The GUI

the slt_ panel

node selector

adapted from
PLoS supp. material by Hermann Cuntz

← the_ged_panel
→ the_ele_panel

The slt_ panel goes hand in hand with the mtr_ panel to browse nodes of that active tree or analyse their properties and change region attributing. The first popup allows to attribute values to nodes individually by means of one of the typical Nx1 vectors. If a vector is selected here the values are mapped onto the colours of the active tree in the mtr_ panel or the plot functions in the plt_ panel (see later) or they are used for the morphing function in the mtr_ panel. More sophisticated Nx1 vectors can be computed using one of the meta-functions (see “Pvec_tree”, “child_tree”, “ratio_tree”, and “asym_tree”). For example the metric path length is the combination of „Pvec“ and „LEN“.

An index (subset) to the nodes can be selected here as well. This can be done directly using one of the options (e.g. all branch points with „iB“) or by thresholding the selected Nx1 vector („t<„ and „<t“) or by selecting a subtree to the last active node of the mtr_ panel, or... by using the edit2 mode of the mtr_ panel, then it becomes very complicated. The selected nodes can be deleted directly or attributed to a new region. Selected nodes are indicated in black on the mtr_ panel plot of the active tree. plt_ panel plotting functions, spines allocation or current injections will be restricted to the selected index of nodes.

In the TREES toolbox, the conventional representation of a tree is as a set of cylinders, where the diameter depends on the daughter node. However, this can easily be altered by adding a „.frustum = 1“ field to the tree structure. In the GUI this is toggled in the slt_ panel as shown here. Differences in total volume or membrane surfaces of more than 10% can occur when switching. Note that POV-Ray and x3d graphical outputs do not support frustum, while NEURON to our knowledge supports only frustum.

Region assignment is a bit complicated. To visualize which nodes belong to the selected region use the „iR“ selection in the node selector. The popup allows to switch from one region to another. The edit-select mode in the mtr_ panel allows together with the node selector of the slt_ panel to chose a set of specific nodes. These can then be assigned to the currently active region or form together a new region by the control „NEW“. When this happens they are extracted from the other region sets. In some cases regions remain empty after such a procedure: The „c“ control is there to clear such regions. In some select cases still deletion of nodes might result into problematic region assignements and this bug was not identified yet.