PhD Position: Deep Learning & Mathematical Morphology for Biomedical Imaging

About the project

About the Project PhD Position: Deep Learning & Mathematical Morphology for Biomedical Imaging Faculty of Informatics, Masaryk University (FI MU), Brno, Czech Republic Supervisor: Petr Matula Host centre: Centre for Biomedical Image Analysis ( CBIA ), FI MU Study programme: Ph.D. in Informatics Form: Full-time (preferred) Start: Spring 2027 Application deadline: November 30, 2026 Research Topic We invite applications for a PhD position at the intersection of deep learning and mathematical morphology , with primary applications in biomedical image analysis . The PhD project will be conducted within the Centre for Biomedical Image Analysis ( CBIA ) at the Faculty of Informatics, Masaryk University. CBIA provides a multidisciplinary research environment combining computer science, biomedical imaging, and clinical collaboration. The research will focus on integrating 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 Morphological operators and layers in CNNs / Vision Transformers Learnable connected filters (min/max trees, component trees, shape trees) Topology-preserving segmentation and explainable AI Morphology-aware representation learning Weakly supervised / few-shot biomedical segmentation Efficient and scalable morphological pipelines The exact topic will be specified jointly with the supervisor. Programme & Study Environment 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 Participate in conferences and research stays Funding & Employment Conditions Tuition fee: 0 CZK (also for English-language doctoral study) Standard funding package (full-time students): - Basic doctoral scholarship: 18,000 CZK / month - Employment contract (20% FTE): ~ 7,000 CZK net / month - Publication-performance scholarship: up to 7,000 CZK / month - Active PhD students typically reach ~32,000 CZK net monthly income during the standard study period. Candidate Profile Required MSc in Computer Science, Applied Mathematics, Biomedical Engineering, or related field Strong background in deep learning / machine learning Programming skills (Python, PyTorch / TensorFlow) Solid mathematical foundation Preferred Experience with mathematical morphology or image processing Biomedical imaging background Publication or open-source track record C++ / GPU / HPC experience Application Procedure Apply through the Masaryk University e-application system https://www.fi.muni.cz/admission/doctoral/ https://www.fi.muni.cz/admission/doctoral/application.html Contact For informal inquiries about the research topic: Petr Matula Faculty of Informatics, Masaryk University Email: pem@fi.muni.cz Web: https://www.muni.cz/en/people/3019

Research areas