There is a strong interest in understanding community assembly and dynamics. Experimental approaches using phytoplankton have proven to be extremely insightful to unravel underlying biological processes. Imaging flow cytometry is an emerging method becoming more and more popular in different fields. It allows us to capture changes within a community or population in a more efficient way. As part of this project, we develop interactive and AI-based approaches to automatically quantify these experiments. The tools we develop are independent of application and will support all kinds of researchers inside and outside of Helmholtz working with imaging flow cytometry.