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Detecting & editing varicosities (3D)

Before you start detecting, trace the trees associated with the varicosities of interest.

Varicosities placed manually in 2D are represented by 2D markers in the 3D window.

Varicosities can be analyzed in Neurolucida Explorer using the Varicosities analysis in the Branched Structure group of analyses.

See Detect Varicosities Panel (3D), Edit Varicosities Panel (3D), video

Detecting varicosities

  1. Click the Varicosities button.
  2. Click Detect All for an initial detection with the default settings. Automatic detection may take a few seconds (see How are spines detected? below to learn about the detection process).

    The program renders the varicosities that meet the criteria defined below using a surface mesh. Because rendering is based on a different algorithm than the one used for detection, it might not reflect exactly the profiles generated by the detection process.

  3. Inspect the results of the detection and adjust the detection settings before detecting again.
    • Minimum thickness ratio: [Varicosity diameter at middle point] / [Underlying branch thickness] where [branch thickness] = [diameter at varicosity's first point + diameter at varicosity's last point] / 2
    • Maximum length ratio:[Varicosity length] / [Diameter at varicosity middle point]
    • Image sensitivity: Used by the detector during image segmentation. Higher percent values result in image appearing brighter to the detector.
  4. Optional: To detect varicosities in addition to varicosities already detected with Detect All, check the Keep existing varicosities box.
  5. Click Detect All to detect again.
  1. Zoom, rotate, and pan as needed to view the varicosity of interest clearly.
  2. Adjust settings as necessary.
  3. Click the varicosity of interest. The detected varicosity is displayed with a color overlay.

    4. You may see a warning: "Unable to detect a varicosity at the selected location." Under Detection Settings, increase the Image sensitivity (e.g., from 100% to 125%) then click the varicosity again to detect it.

This is useful for testing the detection settings on a small region of a large image.

  1. Under Detection, adjust the settings.
  2. Check the box Click image to detect all on nearest branch.
  3. Click the desired branch to select it and detect all the varicosities on that branch.

Optional

Editing trees (by deleting or moving points) after detecting varicosities may result in deleted varicosities.

Editing varicosities

First, click the Edit button to access the Edit varicosities panel.

To see all the options, select varicosities first.

Click Select All or click a varicosity in the tracing window. Selected varicosities are displayed with wireframes.

Press the Delete key OR click Remove in the panel.

You can't undo this action.

  1. Click a single varicosity OR hold down CTRL and click several varicosities to select them OR click the Select All button. Additional options are displayed in the Edit varicosities panel.
  2. Click the arrow near the colored square to access the Color menu.
  3. Select a new color.

  • Use Show as, ball, solid, or wireframe.

How are varicosities detected?

Once you've clicked the Detect All button or clicked individual varicosities to detect them, the program takes a series of steps.

  1. For each traced branch, the program performs a 2D Rayburst sample at consecutive (and closely-spaced) points along its centerline to estimate the Rayburst diameter at each point.
  2. At each point, a thickness metric is computed: [Rayburst diameter] * [Image intensity].
  3. The program analyzes the metrics obtained to determine the location of potential varicosities and their boundaries (i.e., start and end location) along the branch centerline.
  4. Only the objects that meet the detection criteria are modeled as varicosities. They can be rendered as either a sphere or as a 5-point tubular segment.