3 Jul 2020

Interactive Top-Hat by Reconstruction.

This module provides an interactive Top-Hat segmentation that prevents from segmenting false positive porosity on the edges.


This module is a specialized version of the embedded Top-Hat segmentation within Amira and Avizo (tool selection of the Segmentation Editor and Interactive Top-Hat module).

This specialization of the Top-Hat segmentation is better suited for segmenting porosity as it prevents small cavities on the edges to be identified as such.

By decomposing the internal workflow of the Top-Hat segmentation and replacing the "simple" closing/opening operation (segmentation of white/back elements) by a closing by reconstruction/opening by reconstruction operation, the Top-Hat image generated is then edge-preserved. The key of the technique here is to use the closed/opened image as a marker image for the grayscale reconstruction, rather than directly subtracting the input image from it to compute the Top-Hat image. Instead the grayscale reconstruction will erode/dilate the marker image progressively and keep the maximum/minimum value for each voxel between the eroded/dilated marker image and the input image. This does guarantee that the edges will be preserved. After that process has finally converged then the subtraction is eventually performed to compute the Top-Hat image.

Besides, the Interactive Top-Hat by Reconstruction module will have the exact same look as the Interactive Top-Hat module and will share the same characteristics:

  • 2 steps wizard module:
    - Generation of the Top-Hat image.
    - Interactive thresholding of the Top-Hat image.
  • Same ports (but here the Neighborhood and Kernel Size ports drive the internal Closing by Reconstruction/Opening by Reconstruction module instead of the old internal Closing/Opening module).