Student projects

Research topics and projects

The following is a non-exhaustive list of topics for research projects for which students (all levels) are welcome to apply. If you have an idea or a project, but you do not find something that fits below, you can still inquire about it and we may find an arrangement.

Contact: Vlad Popovici, popovici@iba.muni.cz

Digital pathology annotation tool

Digital pathology is a special case of medical image processing, where the main interest is the analysis of microscopy images. The technological development allows the scanning and storage of large collections of images histology microscope slides. However, making full use of such content-rich images is extremely challenging.

The goal of the project is the design and implemention of a tool for annotating digital pathology images. The tool will be used by pathologists/researchers to annotate new images or to detect, analyze and import existing annotation markings on the microscope slides.

The tool will allow the annotation of extremely large images by selecting circular or polygonal regions; adding free-text or dictionary-based labels. At the same time, the tool must allow importing existing annotation (like hand-drawn regions) from the scanned images, by (semi-)automatically detecting them. Finally, the tool will handle multiple annotations, created by different experts.

Requirements: Python or Java; image processing; pattern recognition; ImageJ API is a plus


Parallel tools for digital microscopy image processing

Digital pathology is a special case of medical image processing, where the main interest is the analysis of microscopy images. The technological development allows the scanning and storage of large collections of images histology microscope slides. However, making full use of such content-rich images is extremely challenging.

The goal of the project is to design and implement a library of routines for basic parallel image processing of large microscopy images.

The library will address the needs of image processing (e.g. image restoration, denoising, pyramidal decomposition, etc) specific to microscopy imaging. The routines will be implemented on a mixed environment in which both the grid computing infrastructure and the multi-core  architecture of individual computing nodes will be exploited.

Requirements: Python or C++ or Java; image processing; parallel computing