Editing vessels (3D)

Available with the Neurolucida 360 Ultra package only. Click here for more information.

Purpose

Use the Edit Vessels panel in the 3D Environment to change vessels that have already been modeled.

See also Edit Vessels Panel (3D)

Before you start

  • In the 3D Environment, click the Edit button to display the Edit Vessels panel. More editing options are available after selecting vessels or clicking the Points button.

  • If vessels are associated with a single color-channel (that is, if a color channel was selected prior to tracing or detecting the vessels), select that color channel to access all of the vessel-editing functions. Select the color channel in either the Channel panel in the 3D environment or in the Image Adjustment tool in the 2D window.

  • When editing, vessels can be visualized as continuous lines or as series of points.

  • Use this panel to set directionality of vessel flow.

If you're working with very dense networks, use the partial projection view (available on the Image panel).

It is likely that you will need to adjust the image zoom/position for some of these operations:

  • Zoom in/out by scrolling the mouse wheel.

  • Pan to position the image by pressing shift and dragging with your mouse.

Selecting vessels and vessel segments

  • To select a single vessel or vessel segment, click it with your mouse.
  • To select all vessels, click Select All.
  • To select several adjacent segments, press the CTRL key and draw a marquee (rectangle) around the segments of interest.
  • To deselect all vessels, click away from the selected objects. CTRL-click to deselect individual segments while leaving the rest selected.
  • To select a single point on a vessel, click the Points button then click the point of interest.
  • To select multiple adjacent points, press the CTRL key and draw a marquee (rectangle) around the points of interest.

    Once multiple points are selected, clicking a single point in your selection has no effect and will NOT deselect that point.

  • To deselect all points, click away from the selected objects. CTRL-click to deselect individual points while keeping the rest selected.
  • Click the Points button again to exit points-editing.

Showing/hiding vessels

Click Hide selection to hide all selected vessels.

The button will change to Show selection; click it to show hidden vessels that are still selected.

To show hidden vessels, click Show all hidden.

Editing vessels and vessel segments

  1. Click a vessel to select it.
  2. Click the Detach button.
  3. Click on the segment to detach.
    • If you click a single segment, it is split into two segments.
    • If you click a bifurcation, the segment is split into three segments.
  1. Zoom in and rotate as needed.
  2. Click the Connect button. Vessels are now represented by series of points along colored lines.
  3. Click and drag an end point toward the area you want to connect to. The end point briefly turns green and a green line appears.
  4. Release the mouse button to connect the segments.

Select points in order to edit them (see Selecting points on vessels above)

Moving points

  1. Zoom in and rotate as needed.
  2. Click the Points button. Segments are now represented by series of points along colored lines.
  3. Select the point(s) you want to move. Selected points are displayed in green.
  4. Drag the point(s) to the desired location.

Deleting points

  1. Zoom in and rotate as needed.
  2. Click the Points button.
  3. Select the point(s) you want to delete.
  4. Press Delete or click the Remove button.

Changing vessel thickness at selected points

  1. Zoom in and rotate as needed.
  2. Click the Points button.
  3. Select the point(s) for which you want to adjust the thickness.
  4. In the Edit Vessels panel, drag the slider under Thickness Adjustment.

You can change the thickness of an entire vessel, or you can modify the thickness at a single point or a group of points that represent part of the tree.

  1. Click a vessel to select it or click the Points button and select the points you want to adjust.
  2. Drag the slider or type a value in µm for the thickness you want in the Thickness subpanel at the bottom of the Edit Vessels panel.

To make it easier to see the points, you can change their display without changing their thickness; see Changing point-size display below.

After tracing complex structures, there may be fragments. This tool identifies these issues to help enable you to resolve them quickly.

  • To view a list of issues, click the CLEANUP button.

    Fix column:

    • Indicates that the fragment can be deleted automatically.

    • Indicates that manual editing is recommended (e.g., merging).

  • To delete all the fragments that can be automatically deleted (in the list), click the CLEAN ALL button.

  • To inspect a specific issue, click the description of the issue; the corresponding area in the tracing gains focus in the display.

  • To resolve a specific issue, click in the FIX column.

  • No branch points: The vessel doesn't include any node or branch point: Edit manually to fix this issue.
  • Vessel fragment found: The vessel has two or less points: clicking Fix will delete the vessel.
  • Ending not at image boundary: The ending point is not at the image boundary: Edit manually to fix this issue.

Use classify to categorize segments for later analysis in Vesselucida Explorer.

If applicable, see separate instructions for SPARC users below.

  1. Click to select a segment; a selected segment is indicated by three white squares (beginning, middle, and end of segment).

