April 2020
Intermediate to advanced
438 pages
12h 2m
English
Content preview from Python Image Processing Cookbook
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Segmentation with watershed
In this example, you will learn how to use the SimpleITK library functions to segment bacteria from a three-dimensional focused ion beam-scanning electron microscopy (FIB-SEM) image. The name of the bacterium is bacillus subtilis—it is a rod-shaped organism and is naturally found in plants and soil. Here are the steps involved:
- Read the bacteria image and separate the foreground (bacteria) from the background (resin) using thresholding with a manually chosen threshold. Use morphological opening and closing to get rid of small components/holes with the following code block:
img = sitk.ReadImage('images/fib_sem_bacillus_subtilis_slice_118.png', sitk.sitkFloat32)f = sitk.RescaleIntensityImageFilter()img = f.Execute(img, ...Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
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