Trapalyzer: A computer program for quantitative analyses in fluorescent live-imaging studies of Neutrophil Extracellular Trap formation

Neutrophil extracellular traps (NETs), pathogen-ensnaring structures formed by neutrophils by expelling their DNA into the environment, are believed to play an important role in immunity and autoimmune diseases. In recent years, a growing attention has been put into developing software tools to quantify NETs in fluorescent microscopy images. However, current solutions require extensive training data sets, are difficult to use for users without background in computer science, or have limited capabilities. In this work we present Trapalyzer, a computer program for an automatic quantification of NETs in terms of their area and an approximation of their number. In addition, Trapalyzer counts neutrophils at different stages of NET formation, and is the first tool that makes this possible without extensive training data sets. We validate our approach on a publicly available benchmark data set and apply it in a neutrophil-bacteria co-culture experiment. The software and usage tutorials are available at https://github.com/Czaki/Trapalyzer.