    Use CTRL-click to select several segments.

  2. Select a name from the Segment Namedrop-down menu to classify the selected segments.

    To customize the names in the list, click the Color sets button, highlight a name and type a new name.

  3. When you save, then open, the data file in Vesselucida Explorer, the classified structures are listed in the Networks tab of the Traced Structures panel.

SPARC users will see a slightly different interface that displays anatomic terms associated with the subject information entered when Neurolucida 360 software was launched. To classify vessel segments in SPARC mode, do the following:

  1. Select the segment(s) you want to classify.

  2. Find the classification for the selected segment(s) by scrolling or searching the anatomical terminology list.

    To search the list, start typing into the Search Terms box.

  3. Click the classification to apply it to the selected segment(s).

  • Change direction: Click to change the direction of the segment; direction can be changed for individual segments, but not for entire vessels.

    To reverse the direction of a segment, click a segment to select it, then click Change direction. When a segment is selected, you can see three squares (beginning, middle and end of segment). As a result, the segment is recolored and the beginning point is now red.

    You can only change the direction of a segment that has one open endpoint and is connected to another segment.

  • Set/Clear origin: You can define origins for segments that have one open end and are connected to other segments. \

    • Click a segment to select it then click the Set origin button. This will update the flow direction and set the origin to the open endpoint.

    • Clear origin: Click to undo SET origin. Note, however, that the direction of the flow is NOT automatically reverted. Use the Change flow direction button if needed to change the flow direction.

  1. Click a vessel to select it or click the Select All button.
  2. Press the Delete key or click the Remove button. You can’t undo this action!

Changing vessel appearance

These features are for visualization only (e.g., snapshots for publications); they don't affect your data.

You may want to adjust the displayed size of the points in your vessels to make them easier to view and edit.

  1. Click a vessel to select it, hold down CTRL and click several vessels to select them, or click the Select All button to select all vessels.
  2. Click Points.
  3. Drag the Adjust point display slider to change the size of the selected points.

The Show as drop-down menu offers choices for display of vessels.

  1. Click a vessel to select it, hold down CTRL and click several vessels to select them, or click the Select All button to select all vessels.
  2. Click the arrow next to the Show as drop-down menu and choose one of the display options.
  1. Click a vessel to select it, hold down CTRL and click several vessels to select them, or click the Select All button to select all vessels.
  2. Access the color picker by clicking the arrow near the colored square (next to the Show as: drop-down menu).
  3. Select a new color by clicking on it or click Custom Color… for more options.

In images with more than one color channel, use the drop-down menu to associate the selected vessels with a specific color channel.

  1. Click a vessel to select it, hold down CTRL and click several vessels to select them, or click the Select All button to select all vessels.

  2. Click the arrow next to the Channel drop-down menu and choose the desired channel.

Changing a vessel color-channel does affect the data associated with the image.

  1. Click a vessel to select it, hold down CTRL and click several vessels to select them, or click the Select All button to select all vessels.

  2. Slide the Transparency slider to adjust the display of the selected spine or spines.

If you want a vessel to be entirely invisible, use the Hide selection button.

Use this option to obtain a less jagged tracing.

  1. Click a vessel to select it, hold down CTRL and click several vessels to select them, or click the Select All button to select all vessels.
  2. Check the Smooth box.
  3. Drag the slider to the right for more smoothing or to the left for less smoothing.

  1. Click a vessel to select it, hold down CTRL and click several vessels to select them, or click the Select All button to select all vessels.

  2. Use the drop-down menu to choose one of the following surface effects:

    • Vessel Color: Displays vessels as the color they were originally traced as, or as the color chosen from the Color Picker.

    • Class: Displays vessels in classification colors if they have been Classifying segments.

    • Diameter: Displays the diameter (µm) of the vessels as a color gradient.

    • Direction: Displays direction of vessels as they move away from their origin as a color gradient.

    • Distance to Markers: Displays distance (µm) between vessels and markers as a color gradient. Must have a marker present.

    • Distance to Puncta : Displays distance (µm) between vessels and puncta as a color gradient. Must have a punctum present.

    • Distance to Spines: Displays distance (µm) between vessels and spines as a color gradient. Must have a spine present.

    • Distance to Varicosities: Displays distance (µm) between vessels and varicosities as a color gradient. Must have a varicosity present.

    • Texture: Allows you to select an image from a browser window and apply it to the surface of selected vessels. The image must be one of the following formats: .png, .tif, .jpg, or .bmp.

  3. Click to access additional surface specific controls including gradient colors, transparency, and other context dependent settings.

Editing vessels (2D) in 2D