RT Journal Article
SR Electronic
T1 BiofilmQ, a software tool for quantitative image analysis of microbial biofilm communities
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 735423
DO 10.1101/735423
A1 Raimo Hartmann
A1 Hannah Jeckel
A1 Eric Jelli
A1 Praveen K. Singh
A1 Sanika Vaidya
A1 Miriam Bayer
A1 Lucia Vidakovic
A1 Francisco Díaz-Pascual
A1 Jiunn C.N. Fong
A1 Anna Dragoš
A1 Olga Besharova
A1 Carey D. Nadell
A1 Victor Sourjik
A1 Ákos T. Kovács
A1 Fitnat H. Yildiz
A1 Knut Drescher
YR 2019
UL http://biorxiv.org/content/early/2019/08/15/735423.abstract
AB Biofilms are now considered to be the most abundant form of microbial life on Earth, playing critical roles in biogeochemical cycles, agriculture, and health care. Phenotypic and genotypic variations in biofilms generally occur in three-dimensional space and time, and biofilms are therefore often investigated using microscopy. However, the quantitative analysis of microscopy images presents a key obstacle in phenotyping biofilm communities and single-cell heterogeneity inside biofilms. Here, we present BiofilmQ, a comprehensive image cytometry software tool for the automated high-throughput quantification and visualization of 3D and 2D community properties in space and time. Using BiofilmQ does not require prior knowledge of programming or image processing and provides a user-friendly graphical user interface, resulting in editable publication-quality figures. BiofilmQ is designed for handling fluorescence images of any spatially structured microbial community and growth geometry, including microscopic, mesoscopic, macroscopic colonies and aggregates, as well as bacterial biofilms in the context of eukaryotic hosts.