Detect Varicosities Panel (3D)

See Detecting & editing varicosities (3D) for instructions.

 

Available when trees have been traced.

Varicosities are modeled using five points along the centerline of a process.

Optional: To associate varicosities with a specific color channel, select a single channel using either the Channel panel on the left side of the 3D environment window or the Image Adjustment tool (on the Image and Workspace ribbons) in the main window (2D).

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

Detection Settings

Minimum thickness ratio

Minimum thickness ratio = Thickness metric at the center of the varicosity / Thickness metric of the dendrite just outside the varicosity

Where thickness metric = diameter X image intensity.

Maximum length ratio

Maximum length ratio = [Varicosity length] / [Diameter at middle point of varicosity]

Varicosities are modeled using five points along the centerline of a process.

Varicosity length is the distance between the first point and the last point.

Image sensitivity

Used by the detector during image segmentation. Higher percent values result in image appearing brighter to the detector.

Keep existing varicosities checkbox

The default behavior for Detect All varicosities is to delete any previously detected varicosities before detecting with the current varicosity-detection settings; use the Keep existing varicosities checkbox to override this.

Check this box if:

  • You placed varicosities manually prior to using Detect All and want to maintain them.
  • You used Detect all then decided to use different settings to detect more varicosities, but want to maintain the varicosities already detected.
  • You notice that, when you click a varicosity to detect it, the model of an adjacent varicosity is removed. This may happen when varicosities touch each other. Keep existing varicosities prevents the new varicosity from removing the existing adjacent one.

Detect All button

Automatically detects varicosities based on the settings defined in Detection.

Detection is restricted to varicosities with centers located at least one radius away from the start or the end of a branch. We use the middle point radius of the varicosity in this determination.

Click image to detect all on nearest branch button

This option enables you to restrict the automatic detection to a single branch instead of the entire image.

  1. Adjust the detection settings under Detection.
  2. Check the box.
  3. Click near the desired branch.

 

Options

 

Center after each manual detection

Use to avoid panning manually while tracing. The last point clicked is automatically re-positioned at the window center.

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.