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Labeling the Model

You can apply a function label to the vertices of the model prior to saving. Many modeling packages use this information during their simulations. Currently the labels that can be applied are soma, basal dendrite, apical dendrite, and axon. By default all vertices (and edges) are marked as unknown when a model is first created. To apply a label, simply select as many vertices as you would like and right-click while the Neurite Tool neurite tool is active to bring up the following context menu. See the image below.

Labeling The Model

All selected vertices will be labeled with the chosen type. There is no restriction on the number of vertices that can be labeled this way except when setting the soma function. In this case, the existing soma is not allowed to be split, and only one soma is allowed for any connected group of vertices.

TIP: You can use the select sub-trees function to more easily select entire trees of the model. Any set of connected vertices that is attached to the soma is considered a tree. To select the entire tree simply select 1 or more of the vertices of the tree and choose the menu item Edit >> Select Sub-Trees. Note in the above image that this operation is available in the context menu for convenience.

The labeling is saved along with the model if the file format supports it. At the time of this writing both the SWC and HOC file format support a label field.

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Send questions or comments to: alfredo.rodriguez@mssm.edu