Placing spines (2D)

Before you start

  • Before placing a spine, click Spines from Trace>Neurons>Spines (make sure that Neuron mode is selected) and select a spine type from the bar.

    • Although the spine types are represented by different shapes in the toolbar, each spine placed manually is represented as a sphere regardless of the spine type selected.

  • For live-camera images: We recommend that you trace the tree(s) and place the spines associated with the tree(s) during the same session.

    If you traced the tree during a previous session: Be aware that as you re-open the software, you may place the reference point at a slightly different Z position. As a result, spine length data may not be valid. To avoid this issue, re-align your tracing in Z (before placing spines) by using the Joy Free mode and the Z filter in the Orthogonal View.

Placing spines manually

There are three methods to place spines manually: Two-click & single-click methods (for which you need to trace the dendrite before placing spines) and spine-to-tracing method (for which you can place spines while tracing):

  1. The dendrite is already traced.
  2. Select a spine type from the Spines toolbar.
  3. Optional: Adjust the size of the spine head by scrolling the mouse wheel. If mouse wheel focus is enabled, hold down CTRL and scroll the mouse wheel.
  4. Click to place the spine head center.
  5. Move your cursor over the traced dendrite; a rubber line appears.
  6. Click and release the mouse; the spine is placed.
  7. Click the spine icon again to disable the Spines mode and return to tracing.
  1. The dendrite is already traced.
  2. Select a spine type from the Spines toolbar.
  3. Right-click and select Spine Settings.
  4. Under Anchor Points, check the Use closest branch point (single click mode) box.
  5. Optional: Adjust the size of the spine head by scrolling the mouse wheel. If mouse wheel focus is enabled, hold down CTRL and scroll the mouse wheel.
  6. Click to place the spine head center; the spine's neck is placed on the closest branch point.
  7. Click the spine icon again to disable the Spines mode and return to tracing.
  1. Select a spine type from the Spines toolbar.
  2. Right-click and select Spine Settings.
  3. Make sure that One-shot spine placement (only while tracing) is selected.
  4. Optional: Adjust the size of the spine head by scrolling the mouse wheel. If mouse wheel focus is enabled, hold down CTRL and scroll the mouse wheel.
  5. Use the two-click or the single-click method to place one spine. The program automatically returns to the tracing mode.

 

To perform a quantitative analysis of the spines, use the Spines analysis available in Neurolucida Explorer.