Quantitative image analysis of microbial communities with BiofilmQ
Raimo Hartmann(Max Planck Institute for Terrestrial Microbiology), Hannah Jeckel(Philipps University of Marburg), Eric Jelli(Philipps University of Marburg), Praveen K. Singh(Max Planck Institute for Terrestrial Microbiology), Sanika Vaidya(Max Planck Institute for Terrestrial Microbiology), Miriam Bayer(Max Planck Institute for Terrestrial Microbiology), Daniel K.H. Rode(Philipps University of Marburg), Lucia Vidakovic(Max Planck Institute for Terrestrial Microbiology), Francisco Díaz-Pascual(Max Planck Institute for Terrestrial Microbiology), Jiunn C. N. Fong(University of California, Santa Cruz), Anna Dragoš(Technical University of Denmark), Olga Lamprecht(Max Planck Institute for Terrestrial Microbiology), Janne G. Thöming(Copenhagen University Hospital), Niklas Netter(Philipps University of Marburg), Susanne Häußler(Copenhagen University Hospital), Carey D. Nadell(Dartmouth College), Victor Sourjik(Loewe Center for Synthetic Microbiology), Ákos T. Kovács(Technical University of Denmark), Fitnat H. Yildiz(University of California, Santa Cruz), Knut Drescher(Philipps University of Marburg)
Cited by 357Open Access
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.
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