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Luis Ibanez commented on the mailing list's thread 'watershedImageFilter parameters for 3D CT images':

  • [If] you are working on a CT Image, it tends to be useful to do some denoising before running a Watershed filter.
  • A rule of thumb is to set the Threshold to be about 1 / 100 of the Level.
  • Typical values of level are 0.2 ~ 0.3. But of course, they vary with the structure that you want to extract, and the image that you are providing as input.
  • Please not that usually you want to run the watershed filter not in the image directly but in its GradientMagnitude image, ... unless... you are lucky enough to be searching for an anatomical structure that is dark and it is fully surrounded by brighter objects.
  • Note also, that the watershed filter will rarely provide a segmentation solution by looking at a single level. It is common to have to construct your segmentation by combining fragments that are extracted at different water levels.