Quantitative image analysis of microbial communities with BiofilmQ
Raimo Hartmann, Hannah Jeckel, Eric Jelli, Praveen K. Singh, Sanika Vaidya, Miriam Bayer, Daniel K.H. Rode, Lucia Vidakovic, Francisco Díaz-Pascual, Jiunn C. N. Fong, Anna Dragoš, Olga Lamprecht, Janne G. Thöming, Niklas Netter, Susanne Häußler, Carey D. Nadell, Victor Sourjik, Ákos T. Kovács, Fitnat H. Yildiz, Knut Drescher
Abstract
Biofilms are microbial communities that represent a highly abundant form of microbial life on Earth. Inside biofilms, phenotypic and genotypic variations occur in three-dimensional space and time; microscopy and quantitative image analysis are therefore crucial for elucidating their functions. Here, we present BiofilmQ-a comprehensive image cytometry software tool for the automated and high-throughput quantification, analysis and visualization of numerous biofilm-internal and whole-biofilm properties in three-dimensional space and time.