Euro-BioImaging ISIDORe project “Automatic pipeline for brain autoradiography image analysis”

Turku BioImaging, in collaboration with Zuzana Čočková (Charles University, Prague) and Francisco Lopez-Picón (Turku PET Centre) developed the Mouse Brain Alignment Tool (MBAT), a Python-based software for processing autoradiographic (ARG) images of mouse brain tissue sections and analyzing them using topographical data from the Allen Institute’s Mouse Brain Atlas. The ARG images of mouse brain were from a study that investigates brain damage caused by COVID-19. This project was funded by the ISIDORe project of Euro-BioImaging through the Finnish Advanced Microscopy Node.

In June 2023, Zuzana visited TBI and developed the software together with Junel Solis, one of TBI’s image data analysts. The image is taken by Joanna Pylvänäinen.

The developed pipeline for analysis of ARG images will increase reliability and reproducibility as well as enable end-users to focus on image analysis without technical interruptions”, explains Junel. The source code repository will soon be made public and open source.

The project results were already presented by Zuzana and Junel at multiple events organised by Euro-BioImaging and Turku BioImaging such as Special Edition Virtual Pub “Showcasing Research & Stories from ISIDORe Users“, Image Data Expert Group, and Turku Imaging Day. In addition, there is an opportunity to learn more details about the MBAT development from Junel at CytoData2023 symposium on October 24, 2023.

This project an excellent opportunity for TBI to participate in an Euro-BioImaging image analysis project, and the TBI team is very proud of the outcomes!