Quantitative image analysis of microbial communities with BiofilmQ
Raimo HartmannMax Planck Institute for Terrestrial Microbiology, Marburg, GermanyHannah JeckelDepartment of Physics, Philipps-Universität Marburg, Marburg, GermanyEric JelliDepartment of Physics, Philipps-Universität Marburg, Marburg, GermanyPraveen K. SinghMax Planck Institute for Terrestrial Microbiology, Marburg, GermanySanika VaidyaMax Planck Institute for Terrestrial Microbiology, Marburg, GermanyMiriam BayerMax Planck Institute for Terrestrial Microbiology, Marburg, GermanyDaniel K.H. RodeDepartment of Physics, Philipps-Universität Marburg, Marburg, GermanyLucia VidakovicMax Planck Institute for Terrestrial Microbiology, Marburg, GermanyFrancisco Díaz-PascualMax Planck Institute for Terrestrial Microbiology, Marburg, GermanyJiunn C. N. FongDepartment of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, USAAnna DragošBacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, DenmarkOlga LamprechtEawag, Swiss Federal Institute of Aquatic Science and Technology, Dubendorf, SwitzerlandJanne G. ThömingDepartment of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, DenmarkNiklas NetterDepartment of Physics, Philipps-Universität Marburg, Marburg, GermanySusanne HäußlerDepartment of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, DenmarkCarey D. NadellDepartment of Biological Sciences, Dartmouth College, Hanover, NH, USAVictor SourjikMax Planck Institute for Terrestrial Microbiology, Marburg, GermanyÁkos T. KovácsBacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, DenmarkFitnat H. YildizDepartment of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, USAKnut DrescherDepartment of Physics, Philipps-Universität Marburg, Marburg, Germany. [email protected]
2021en
ABI
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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Citations and references
Cited by 20 references