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3D visualization

Use this environment to visualize your tracings in 3D or as cross-sections and to edit trees, somas, spines, markers and contours. See Take a tour of the 3D visualization environment for details.

To open the 3D Visualization window, click Trace>View>3D visualize.

ClosedNavigating image stacks with the mouse
  • Drag to rotate (3D view only).
  • Scroll the mouse wheel to zoom.
  • Hold down SHIFT and drag to pan (3D only).
  • Drag to pan (projection views only).
ClosedAdditional rotation options

To spin a stack that was saved in an improper orientation, use the 2D rotation tool.

  1. Click the button in the toolbar.
  2. Drag to rotate clockwise or counterclockwise.

To use of different rotation axis, use the pivot point tool.

  1. Click the button in the toolbar.
  2. Click a point in the image.
  3. Drag to rotate relative to the new rotation point.
ClosedReturning to the original orientation of the stack

Click the icon.

Closed3D view vs. cross-sections view

3D Volume is the default but you can switch to the Image Slice mode:

  1. Click the Image button to access the Change Image Display dialog box.
  2. Under Display Image as, select Image Slice.
ClosedImage adjustments in 3D

Use the Image panel to adjust gamma, black point and white point.

To work with a single channel on a multichannel image:

  1. Open the multichannel image and go to Image>Image Adjustment.
  2. In the Image Adjustment window, select a channel.
  3. In the 3D Visualization window, click Image to view the Image panel:
    1. Click Image Sync with 2D to apply the changes made in Image Adjustment.
    2. Use the sliders to adjust gamma, black point and white point.