ScatterJ: An ImageJ plugin for the evaluation of analytical microscopy datasets

Zeitvogel, Fabian; Schmid, Gregor; Hao, Likai; Ingino, Pablo; Obst, Martin

doi:10.1111/jmi.12187

Cited by 49 publications

(42 citation statements)

References 35 publications

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“…The colocalization of iron and Psl matrix was analyzed by using the Interactive 3D Surface Plot plugin of the ImageJ software (version 1.43u; NIH). The colocalization of iron and Psl in biofilm images was analyzed and calculated as previously described (41). Swarming assay.…”

Section: Methodsmentioning

confidence: 99%

A Survival Strategy for Pseudomonas aeruginosa That Uses Exopolysaccharides To Sequester and Store Iron To Stimulate Psl-Dependent Biofilm Formation

Wei

Zhao

et al. 2016

Appl Environ Microbiol

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Exopolysaccharide Psl is a critical biofilm matrix component in Pseudomonas aeruginosa, which forms a fiber-like matrix to enmesh bacterial communities. Iron is important for P. aeruginosa biofilm development, yet it is not clearly understood how iron contributes to biofilm development. Here, we showed that iron promoted biofilm formation via elevating Psl production in P. aeruginosa. The high level of iron stimulated the synthesis of Psl by reducing rhamnolipid biosynthesis and inhibiting the expression of AmrZ, a repressor of psl genes. Iron-stimulated Psl biosynthesis and biofilm formation held true in mucoid P. aeruginosa strains. Subsequent experiments indicated that iron bound with Psl in vitro and in biofilms, which suggested that Psl fibers functioned as an iron storage channel in P. aeruginosa biofilms. Moreover, among three matrix exopolysaccharides of P. aeruginosa, Psl is the only exopolysaccharide that can bind with both ferrous and ferric ion, yet with higher affinity for ferrous iron. Our data suggest a survival strategy of P. aeruginosa that uses exopolysaccharide to sequester and store iron to stimulate Psl-dependent biofilm formation. IMPORTANCEPseudomonas aeruginosa is an environmental microorganism which is also an opportunistic pathogen that can cause severe infections in immunocompromised individuals. It is the predominant airway pathogen causing morbidity and mortality in individuals affected by the genetic disease cystic fibrosis (CF). Increased airway iron and biofilm formation have been proposed to be the potential factors involved in the persistence of P. aeruginosa in CF patients. Here, we showed that a high level of iron enhanced the production of the key biofilm matrix exopolysaccharide Psl to stimulate Psl-dependent biofilm formation. Our results not only make the link between biofilm formation and iron concentration in CF, but also could guide the administration or use of iron chelators to interfere with biofilm formation in P. aeruginosa in CF patients. Furthermore, our data also imply a survival strategy of P. aeruginosa under high-iron environmental conditions. P seudomonas aeruginosa is a ubiquitous environmental microorganism. It is also an opportunistic pathogen that is often found in the hospital environment. P. aeruginosa can cause severe acute nosocomial infections in immunocompromised individuals or chronic lung infections in cystic fibrosis (CF) patients (1). These infections generally persist despite the use of intensive antimicrobial therapy and have been linked to the formation of antibiotic-resistant biofilms, wherein bacterial cells were encased in an extracellular polymeric substance (EPS) matrix (2, 3). It is generally accepted that the biofilm matrix functions as both a structural scaffold and protective barrier for bacteria in biofilms (4, 5). The iron content of CF sputum is often highly increased compared to that in the sputum of healthy controls, which has also been considered a potential factor in the persistence of P. aeruginosa (6-8). Mineral elem...

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Section: Methodsmentioning

confidence: 99%

A Survival Strategy for Pseudomonas aeruginosa That Uses Exopolysaccharides To Sequester and Store Iron To Stimulate Psl-Dependent Biofilm Formation

Wei

Zhao

et al. 2016

Appl Environ Microbiol

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“…It is published under the GNU GPL v.3 license and available at https://savannah.nongnu.org/projects/ scatterjn. The plugin was written in Java and is partly based on ScatterJ [1], a scatterplot tool for pairwise analysis of images.…”

Section: Implementation and Architecturementioning

confidence: 99%

“…Therefore, the density of datapoints in the scatterplots is visualized using an adaptable colour scale. For a more detailed description see [1]. It is possible for the user to adjust display parameters such as the colour scale used for the scatterplots and labels in the scatterplot matrix image.…”

Section: User-defined Display Settingsmentioning

confidence: 99%

“…The resulting maps (as shown in the figure) of course no longer represent exact matrices of measured values, but probability distributions of the respective elements. This procedure is sometimes helpful when dealing with EDX maps [1,17] or any other, similar image data.…”

Section: Example Dataset: Acquisition and Pre-processingmentioning

confidence: 99%

“…From spatially resolved chemical information of samples such as elemental or species maps, it is possible to derive information about reaction mechanisms and processes [1]. Methods that allow for the spatially resolved chemical analysis of samples on the micron and submicron scales include scanning electron microscopy (SEM) and transmission electron microscopy (TEM), both in combination with energy-dispersive X-ray spectroscopy (EDX) mapping, nanoscale secondary ion mass spectrometry (nanoSIMS), scanning transmission X-ray microscopy (STXM), and confocal laser scanning microscopy (CLSM).…”

Section: Introductionmentioning

confidence: 99%

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ScatterJn: An ImageJ Plugin for Scatterplot-Matrix Analysis and Classification of Spatially Resolved Analytical Microscopy Data

Zeitvogel¹,

Obst

2016

JORS

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We present ScatterJn, an ImageJ (and Fiji) plugin for scatterplot-based exploration and analysis of analytical microscopy data. In contrast to commonly used scatterplot tools, it handles more than two input images (or image stacks, respectively) by creating a matrix of pairwise scatterplots. The tool offers the possibility to manually classify pixels by selecting regions of datapoints in the scatterplots as well as in the spatial domain. We demonstrate its functioning using a set of elemental maps acquired by SEM-EDX mapping of a soil sample. The plugin is available at https://savannah.nongnu.org/projects/scatterjn.

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Dreidimensionale Tomographie im mittleren Infrarotbereich von endogenen und exogenen Molekülen in einer einzelnen Zelle mit subzellulärer Auflösung

et al. 2014

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ScatterJ: An ImageJ plugin for the evaluation of analytical microscopy datasets

Cited by 49 publications

References 35 publications

A Survival Strategy for Pseudomonas aeruginosa That Uses Exopolysaccharides To Sequester and Store Iron To Stimulate Psl-Dependent Biofilm Formation

A Survival Strategy for Pseudomonas aeruginosa That Uses Exopolysaccharides To Sequester and Store Iron To Stimulate Psl-Dependent Biofilm Formation

ScatterJn: An ImageJ Plugin for Scatterplot-Matrix Analysis and Classification of Spatially Resolved Analytical Microscopy Data

Dreidimensionale Tomographie im mittleren Infrarotbereich von endogenen und exogenen Molekülen in einer einzelnen Zelle mit subzellulärer Auflösung

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