Automatic contour tracing

Purpose

Trace contours on live or acquired images interactively and quickly using Auto Contour.

Although automatic contour tracing is a powerful function, we recommend that you examine auto-traced contours and refine them manually.

Before you start

  1. Open an image.

  2. In the Main window, click Contour mode on the Trace ribbon.

Procedure

  1. If the region of interest that you want to trace is just a small portion of your image, zoom in so that it is easily visible.
  2. In the Main window, go to the Pipelines ribbon and click Auto contour.
  3. Optional Click Show Advanced Settings.
    1. Click Start Initialization. Initialization enables you to guide the program in placing the first contour points.
    2. Place two contour points manually. Neurolucida highlights the segments between the contour points in blue and suggests a path for the next contour points represented by orange circles.
    3. Click Stop Initialization.

      If you are not satisfied with the path suggested, click Restart Initialization.

      Global Options

      • Point Density: Controls the frequency of the point placement during tracing. A lower setting means fewer points placed.

      • Auto-close within: Closes the current contour as soon as an added point comes within the set number of pixels of the contour start. 0 turns disables this feature. We recommend starting with a value of 30.

      • Deletion prompt: Controls a message box displayed when the number of points to be deleted exceeds the value set for the prompt. This helps protect you against accidental deletion of a large contour.

      Intensity, Texture, and Hue

      Each of these methods has the following controls:

      • Force: Controls the amount of force that a particular method has on each point placed. A lower Force value tends to move on more of a straight line.

      • Sensitivity: Controls when automatic contouring needs to stop and ask you for help—you will need to examine the tracing and make some decisions. A lower Sensitivity value requires less interaction, but it is more likely to wander into undesirable image areas.

      • Sample Width: Defines a region on either side of the contour which is sampled during contouring for making point-placement decisions. A larger Sample Width samples farther away from the contour.

      Which control should I use? It is possible to use multiple methods simultaneously. However, you may get the best results by using one method at a time. To disable a method, set its forces to 0.

      Presets

      The presets are good starting points to create your own settings. Experimenting with them will give you a sense of how different parameters and options affect the results.

      • To use the presets, click the Presets button and select a preset from the list.

  4. In the Control area, click the Forward arrow. The automatic contouring process starts.

    • To interrupt automatic contouring, click the Pause icon.

    • To delete points, click the Back arrow or CTRL-Z on your keyboard.

    • To resume manual tracing, click the Pause icon then place contour points manually.