PhD Position: Deep Learning & Mathematical Morphology for Biomedical Imaging Masaryk University in Czech Republic

This PhD position at Masaryk University, Faculty of Informatics, offers an exciting opportunity to conduct research at the intersection of deep learning and mathematical morphology, with a primary focus on biomedical image analysis. The project is hosted by the Centre for Biomedical Image Analysis (CBIA), a multidisciplinary research environment that brings together computer science, biomedical imaging, and clinical collaboration. CBIA is renowned for its innovative approaches to image analysis and provides access to state-of-the-art facilities and expertise.

The research will explore the integration of morphological operators, connected filters, and shape-based representations into modern machine learning frameworks. Potential application domains include fluorescence microscopy, radiology (CT/MRI), and multimodal imaging. Possible research directions encompass morphological operators and layers in CNNs/Vision Transformers, learnable connected filters (min/max trees, component trees, shape trees), topology-preserving segmentation, explainable AI, morphology-aware representation learning, weakly supervised or few-shot biomedical segmentation, and efficient, scalable morphological pipelines. The exact research topic will be determined in consultation with the supervisor, Dr Petr Matula.

The position is embedded in the four-year doctoral programme in Informatics at Masaryk University, delivered in English or Czech. Doctoral students are expected to conduct independent research under supervision, publish at international venues, and participate in conferences and research stays. The programme offers a vibrant academic environment and opportunities for collaboration with leading researchers in the field.

Funding is available for full-time students, including a basic doctoral scholarship of 18,000 CZK per month, an employment contract (20% FTE) with ~7,000 CZK net per month, and a publication-performance scholarship of up to 7,000 CZK per month. Tuition fees are waived (0 CZK), even for English-language study. Active PhD students typically reach a net monthly income of approximately 32,000 CZK during the standard study period.

Applicants must hold an MSc in Computer Science, Applied Mathematics, Biomedical Engineering, or a related field. Required qualifications include a strong background in deep learning and machine learning, programming skills in Python (PyTorch/TensorFlow), and a solid mathematical foundation. Preferred qualifications are experience with mathematical morphology or image processing, biomedical imaging background, publication or open-source track record, and C++/GPU/HPC experience. The programme is delivered in English or Czech, so proficiency in one of these languages is necessary.

To apply, candidates should submit their application through the Masaryk University e-application system. For further information or informal inquiries about the research topic, contact Dr Petr Matula at [email protected]. The application deadline is 30 April 2026, and the position is expected to start in Autumn 2026. For more details, visit the CBIA website and the supervisor's academic profile.