3 Jul 2020

Interactive Top-Hat by Reconstruction

This module provides an interactive Top-Hat segmentation that prevents the segmentation of "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 because 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 edge-preserved. The key to this technique 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 erodes/dilates the marker image progressively and keeps the maximum/minimum value for each voxel between the eroded/dilated marker image and the input image. This guarantees that the edges are preserved. After that process has finally converged, then a subtraction is performed to compute the Top-Hat image.

The Interactive Top-Hat by Reconstruction module has the exact same look as the Interactive Top-Hat module and shares the same characteristics:

  • Two step wizard module:
    - Generation of the Top-Hat image.
    - Interactive thresholding of the Top-Hat image.
  • Same ports (however, the Neighborhood and Kernel Size ports drive the internal Closing by Reconstruction/Opening by Reconstruction module instead of the old internal Closing/Opening module).

Download a compatible version from Amira-Avizo 2019.4 until Amira-Avizo 2020.2 HERE, with Amira-Avizo 2020.3 HERE, and with Amira-Avizo 2021.1 HERE.