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.

The research aims to integrate morphological operators, connected filters, and shape-based representations into modern machine learning frameworks. Example biomedical domains include fluorescence microscopy, radiology (CT/MRI), and multimodal imaging. Possible research directions include 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/few-shot biomedical segmentation, and efficient, scalable morphological pipelines. The exact topic will be specified jointly with the supervisor, Dr Petr Matula.

The position is embedded in the four-year doctoral programme in Informatics at FI MU, 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 study environment is highly collaborative, with access to state-of-the-art facilities and expertise in biomedical image analysis.

Funding and employment conditions are highly competitive. Tuition fees are fully waived (0 CZK), including for English-language doctoral study. The standard funding package for full-time students includes a basic doctoral scholarship of 18,000 CZK/month, an employment contract (20% FTE) of approximately 7,000 CZK net/month, and a publication-performance scholarship of up to 7,000 CZK/month. Active PhD students typically reach a net monthly income of around 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 skills include a strong background in deep learning or machine learning, programming proficiency (Python, PyTorch or TensorFlow), and a solid mathematical foundation. Preferred qualifications include experience with mathematical morphology or image processing, biomedical imaging background, publication or open-source track record, and C++/GPU/HPC experience. English or Czech language proficiency is required for the doctoral programme.

To apply, submit your application through the Masaryk University e-application system. The deadline for applications is November 30, 2026. For informal inquiries about the research topic, contact Dr Petr Matula at [email protected]. More information about CBIA can be found at https://cbia.fi.muni.cz/ and about the supervisor at https://www.muni.cz/en/people/3019.

This position is ideal for candidates seeking to advance the state-of-the-art in biomedical image analysis using deep learning and mathematical morphology, within a supportive and innovative research environment.