Biofilm image reconstruction for assessing structural parameters

Renslow, Ryan; Lewandowski, Zbigniew; Beyenal, Haluk

doi:10.1002/bit.23060

Cited by 24 publications

(13 citation statements)

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“…Beyond the reproducibility of the biofilm electrode surface, simply characterizing biofilm structure itself has historically been difficult (Yang et al 2000, 2001; Renslow et al 2011b). Furthermore, the result of biofilm heterogeneity is the local variation of not only diffusion coefficients, but local flow velocities as well (Beyenal et al 1998; Beyenal and Lewandowski 2001, 2002; Renslow et al 2010).…”

Section: Electrochemical Techniques For Studying Extracellular Electrmentioning

confidence: 99%

Electrochemically active biofilms: facts and fiction. A review

et al. 2012

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This review examines the electrochemical techniques used to study extracellular electron transfer in the electrochemically active biofilms that are used in microbial fuel cells and other bioelectrochemical systems. Electrochemically active biofilms are defined as biofilms that exchange electrons with conductive surfaces: electrodes. Following the electrochemical conventions, and recognizing that electrodes can be considered reactants in these bioelectrochemical processes, biofilms that deliver electrons to the biofilm electrode are called anodic, ie electrode-reducing, biofilms, while biofilms that accept electrons from the biofilm electrode are called cathodic, ie electrode-oxidizing, biofilms. How to grow these electrochemically active biofilms in bioelec-trochemical systems is discussed and also the critical choices made in the experimental setup that affect the experimental results. The reactor configurations used in bioelectrochemical systems research are also described and the authors demonstrate how to use selected voltammetric techniques to study extracellular electron transfer in bioelectrochemical systems. Finally, some critical concerns with the proposed electron transfer mechanisms in bioelectrochemical systems are addressed together with the prospects of bioelectrochemical systems as energy-converting and energy-harvesting devices.

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Section: Electrochemical Techniques For Studying Extracellular Electrmentioning

confidence: 99%

Electrochemically active biofilms: facts and fiction. A review

et al. 2012

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“…For example, Xavier et al (2003) developed an automated biofilm morphology software toolbox based on three-dimensional confocal laser scanning microscopy (CLSM) images, which allows the automated quantification of such features as area of microbial colonization, biovolume, colony height, and more. Renslow et al (2011) used computerized biofilm binary image reconstructions to compare such structural parameters as cell cluster shapes and their spatial relations within the biofilm. Bridier et al (2010) performed a three-dimensional computerized analysis of 60 opportunistic pathogens with biovolume, thickness, substratum coverage, and roughness values for each.…”

Section: Introductionmentioning

confidence: 99%

Bacillus subtilis Biofilm Development – A Computerized Study of Morphology and Kinetics

et al. 2017

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Biofilm is commonly defined as accumulation of microbes, embedded in a self-secreted extra-cellular matrix, on solid surfaces or liquid interfaces. In this study, we analyze several aspects of Bacillus subtilis biofilm formation using tools from the field of image processing. Specifically, we characterize the growth kinetics and morphological features of B. subtilis colony type biofilm formation and compare these in colonies grown on two different types of solid media. Additionally, we propose a model for assessing B. subtilis biofilm complexity across different growth conditions. GFP-labeled B. subtilis cells were cultured on agar surfaces over a 4-day period during which microscopic images of developing colonies were taken at equal time intervals. The images were used to perform a computerized analysis of few aspects of biofilm development, based on features that characterize the different phenotypes of B. subtilis colonies. Specifically, the analysis focused on the segmented structure of the colonies, consisting of two different regions of sub-populations that comprise the biofilm – a central “core” region and an “expanding” region surrounding it. Our results demonstrate that complex biofilm of B. subtillis grown on biofilm-promoting medium [standard lysogeny broth (LB) supplemented with manganese and glycerol] is characterized by rapidly developing three-dimensional complex structure observed at its core compared to biofilm grown on standard LB. As the biofilm develops, the core size remains largely unchanged during development and colony expansion is mostly attributed to the expansion in area of outer cell sub-populations. Moreover, when comparing the bacterial growth on biofilm-promoting agar to that of colonies grown on LB, we found a significant decrease in the GFP production of colonies that formed a more complex biofilm. This suggests that complex biofilm formation has a diminishing effect on cell populations at the biofilm core, likely due to a combination of reduced metabolic rate and increased levels of cell death within this region.

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“…2d). Biofilm segmentation algorithms have received significant attention in the literature [15][16][17][18][19][20][21] . BiofilmQ therefore offers different segmentation workflows: either semi-manual segmentation supported by immediate visual feedback, or via automatic segmentation algorithms, such as Otsu, Ridler-Calvard, robust background, or maximum correlation thresholding.…”

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confidence: 99%

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

Hartmann

Jeckel

Jelli

et al. 2019

Preprint

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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 singlecell 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. Main TextMicrobial biofilm communities shape the Earth by contributing to the biogeochemical cycles in soil, sediments, oceans, and the plant microbiota 1 . Microbial communities are also an integral part of human health, due to their functions in the intestinal and oral microbiota, as well as in infections, where cells that are bound in biofilms can display a 1000-fold higher tolerance to antibiotics than planktonic cells 2 . Biofilms are generally three-dimensional (3D) communities that display spatial gradients of nutrients and many other diffusible molecular compounds, as well as spatiotemporal variation in species composition and cellular differentiation 3,4 . Due to the spatial heterogeneity of phenotypes and genotypes inside biofilms, studies of biofilms often rely on 3D fluorescence imaging, e.g. using confocal microscopy. For biofilm phenotyping, and for characterizing phenotypes of particular cells within biofilms, it is critical to be able to perform image-based quantitative measurements of fluorescent reporters and structural features for particular regions inside the biofilm.Extracting the desirable information from 3D images relies on non-trivial automated image analysis. The most widely-used tool for biofilm image analysis in the literature is COMSTAT 5 , which was released almost 20 years ago and provided one of the first tools to objectively determine differences in biofilm morphology. More recent software tools 6-8 were released 10

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Biofilm image reconstruction for assessing structural parameters

Cited by 24 publications

References 47 publications

Electrochemically active biofilms: facts and fiction. A review

Electrochemically active biofilms: facts and fiction. A review

Bacillus subtilis Biofilm Development – A Computerized Study of Morphology and Kinetics

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

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