scholarly journals Quantitative image analysis of microbial communities with BiofilmQ

2021 ◽  
Author(s):  
Raimo Hartmann ◽  
Hannah Jeckel ◽  
Eric Jelli ◽  
Praveen K. Singh ◽  
Sanika Vaidya ◽  
...  
Keyword(s):  
Image Analysis ◽  
Microbial Communities ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Software Tool ◽  
Image Cytometry ◽  
Quantitative Image Analysis ◽  
Space And Time ◽  
Quantitative Image ◽  
Three Dimensional Space

AbstractBiofilms 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.

scholarly journals BiofilmQ, a software tool for quantitative image analysis of microbial biofilm communities

2019 ◽  
Author(s):  
Raimo Hartmann ◽  
Hannah Jeckel ◽  
Eric Jelli ◽  
Praveen K. Singh ◽  
Sanika Vaidya ◽  
...  
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Software Tool ◽  
Image Cytometry ◽  
Microbial Life ◽  
Space And Time ◽  
Quantitative Image ◽  
Life On Earth ◽  
User Friendly ◽  
Three Dimensional Space

AbstractBiofilms 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.

BiofilmQ, a software tool for quantiative image analysis of microbial biofilm communities

2020 ◽  
Author(s):  
Hannah Jeckel ◽  
Raimo Hartmann ◽  
Eric Jelli ◽  
Knut Drescher ◽  
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Software Tool ◽  
Image Cytometry ◽  
Microbial Life ◽  
Space And Time ◽  
Life On Earth ◽  
User Friendly ◽  
Friendly Graphical User Interface ◽  
Three Dimensional Space

<p>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.</p>

Stereological Analysis Of Sem Images

1977 ◽  
Vol 35 ◽  
pp. 212-213
Author(s):  
H. S Schmiβer ◽  
R. A. Swensson
Keyword(s):  
Image Analysis ◽  
Three Dimensional ◽  
Quantitative Information ◽  
Quantitative Image Analysis ◽  
Sem Images ◽  
Detection Systems ◽  
The Past ◽  
Quantitative Image ◽  
Electron Microscopes ◽  
Scanning Electron Microscopes

Development of new signal detection systems for STEREOSCAN scanning electron microscopes has greatly increased the applicability of quantitative image analysis to pictures obtained with an s.e.m. While quantitative image analysis has proven to be a powerful technique to draw quantitative information from pictures obtained from light microscopes as well as various other sources of images, the field of scanninq electron microscopy has largely been uncovered in the past.This was mainly due to the particular appearance of “normal” s.e.m. pictures. Exactly those features which make s.e.m. pictures easy to interpret intuitively an aesthetically attractive i.e. the pseudo three dimensional appearance made it virtually impossible to treat these images with the well known methods of electronic image analysis.

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