PhD Position: Improving Evaluation Frameworks for Microscopy Image Analysis

This PhD position at the Faculty of Informatics, Masaryk University, offers an exciting opportunity to advance evaluation frameworks for microscopy image analysis. Hosted by the Centre for Biomedical Image Analysis (CBIA), the project is situated at the intersection of computer science, machine learning, and biological imaging. CBIA provides a multidisciplinary environment, fostering collaboration between computer vision experts, biologists, and biomedical researchers. The research aims to address current limitations in evaluating segmentation, tracking, and lineage-reconstruction methods in microscopy. The goal is to design biologically meaningful, uncertainty-aware, and robust evaluation approaches that better reflect the needs of cell biology and biomedical imaging. Possible research directions include developing new metrics for segmentation and tracking, modeling inter-annotator variability, uncertainty-aware scoring, biology-driven composite metrics, stress-testing pipelines under various conditions, and creating open-source tools for reproducible evaluation. The exact topic will be tailored to the candidate’s background and interests in consultation with the supervisor. The position is part of a four-year doctoral programme in Informatics, delivered in English or Czech. Doctoral students are expected to conduct independent research, publish in international venues, participate in conferences and research stays, and contribute to the scientific community at CBIA and FI MU. Funding is available for full-time students, including a basic doctoral scholarship (18,000 CZK/month), an employment contract (20% FTE, ~7,000 CZK net/month), and a publication-performance scholarship (up to 7,000 CZK/month). Tuition is free for both Czech and English-language study. Active PhD students typically achieve a net monthly income of approximately 32,000 CZK during the standard study period. Applicants should have an MSc in Computer Science, Applied Mathematics, Biomedical Engineering, or a related field, with a strong background in machine learning, image analysis, and Python programming. Preferred qualifications include experience with microscopy image analysis, knowledge of image-processing metrics and benchmarking, familiarity with segmentation and tracking pipelines, C++/GPU/HPC experience, and publication or open-source contributions. To apply, submit your application through the Masaryk University e-application system. For further information or informal inquiries, contact the supervisor, Pavel Matula, at [email protected]. The application deadline is 30 April 2026, and the position is expected to start in Autumn 2026. For more details about CBIA and the research environment, visit CBIA . Supervisor profile: Pavel Matula .