Dataset Information

Quantitative image analysis of microbial communities with BiofilmQ.

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.

SUBMITTER: Hartmann R

PROVIDER: S-EPMC7840502 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Publications

Quantitative image analysis of microbial communities with BiofilmQ.

Hartmann Raimo R Jeckel Hannah H Jelli Eric E Singh Praveen K PK Vaidya Sanika S Bayer Miriam M Rode Daniel K H DKH Vidakovic Lucia L Díaz-Pascual Francisco F Fong Jiunn C N JCN Dragoš Anna A Lamprecht Olga O Thöming Janne G JG Netter Niklas N Häussler Susanne S Nadell Carey D CD Sourjik Victor V Kovács Ákos T ÁT Yildiz Fitnat H FH Drescher Knut K

Nature microbiology 20210104 2

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 prope ...[more]

PMID: 33398098

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Project description:BackgroundOptical coherence tomography (OCT) is an invaluable diagnostic tool for the detection and follow-up of retinal pathology in patients and experimental disease models. However, as morphological structures and layering in health as well as their alterations in disease are complex, segmentation procedures have not yet reached a satisfactory level of performance. Therefore, raw images and qualitative data are commonly used in clinical and scientific reports. Here, we assess the value of OCT reflectivity profiles as a basis for a quantitative characterization of the retinal status in a cross-species comparative study.MethodsSpectral-Domain Optical Coherence Tomography (OCT), confocal Scanning-Laser Ophthalmoscopy (SLO), and Fluorescein Angiography (FA) were performed in mice (Mus musculus), gerbils (Gerbillus perpadillus), and cynomolgus monkeys (Macaca fascicularis) using the Heidelberg Engineering Spectralis system, and additional SLOs and FAs were obtained with the HRA I (same manufacturer). Reflectivity profiles were extracted from 8-bit greyscale OCT images using the ImageJ software package (http://rsb.info.nih.gov/ij/).ResultsReflectivity profiles obtained from OCT scans of all three animal species correlated well with ex vivo histomorphometric data. Each of the retinal layers showed a typical pattern that varied in relative size and degree of reflectivity across species. In general, plexiform layers showed a higher level of reflectivity than nuclear layers. A comparison of reflectivity profiles from specialized retinal regions (e.g. visual streak in gerbils, fovea in non-human primates) with respective regions of human retina revealed multiple similarities. In a model of Retinitis Pigmentosa (RP), the value of reflectivity profiles for the follow-up of therapeutic interventions was demonstrated.ConclusionsOCT reflectivity profiles provide a detailed, quantitative description of retinal layers and structures including specialized retinal regions. Our results highlight the potential of this approach in the long-term follow-up of therapeutic strategies.

Dataset Information

Quantitative image analysis of microbial communities with BiofilmQ.

Publications

Quantitative image analysis of microbial communities with BiofilmQ.

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