Biofilms – highly organised microbial communities – are often the hidden cause of recurrent infections in humans and animals, as well as contamination in food and pharmaceutical production. As these communities grow into 3D structures, microscopy is becoming increasingly important for their investigation, while imaging data processing requires multidisciplinary expertise. At the IJS, through collaboration between three departments (Biotechnology – B3, Knowledge Technologies – E8 and Condensed Matter Physics – F5), we have developed a new tool for analysing biofilm images called MicroICS, currently the only tool that combines analysis of confocal fluorescence images of biofilms with machine learning. It consists of three modules: the first converts images into quantitative structural features; in the second, we train models to understand how these features relate to the biological context; and in the third, we use the trained models to predict and classify new images. We have published an article on its development and functionalities in the journal npj Biofilms and Microbiomes.