PhD Position: Improving Evaluation Frameworks for Microscopy Image Analysis

About the project

About the Project PhD Position: Improving Evaluation Frameworks for Microscopy Image Analysis Faculty of Informatics, Masaryk University (FI MU), Brno, Czech Republic Supervisor: Pavel 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 focused on next-generation evaluation frameworks for microscopy image analysis , combining ideas from computer vision, machine learning, and biological imaging. The project will be carried out within the Centre for Biomedical Image Analysis (CBIA) at the Faculty of Informatics, Masaryk University. CBIA offers a multidisciplinary environment working at the interface of computer science, microscopy, image analysis, and biomedical research. The PhD research will address current limitations in how segmentation, tracking, and lineage-reconstruction methods are assessed in microscopy. The aim is to design biologically meaningful, uncertainty-aware, and robust evaluation approaches that better reflect the actual needs of cell biology and biomedical imaging. Possible Research Directions Evaluation metrics for segmentation, tracking, and lineage reconstruction Modelling inter-annotator variability & imperfect ground truth Uncertainty-aware scoring and confidence intervals for algorithm performance Biology-driven composite metrics (shape, cell counts, division timing, migration behaviour) Stress-testing pipelines under noise, bleaching, drift, and domain shift Benchmark design and simulation of realistic error modes Development of open-source tools for reproducible evaluation The exact topic will be specified jointly with the supervisor based on the candidate’s background and interests. 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 in international venues Participate in conferences and research stays Contribute to the scientific community of CBIA and FI MU 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 achieve ~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 Solid background in machine learning / image analysis Programming skills (Python) Strong mathematical foundation Preferred Experience with microscopy image analysis or biomedical imaging Knowledge of image-processing metrics, benchmarking, or statistical evaluation Familiarity with segmentation / tracking pipelines C++ / GPU / HPC experience Publication or open-source contributions 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: Pavel Matula Faculty of Informatics, Masaryk University Email: pam@fi.muni.cz Web: https://www.muni.cz/en/people/2927

Research areas