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Editing the Spines

There are a few editing operations that can be performed on the spines of the project. Most of these functions are accomplished by using the Spine Tool spine tool.

Deletion

Deletion of one or more spines is accomplished by selecting the desired spines, and then hitting either the Delete key or using the menu item Edit >> Delete Selected.

IMPORTANT: The current tool must be the spine tool Spine Tool for deletion of spines to occur.

Example:

1) In the image shown below spines to be deleted have been selected using the spine tool.

Edit Spines Example 1 Image 1

2) With the spine tool active, press the Delete key and the selected spines are removed. See image below.

Edit Spines Example 1 Image 2

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

Addition

You can also manually add spines by selecting the spine tool Spine Tool and clicking within the 2D or 3D window. NeuronStudio will try to determine the optimal 3D position within the data from the mouse position. After this new spine is placed in an (X,Y,Z) location it will become selected, while all other spines become deselected. This is to allow you to more easily set the type of this one spine without accidentally altering other spines. See also Setting Types below. Note that when a new spine is added in this manner it's type is initially set to other.

If the slice viewer is active, adding a spine while viewing from the forward (along the optical axis) direction will force the Z coordinate of the newly added spine to be placed at the Z position of the current slice.

Note that if the location of your mouse click falls outside the boundaries of the region of interest, then no new spine will be created.

TIP: Hold down the Ctrl key while clicking to "redo" the selected spine or if none is selected, the last manual spine that was added.

TIP: You should aim for what you perceive as the approximate head of the spine when clicking, since NeuronStudio automatically calculates a head diameter at that location.

Example:

1) Identify a spine that has not yet been found. See image below.

Edit Spines Example 2 Image 1

2) With the spine tool active, click on the approximate head of the spine. See image below. Note that the spine becomes selected.

Edit Spines Example 2 Image 2

3) The 3rd coordinate is found automatically for you. See image below.

Edit Spines Example 2 Image 3

4) Since this new spine is selected, you can choose to set its type now, or leave it marked as other.

Edit Spines Example 2 Image 4

Setting Types

At any time you can set the type of one or more spines. With the spine tool Spine Tool active, simply right-click anywhere within the 2D or 3D display window to bring up a context menu containing the various types that the selected spines can be set to (see image below). For convenience, a delete option is also present in the menu.

IMPORTANT: The type of ALL currently selected spines is set by this operation. When a spine is manually added, it will become the only spine selected to help you avoid mistakes.

Setting Spine Types

Changing ID's

Spine ID's can be visualized in the 2D display if the menu item View >> Spine ID's (2D Only) is checked. There are two keyboard commands to change spine ID's:

  • Press the plus (+) key to increase the ID of the selected spine to the next available larger ID.
  • Press the minus (-) key to decrease the ID of the selected spine to the next available smaller ID (if any).

Plus and minus can be hit multiple times or held down to achieve the desired ID. These commands, along with the ability to delete and add spines, give enough flexibility to skip any missing spines as well as make corrections without having to start over.

IMPORTANT: These keyboard commands are only enabled if the spine tool Spine Tool is currently active, and only one spine is selected.

Changing Radii

You may also choose to increase or decrease the radius of any number of selected spines (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 spine tool Spine Tool to be able to change radii.

Translation and Rotation

In some cases, repositioning selected spines may also be necessary. You may alter the position of any selected spines by a translation or rotation operation. The first step is to select the spines using the spine 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 spines.

  • 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 spines.

Example:

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

Edit Spines Example 3 Image 1

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

Edit Spines Example 3 Image 2

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

Edit Spines Example 3 Image 3

Hiding and Unhiding

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

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

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