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Editing The Model

There are numerous editing operations that can be performed on a model. Most of these functions can be accessed in the top level Edit menu of the main window.

Deletion

Deletion of sections of the model is accomplished by selecting the desired vertices, and then hitting either the Delete key or using the menu item Edit >> Delete Selected.

IMPORTANT: The current tool must be the neurite tool Neurite Tool for deletion of vertices to occur.

Example:

1) Vertices to be deleted have been selected using the neurite tool. See image below.

Edit Model Example 1 Image 1

2) With the neurite tool active, press the Delete key and the section is removed. See image below.

Edit Model Example 1 Image 2

TIP: To delete the entire model, select Edit >> Delete Neurites from the main menu. You can also accomplish this by using the key combination X+N. Deletion of the whole model will occur no matter what tool is active. Since this is a potentially risky operation, a confirmation window will appear.

Joining and Unjoining

Another common editing operation performed on a model is to join or unjoin vertices. This amounts to adding or removing a connection (edge) between a selected pair of vertices. If the selected vertices already have a connection, it is removed. Otherwise a connection is created. You may use either the J key or menu item Edit >> Join/Unjoin 2-Selected to perform this operation.

IMPORTANT: There are 2 restrictions for this operation to occur. The current tool must be the neurite tool Neurite Tool and exactly 2 vertices must be selected.

Example:

1) 2 vertices have been selected using the neurite tool. Since they do not yet have a connection between them, one will be created. See image below.

Edit Model Example 2 Image 1

2) With the neurite tool active, press the J key and a connection is created. See image below.

Edit Model Example 2 Image 2

3) 2 vertices have been selected using the neurite tool. In this case they are the same two vertices as before so they now have a connection between them. See image below.

Edit Model Example 2 Image 3

4) With the neurite tool active, press the J key and the connection is removed. See image below.

Edit Model Example 2 Image 4

Setting the Soma

NeuronStudio selects one vertex from each connected component of the model to be the origin (soma). A connected component is made up of vertices where a path (series of connections) can be followed to reach every other vertex in that component. For traced components, NeuronStudio selects the vertex with the largest radius to be the soma. You may at any time reset which vertex is the soma by selecting exactly one vertex and using the menu item Edit >> Set 1-Selected as Origin.

TIP: NeuronStudio colorizes the vertices of the model according to their "type". For example the default color for a soma vertex is red.

IMPORTANT: Only exactly 1 vertex must be selected for this operation to occur.

Example:

1) A small component with one vertex selected using the neurite tool. The current origin vertex is colored in red. See image below.

Edit Model Example 3 Image 1

2) Select Edit >> Set 1-Selected as Origin from the main menu. Note how the old origin is cleared and reset as the selected vertex. See image below.

Edit Model Example 3 Image 2

Changing Radii

You may also choose to increase or decrease the radius of any number of selected vertices (by 5% of its current size). This can be accomplished by using the up ↑ or down ↓ arrow keys.

  • up ↑ is used to increase radii.
  • down ↓ is used to decrease radii.

IMPORTANT: The current tool must be the neurite tool Neurite Tool to be able to change radii.

Example:

1) A number of vertices selected using the neurite tool. See image below.

Edit Model Example 4 Image 1

2) up ↑ key pressed a number of times. All radii have proportionately increased. See image below.

Edit Model Example 4 Image 2

3) down ↓ key pressed a number of times. All radii have proportionately decreased. See image below.

Edit Model Example 4 Image 3

Translation and Rotation

To provide a full range of editing possibilities for the model, repositioning selected vertices is also provided. You may alter the position of any selected vertices by a translation or rotation operation. The first step is to select the vertices using the neurite tool. Next, switch modes to the move tool Move Tool and click and drag while holding the Ctrl or Shift keys. Rotation occurs around the center of mass of the selected vertices.

  • Ctrl is used to translate.
  • Shift is used to rotate.

IMPORTANT: The current tool must be the move tool Move Tool to be able to translate or rotate vertices.

Example:

1) A number of vertices have been selected using the neurite tool. Now switch to the move tool. See image below.

Edit Model Example 5 Image 1

2) While holding the Ctrl key, click and drag in the display window. Note how the vertices are translated. A yellow rectangle is drawn around the vertices to indicate translation. See image below.

Edit Model Example 5 Image 2

3) While holding the Shift key, click and drag in the display window. Note how the vertices are rotated. A yellow circle is drawn around the vertices to indicate rotation. See image below.

Edit Model Example 5 Image 3

You may also use the magnet tool Magnet Tool to quickly translate vertices of the model. See also Selection and Deselection for an example.

IMPORTANT: If there are no intersecting vertices when the magnet tool is clicked and dragged within the display, then translation of the display will occur.

TIP: Pressing the G key will switch to the magnet mode as well.

Hiding and Unhiding

Finally, the last edit operation is the ability to hide selected vertices. This can be used to reduce the visual load of a complex model, or to allow occluded sections of the model to show through. Select Edit >> Hide Selected from the menu to hide the selected vertices. Use the menu item Edit >> Unhide All at any time to show all previously hidden vertices.

IMPORTANT: The current tool must be the Neurite Tool neurite tool for hiding or unhiding to occur.

Example:

1) A number of vertices selected using the neurite tool. See image below.

Edit Model Example 6 Image 1

2) Edit >> Hide Selected selected from the menu. The selected vertices now become hidden. See image below.

Edit Model Example 6 Image 1

3) Edit >> Unhide All selected from the menu. Note how all previously hidden vertices are shown again. See image below.

Edit Model Example 6 Image 1

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