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Figure 1 | BMC Systems Biology

Figure 1

From: Accurate, precise modeling of cell proliferation kinetics from time-lapse imaging and automated image analysis of agar yeast culture arrays

Figure 1

An overview of the YeastXtract image analysis algorithm. (a) A limited time series of four replicate cell arrays is shown. The arrays were created from serial 2-fold dilution of a 1:4 dilution of an overnight culture, skipping rows with each dilution and backfilling skipped rows. (b) A time series of one cell array from Panel A is shown at larger magnification. (c) Depiction of the first step of spot detection. A grid is created from the local maximum values after summing row and column pixel intensities over the entire array image (see Materials and Methods). The summed row and column pixel intensities are plotted at the edges of the array. (d) Depiction of the second step of spot detection. A cell containing each spot is defined by the 50 × 50 Pixel square surrounding the grid intersections shown in panel C. Within each cell, the horizontal and vertical diameters of each spot are calculated as the pixel distance between threshold values of summed column and row pixel intensities. An ellipse is drawn around each spot based on the resulting diameters. Spot detection is more precise for darker spots. Hence, the last time point is used for spot detection and those ellipses are used for extracting signal intensities from aligned time series of images of each cell array. (e) After spot detection, the background local to each spot is subtracted and remaining signal intensities are calculated by summing pixel values inside each ellipse. (f) Spot intensities are plotted versus time and used for growth modeling.

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