Color properties of the images were calculated based on the standard HSV model (Hue, Saturation, and Value) using the MATLAB image processing toolbox built-in functions (MATLAB and Image Processing Toolbox Release 2012b, The MathWorks, Inc., Natick, Massachusetts, United States). 1) Hue is the degree to which a stimulus can be described as similar to or different from stimuli that are described as red, green, or blue. Hue describes a dimension of color that is readily experienced (i.e., the dominant wavelength in the color). We calculated the average hue across all image pixels and the average standard deviation of hue across all of an image's pixels for each image. The average hue represents the hue level of the image and the 2) standard deviation of hue (SDhue) represents the degree of diversity in the image's hue. 3) Saturation (Sat) is the degree of dominance of hue mixed in the color, or the ratio of the dominant wavelength to other wavelengths in the color. We calculated the average saturation of each image across all image pixels, as well as the 4) standard deviation of saturation for each image (SDsat). We also measured the overall darkness-to-lightness of a pixel's color depending on the brightness of the pixel. This dimension of color is called 5) Brightness (Bright) or the value of the color. We computed the average brightness of all pixels for each image, as well as the 6) standard deviation of brightness in each image (SDbright). Fig. 5 shows hue, saturation, and brightness maps of a sample image in our experiment, and Fig. 6 compares two images in terms of their color diversity (SDHue, SDSat and SDbright).
To determine if explosive cell lysis was a conserved phenomenon in P. aeruginosa strains, we cultured interstitial biofilms of the common laboratory strains PAK, PAO1, PA103, PA14, ATCC27853, five CF clinical isolates and two non-CF clinical isolates, and quantified the frequency of round cells and sites of eDNA release as a marker for explosive cell lysis. To quantify the frequency of round cells in P. aeruginosa interstitial biofilms, randomly selected fields of view of the interstitial biofilm monolayer were imaged with phase contrast microscopy and analysed via computer vision to identify cells and categorize their morphotypes as rod or round cells. Round cells were observed in all strains, although the frequency of round cells varied from about 1 per 3,000 to 1 per 100,000 rod cells in different strains (Supplementary Fig. 1a). Similar frequencies of punctate eDNA sites were observed in the interstitial biofilms of all strains (Supplementary Fig. 1b). These observations suggest that while eDNA release through explosive cell lysis occurs in many P. aeruginosa strains, the survival times of round cells appear to vary between strains that is reflected in the number of round cells visible in the population at any instant in time.
computer vision toolbox matlab 2012b 15
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L.T., A.L.H., N.K.P., S.R.O., E.S.G., R.C., L.G.M., X.Y., C.B.W., M.T., M.K., G.P., G.C. and S.I. conducted experiments; G.P., U.O. and C.H.A. conducted DNA- and RNA-seq data analyses; R.S. programmed BacFormatics and conducted computer vision analyses; L.T., A.L.H., N.K.P., S.R.O., E.S.G., R.C., L.G.M., I.G.C., C.B.W., M.T., M.K., G.P., G.O., U.O., C.H.A., N.N. and L.E. analysed results; C.B.W., M.T. and L.E. wrote the manuscript; all authors reviewed the manuscript. 2ff7e9595c
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