Detecting & editing varicosities (3D)

Before you start

Because varicosities are always associated with trees, you must trace the trees associated with the varicosities of interest before .

Varicosities placed manually in 2D are represented with 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

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 2D window.

Detecting all varicosities automatically

  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 varicosities 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: [Diameter at the center of the varicosity X Image intensity at the center of the varicosity) ÷ [Diameter of the underlying dendrite X Image intensity of the underlying dendrite]
      Note that the underlying dendrite is measured as the average of the values at both ends of the varicosity.
    • Maximum length ratio:[Varicosity length] ÷ [Diameter at middle point of varicosity]
    • Image sensitivity: Used by the detector during image segmentation. Higher values result in the image appearing brighter to the detector.
  4. Check or uncheck the Keep existing varicosities checkbox keep or delete the varicosities detected before you adjusted the detection settings. .
  5. Click Detect All to detect varicosities again, using the adjusted detection settings.

Detecting individual varicosities manually

  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.

Detecting varicosities on a single branch

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

  • If your image has background noise, it may be beneficial to check the Filter image noise checkbox.
  • To detect varicosities in addition to varicosities previously detected manually, check the Keep existing varicosities box.

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

Editing varicosities

See also Edit Varicosities Panel (3D)

  • Click the Edit button to access the Edit varicosities panel. Click a second time to exit varicosity editing.
  • If varicosities are associated with a single color-channel (that is, if a color channel was selected prior to tracing or detecting the varicosities), select that color channel to edit varicosities. Select the color channel in either the Channel panel in the 3D environment or in the Image Adjustment tool in the 2D window.
  • To see all the editing options, select one or more varicosities.

Selecting varicosities

  • Click Select All
  • Click a varicosity or hold control and click multiple varicosities
  • Hold the Ctrl key on your keyboard and drag a marquee to select varicosities inside the marquee.

Selected varicosities are displayed with wireframes.

Deleting selected varicosities

Select varicosity/varicosities, then do one of the following:

  • Press the Delete key on your keyboard

  • Click Remove in the panel

You can't undo this action if you have selected all varicosities.

Modifying the appearance of selected varicosities

  • Change the display size of varicosities that are set to Show as Ball from 1X to 3X using the slider.

  • Use the Show as drop-down to display as Ball, Solid, or Wireframe.

  • Select a different color for selected varicosities by clicking the arrow near the colored square to access the color picker

  • Set the transparency of varicosities to view other structures using the Transparency slider. The transparency setting specified here will be ignored if a different color channel is displayed, however, the transparency of varicosities and any other traced structures associated with undisplayed color channels can be controlled using the Trace Opacity slider in the Channel panel.

  • Smooth the appearance of varicosities by checking the Smooth checkbox and adjusting smoothness using the slider.

How are varicosities detected?

  1. For each traced branch, Neurolucida 360 software evaluates 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] X [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.