High-throughput bacterial aggregation analysis in droplets

The communal lifestyle of bacteria manifested as bacterial aggregation and potential biofilm formation is posing as a significant contributor to antimicrobial resistance. A key approach to adress the emerging pandemic is to implement novel techniques that enhance the precision and speed of analysis in various microbiological experiments. Droplet-based platforms coupled with image analysis techniques exhibit great potential in advancing the precision of investigating bacterial behaviour and increasing the speed of microbiological experiments. As most of the image analysis techniques require advanced programming skills or implement high-priced fees, open-source software interweaving user-friendly interface is in great demand. In this paper, we introduce two image analysis pipelines constructed in CellProfilerTM to quantify bacterial aggregation responding to a presence of microplastics as well as suboptimal concentrations of antibiotics in droplets.