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Saving the Model

After you have traced the entire dendritic tree or region of interest you may want to save the model to a file. NeuronStudio allows you to save your tracings in SWC format and in HOC format. To save the file select File >> Save Neurites.... This brings up the standard window for exploring your file system. Select the desired location and file format and hit OK. Once a file has been saved the name will appear in the status bar at the bottom of the main window (see image below).

Neuron Studio Status Bar

If there is a file name displayed in the status bar then subsequent selections of the File >> Save Neurites... menu item will NOT bring up the save dialog, but will simply over-write this file. This provides a quick and easy means of saving your work as the model is refined and edited.

TIP: Use the Ctrl+S key combination as a shortcut for saving.

Additionally you may use the menu item File >> Save Neurites As... instead which will always bring up the explorer window. This allows for the creation of any number of model files.

Saving an SWC File

If you choose to save the file in SWC format, the following dialog will appear before the file is actually written.

The SWC Options Dialog

The various fields of the window correspond to the standard headers of an SWC file. It is unclear at the time of this writing whether these are required or optional, but NeuronStudio fills out a few of them automatically for you. See also Importing Models for more details on the SWC file format specification.

If Output Edge Section and Order is checked, then two additional fields will be added to the output of each vertex in the file. Since any given vertex can participate in more than one edge, the branch order and section number output to the file correspond to the parent edge that the vertex is a part of. A parent edge is defined as the edge which "leads back" to the origin (soma) of the model.

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