Figure 3.

Colony Detection and Segmentation Pipeline

The raw image is processed by the difference of erosion and dilation followed by Otsu thresholding to create the first mask. The raw image is also processed by removing the background level through fast Fourier transform, creating a background subtracted image, from which we extract the gradient and local contrast and produce two more masks through Otsu thresholding. The three masks are added together and if the pixel value is greater than 1, the object is incorporated into the final mask. The outline and label of the final mask is added to the raw image to show the outcome of the segmentation. Scale bar, 500 μm.