Seeded Watershed 3D

Classical Watershed 3D Algorithm

Pre-filters to apply before this algorithm

The Algorithm


  • The watershed is seeded with Regional Minima of the watershed map (given as a parameter, which is usually the gradient of the input image), in order to limit over-segmentation
  • Propagation : propagation is done in the ascending order of the watershed map, starting from the seeds. It is a 6-connectivity propagation. Propagation is done on the whole image.
  • As there is no constraint on seed and no limit for propagation, this algorithm detects well the edges of objects.


This algorithm can produce over-segmentation. This can be corrected with (at least) 3 operations:
  • Reducing the noise during before computing the watershed map
  • Increasing the derivation radius and/or applying filters on the watershed map
  • Using the post-filter Merge Regions


  • As the algorithm segments the whole image into regions, regions corresponding to background have to be removed. This can be done using the post-filter Erase Spots. It can be applied several time in order to have several criteria
  • In case of over-segmentation: Merge Regions
  • Classical morphological operations


  • Spots-like objects like chromocenters
  • If objects are too small, they might not be segmented properly.


This procedure is adapted from a procedure developed by Dr. Philippe Andrey and his team