The skl_ panel is there to reduce the binary matrices to a set
of individual carrier points and some starting nodes to be subsequently connected to trees.
The 3D skeletonization is a process which carves off binary voxels
one by one in dependence of their neighborhood (a method introduced by Palagyi and Kuba),
ideally leaving only the carrier nodes of the branched structure
(see “skel_stack”).
Pressing the „skel“ button performs the morphological operation.
If toggle „D“ is pressed,
a diameter value is obtained for each node from the neighborhood relationships
of the binary matrix:
*D* is the distance of the closest zero value in the binary matrix
(see „bwdist“ from the image processing toolbox in Matlab).
If toggle „L“ is pressed, a labeling is performed on the binary matrix:
two nodes are connected if walking on non-zero voxels from one to the other
without gaps is possible.
This is helpful for calculating the connnectivity matrix later.
Also it helps to chose starting points:
two starting points should never show up on the same „label“
(see „bwlabeln“ from the image processing toolbox in matlab).

The skl_panel is equipped with a very basic soma finding function.
This takes the threshold value (** thr**) in the edit field and finds either
all nodes whose diameters were calculated to be higher than

**skl_ edit and edit2 mode**

The skl_panel allows alteration of starting node locations in the edit mode
and of skeletonization carrier point locations in the edit2 mode.
Points are moved in the current viewing plane and can be deleted with the key [c].
A line shows to the closest point.
In edit2 mode key [C] cuts out all carrier points in close vicinity.

Pressing [v] in the edit2 mode previews the result of cleaning.
This process reduces the number of nodes by preventing neighboring nodes
within a distance limit in mm indicated in the edit field.
Pressing [V] or the “clean” key finalizes the sparsening of the nodes.

The nodes and starting nodes are then ready for the tree constructor.
However to improve the result further the MST tree constructor with
“RST” option accepts a distance matrix between the nodes to increase
the probability of connection.
Threshold-linking is a standard way to do this.
The resulting connectivity graph of increased connection probability
is shown when the third radio button is active.

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