Module: Interactive Top-Hat by Reconstruction ()

Description:

This is an experimental module from the Xtra Library: https://xtras.amira-avizo.com.

This module works essentially like the Interactive Top-Hat except that is based on a Closing by Reconstruction, or a Opening by Reconstruction, depending on its type: respectively Black or White Top-Hat.
Because of that it is better suited for porosity segmentation as the morphological grayscale reconstruction operation will preserve the edges of the input image.
The Top-Hat image generated will indeed be free of any false positive porosities on the edges, that the Closing / Opening of the Interactive Top-Hat tend to create out of small concavities on the edges of the input image.

Connections:

Data [required]
The input data to be segmented.

Ports:

Top Hat Type

This port allows selecting the type of Top-Hat to compute.

Neighborhood

Neighborhood is the neighborhood used for the morphological operation (closing by reconstruction for black Top-Hat, opening by reconstruction for white Top-Hat). It defines also the connectivity used for this operation.

Kernel Size

This port defines the kernel size for the closing/opening by reconstruction operation. The smaller is the kernel, the smaller are the elements detected.

Colormap

The colormap used to display the input data.

Slice Number

The number of the slice to display.

Orientation

The orientation of the slice to display.

Intensity Range

This port allows selecting the elements to keep. See the module description for more information.

Preview

Options for the threshold preview. The color of the preview can be chosen in this port. Select 2D to display the threshold on the current displayed slice (default value). Select on 3D to get a 3D preview of the segmentation (slower display).

Input

This port allows displaying the threshold preview:

• On the original image (Original image)
• On the Top-Hat image, computed at the previous step (Top Hat image)
• On nothing (None): only the threshold will be displayed.