Module: Thinner ()

Description:

The module takes as input a label image to be thinned and a distance map scalar field. It removes voxel by voxel from the segmented object until only a string of connected voxels remains. This thinning is ordered according to the distance map input.

Thinner is also used internally by the Auto Skeleton module.

Press the Apply button to start the computation.

Connections:

Data [required]
Label image to be processed. Can be a regular Label Field or of type Large Disk Data in which case the output is of the same type. When used with external data on disk, the Thinner module expects a black border around the data. This border should be at least of size 'length of ends' (see below). The data should have a data parameter BorderWidth specifying border for the 3 dimensions, for instance BorderWidth 15 15 15.

Distmap [required]
Distance map of the label image. The thinning algorithm expects the distance map input to use positive short integers. Also a 15 voxel border must be added in current implementation.

Ports:

Filename

This port is available only if the module is attached to a Large Disk Data object. Specify here the name of the output file.

Temp filename

This port is available only if the module is attached to a Large Disk Data object. Specify here the name of a temporary file needed by the algorithm.

Extended Options

Extended Options

Switch on this port to get extended options.

Len of ends

The value in this field is given in terms of voxels and controls the module's sensitivity to generate branch points. The higher the value the lower the sensitivity.

Note: When using Thinner with disk data, you can set the 'length of ends' parameter manually in the console, for instance: Thinner setVar lenOfEnds 10 will set the length of the ends to 10 voxels before they are detected as unconnected ends.

Max iterations

Enter the number of iterations of the thinning algorithm. In the case of complex data set this port to non-zero values to prevent extraordinary computation times. A value of 0 means that the maximum number of iterations is controlled automatically.