Placing markers (3D)

Purpose

Use markers to quickly mark structures of interest in your images.

Markers can also be used to indicate the center point for Sholl analysis using Neurolucida Explorer, the freely available companion software for Neurolucida 360.

A variety of marker types (i.e., circle shape, star shape, etc.) become available once you click the markers button to enter Place markers mode.

How it works

Tracing and detecting structures in the 3D Environment, with the default 3D Volume image-display mode, relies on visible differences between the structure and the background to determine the appropriate z-position for the marker or tracing. There are different instructions for placing markers on visible structures or in locations without visible structures.

Also see using markers in the main (2D) window, and editing markers in 3D.

Placing markers on visible structures

When the Image Display is set to the default 3D Volume mode, Neurolucida 360 uses image data to determine the Z-position for marker placement. If you attempt to place a marker and the software cannot recognize a visible structure at that location, no marker is placed; you would need to follow the instructions below for Placing markers at locations without visible structures.

  2. Click the marker button in the 3D Environment to enter Place markers mode.

  3. Select a marker type from the list.

  4. Navigate as needed and click on structures to place markers.

    Neurolucida 360

To delete the last marker you placed, press CTRL-Z.

Placing markers at locations without visible structures

In order to place markers where there is no visible structure, display your image as an "Image slice", a 2-dimensional view.

  1. Click the image button to open the Change Image Display panel.
  2. In the Display Image as section of the panel, click the radio button to select Image Slice mode.
  3. In Image Slice mode, position sliders for each of the three axes are displayed.
    • Select the axis that you want to use (i.e., XY, XZ, or YZ) by clicking its checkbox.
    • Position the image slice using the slider for the axis you chose.
  4. Click the marker button in the 3D Environment to enter Place markers mode.

  5. Select a marker type from the list and click in the window to place the marker.

    • Each click places a marker at the cursor location.

    • Select a different marker from the list

Editing markers

With Place markers mode active, select at least one marker and click the edit button to display the editing options.

See Editing markers (3D) for information.