topics of interest for these positions include:

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

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

You will have the opportunity to participate in one or more of our ongoing multidisciplinary research projects:

• 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. One project focuses on the human kidney, while the other explores the human eye and pancreas. Both projects are in close collaboration with Vanderbilt University (Nashville, TN, U.S.A.).
• Two National Institutes of Health projects on the molecular imaging of microbial communities and infectious disease, in collaboration with the Vanderbilt University Medical Center (Nashville, TN, U.S.A.).
• SMART BRAIN, a FLAG-ERA JTC project in collaboration with the University of Modena and Reggio Emilia (Italy) through which our lab is an associated member of Europe’s Human Brain Project Flagship.