Quantitative image analysis of microbial communities with BiofilmQ.
Raimo HartmannHannah JeckelEric JelliPraveen K SinghSanika VaidyaMiriam BayerDaniel K H RodeLucia VidakovicFrancisco Díaz-PascualJiunn C N FongAnna DragošOlga LamprechtJanne Gesine ThömingNiklas NetterSusanne HäußlerCarey D NadellVictor SourjikÁkos T KovácsFitnat H YildizKnut DrescherPublished in: Nature microbiology (2021)
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.