PhD Position: Improving Evaluation Frameworks for Microscopy Image Analysis Masaryk University in Czech Republic

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 in a multidisciplinary environment at the intersection of computer science, microscopy, image analysis, and biomedical research. The research aims to address current limitations in evaluating segmentation, tracking, and lineage-reconstruction methods in microscopy, with a focus on designing biologically meaningful, uncertainty-aware, and robust evaluation approaches that better reflect the needs of cell biology and biomedical imaging.

Possible research directions include developing evaluation metrics for segmentation, tracking, and lineage reconstruction; modeling inter-annotator variability and imperfect ground truth; uncertainty-aware scoring and confidence intervals for algorithm performance; biology-driven composite metrics (such as shape, cell counts, division timing, migration behavior); stress-testing pipelines under noise, bleaching, drift, and domain shift; benchmark design and simulation of realistic error modes; and the development of open-source tools for reproducible evaluation. The exact research topic will be specified in collaboration with the supervisor, based on the candidate’s background and interests.

The position is embedded in a four-year doctoral programme in Informatics, 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, and contribute to the scientific community of CBIA and FI MU.

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 per month, an employment contract (20% FTE) with a net monthly salary of approximately 7,000 CZK, and a publication-performance scholarship of up to 7,000 CZK per month. Active PhD students typically achieve 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. Essential qualifications include a solid background in machine learning and image analysis, programming skills in Python, and a strong mathematical foundation. Preferred qualifications are experience with microscopy image analysis or biomedical imaging, knowledge of image-processing metrics, benchmarking, or statistical evaluation, familiarity with segmentation and tracking pipelines, C++/GPU/HPC experience, and publication or open-source contributions. The doctoral programme is delivered in English or Czech, and proficiency in one of these languages is required.

To apply, candidates should submit their application through the Masaryk University e-application system. For informal inquiries about the research topic, contact Associate Professor Pavel Matula at [email protected]. Further information about CBIA can be found at https://cbia.fi.muni.cz/, and the supervisor’s academic profile is available at https://www.muni.cz/en/people/2927.

The application deadline is November 30, 2026. This position is ideal for candidates seeking to contribute to cutting-edge research in biomedical image analysis, computer vision, and machine learning within a collaborative and supportive academic environment.