The GUI

the skl_ panel

skeletonization

adapted from
PLoS supp. material by Hermann Cuntz

← the_thr_panel
→ the_mtr_panel

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 thr. If none falls in that category the node with the highest diameter is chosen (as in this case). If more than one node falls in that category then smaller starting nodes which appear in distance smaller than thr of larger starting nodes are cleaned away. Starting nodes which appear on the same label are also deleted.

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.