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Robinson, Andrew; Sadr-kazemi, N.; Dickason, Gregory John; Harrison, Susan T.L.

doi:10.1023/a:1008816702162

Cited by 10 publications

(1 citation statement)

References 9 publications

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“…Automation of colony counting has been proposed with epi-illumination or a transillumination [72,73]. Sometimes a full separation of all the objects in view is difficult or not desired when one is interested in the number of elements of a cluster [74,75].Assuming the cells are convex the EDM provides an easy way to count the number of objects as illustrated in Fig. 12: the number of maxima found in the EDM images corresponds to the number of cells.…”

Section: Basic Treatmentmentioning

confidence: 99%

Biomass Quantification by Image Analysis

Pons

Vivier

1999

Bioanalysis and Biosensors for Bioprocess Monitoring

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Microbiologists have always rely on microscopy to examine microorganisms. When microscopy, either optical or electron-based, is coupled to quantitative image analysis, the spectrum of potential applications is widened: counting, sizing, shape characterization, physiology assessment, analysis of visual texture, motility studies are now easily available for obtaining information on biomass. In this chapter the main tools used for cell visualization as well as the basic steps of image treatment are presented. General shape descriptors can be used to characterize the cell morphology, but special descriptors have been defined for filamentous microorganisms. Physiology assessment is often based on the use of fluorescent dyes. The quantitative analysis of visual texture is still limited in bioengineering but the characterization of the surface of microbial colonies may open new prospects, especially for cultures on solid substrates. In many occasions, the number of parameters extracted from images is so large that data-mining tools, such as Principal Components Analysis, are useful for summarizing the key pieces of information.

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Section: Basic Treatmentmentioning

confidence: 99%

Biomass Quantification by Image Analysis

Pons

Vivier

1999

Bioanalysis and Biosensors for Bioprocess Monitoring

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Quantitative analysis of morphological changes in yeast colonies growing on solid medium: the eccentricity and Fourier indices

Prado

Rivas

Silóniz

et al. 2014

Yeast

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The colony shape of four yeast species growing on agar medium was measured for 116 days by image analysis. Initially, all the colonies are circular, with regular edges. The loss of circularity can be quantitatively estimated by the eccentricity index, E i , calculated as the ratio between their orthogonal vertical and horizontal diameters. E i can increase from 1 (complete circularity) to a maximum of 1.17-1.30, depending on the species. One colony inhibits its neighbour only when it has reached a threshold area. Then, E i of the inhibited colony increases proportionally to the area of the inhibitory colony. The initial distance between colonies affects those threshold values but not the proportionality, E i /area; this inhibition affects the shape but not the total surface of the colony. The appearance of irregularities in the edges is associated, in all the species, not with age but with nutrient exhaustion. The edge irregularity can be quantified by the Fourier index, F i , calculated by the minimum number of Fourier coefficients that are needed to describe the colony contour with 99% fitness. An ad hoc function has been developed in Matlab v. 7.0 to automate the computation of the Fourier coefficients. In young colonies, F i has a value between 2 (circumference) and 3 (ellipse). These values are maintained in mature colonies of Debaryomyces, but can reach values up to 14 in Saccharomyces. All the species studied showed the inhibition of growth in facing colony edges, but only three species showed edge irregularities associated with substrate exhaustion.

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