Fig. 1.

Image preprocessing and Colonies Segmentation. a Input image with three colonies (SalPhase movie). b Contourlet based denoising and adaptive histogram equalization used to sharpen cell edges. c Colony masks created using morphological filtering, Otsu’s global thresholding and Canny edge detection; they are used to separate colony regions from image background so that each colony can be processed separately in the pipeline (divide-and-conquer). d Adaptive thresholding is used to remove the colony’s local background pixels. e Multiplication of the image generated by adaptive thresholding with the corresponding extracted mask (Colony in the red rectangle) removes the noise (existing locally in the colony) and the artifacts (produced by the adaptive thresholding algorithm) while revealing cell objects inside the colony