Editing vessels (3D)

• 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.

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.

• 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!

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.