PhD candidate on the project Virtual biopsy of brain tumours – imaging pathomics

With this project we aim to reduce the need for surgical biopsies in patients with a brain tumour by developing artificial intelligence (AI) technology which integrates magnetic resonance imaging (MRI) and histopathology to eventually obtain all clinically relevant diagnostic information non-invasively from MRI only: a virtual biopsy.

As a PhD student, you will develop advanced image analysis and machine learning techniques that will automatically diagnose brain tumour genotypes from tissue samples, and to link tissue sample characteristics with MRI-based features. This is a challenging and multidisciplinary project, bridging technical, biological and clinical disciplines.

This is one of several positions in the Brain Tumour Virtual Biopsy Project. Both conventional and advanced MRI and histopathological staining techniques will be used. A large database of MRI scans, tissue samples and clinical information will be collated for this project, both retrospectively and prospectively. There will be a strong collaboration with the other PhD students and postdoc on this project, whose focus will be on the automated extraction of relevant quantitative features from radiological (‘radiomics’) and pathological (‘pathomics’) images, and on bringing virtual biopsy into clinical practice through an ‘in silico’ trial.
The project is performed at Erasmus MC – University Medical Centre Rotterdam and Radboud University Medical Centre (Radboudumc) in Nijmegen, in collaboration with AmsterdamUMC, Delft University of Technology, Leiden University Medical Centre, Memorial Sloan Kettering Cancer Center (New York, USA), and with advisors from University College London (UK).

As a PhD student you will be based both in the Department of Radiology & Nuclear Medicine of the Erasmus MC in Rotterdam and in the Computational Pathology Group at the Pathology department of Radboudumc in Nijmegen. Both departments have an international character with a good balance between internationally recognised, high-end research and an excellent social working environment. The supervision for the project will be provided by Dr. ir. Stefan Klein and Prof. Marion Smits at Erasmus MC and by Dr. Geert Litjens at Radboudumc. The expectation is that you work a substantial part of the time at Radboudumc.

The Department of Radiology & Nuclear Medicine of the Erasmus MC is one of the largest imaging departments in Europe with 10 clinical MRI scanners at several field strengths and 1 PET-MRI scanner. In Rotterdam, the project is locally embedded in the Applied Physiological Neuroimaging group and Biomedical Imaging group Rotterdam (BIGR). In Nijmegen, the Department of Pathology is a modern, fully digital department with several whole-slide scanning systems and a compute cluster encompassing more than a 100 GPUs.