The CELLIM shared laboratory at CEITEC produces a large number of often sizeable experimental datasets. The lab is involved in optical microscopy and therefore produces mostly image data. The measured data needs to be stored, visualized, further processed, and shared with the scientific community. The entire data workflow of the lab needs to comply with the FAIR principles so that the data and metadata are ready for publication to repositories.

The OMERO system provides tools for visualizing, annotating, managing, and sharing scientific image data within a research group or even the international scientific community. All the mentioned features of the system can improve the way users and lab operators work with data and allow them to apply other, not yet easily accessible methods, for image data processing.

The student will become familiar with the OMERO system and the existing workflow of the laboratory. Based on the information learned, the student will suggest ways in which the OMERO system could be used to improve the laboratory's operations. The work will include the possible implementation of their own automation software. The system will be deployed in test mode in the laboratory and presented to the laboratory staff. According to the feedback received, the student will evaluate the proposed solution and modify it if necessary.

Furthermore, the thesis will deal with the interconnection of the OMERO system and the Onedata distributed data management system. The student will propose a procedure or implement a connector that will allow the processing of data stored in the Onedata system in the OMERO system. Documentation for the proposed solution will be created for its installation and operation.