Editing trees (3D)

• To select a single tree, click the tree.
• Choose a type from the Select by Type: drop-down menu to select all trees of that type.
• To select all the trees, click Select All.
• To select several adjacent trees, press the CTRL key and draw a marquee (rectangle) around the trees of interest.
• To deselect all trees, click away from the selected objects. CTRL-click to deselect individual trees while leaving the rest selected.

• To select a single point on a tree, 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 tree to select it or click Select All.
2. Press the Delete key on your keyboard or click Remove. You can’t undo this action!

1. Click a tree to select it.
2. Click the Detach button.
3. Click on the tree to detach.
   • If you click a single branch, the tree is split in two.
   • If you click a bifurcation, the tree is split in three.
4. Click Detach again to exit.

1. Click Connect. Trees are now represented by series of points along colored lines.
2. Click and drag an end point toward the desired connection area. The end point briefly turns green and a green line appears.
3. Release the mouse button to connect the branches.
4. Click Connect again to exit.

Moving points

1. Select the point(s) you want to move. Selected points are displayed in green.
2. Drag the point(s) to the desired location.

Deleting points

1. Select the point(s) you want to delete.
2. Press Delete on your keyboard or click Remove.

Changing process thickness at selected points

1. Select the point(s) for which you want to adjust the thickness.
2. Drag the slider in the Thickness subpanel near the bottom of the Edit Trees panel. Alternatively type a value (µm) in the open box.

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

1. Click a tree 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 Trees panel.

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

(Available only with the Neurolucida 360 Studio or Ultra package)

After tracing complex structures with the user-guided or automatic tracing mode, there may be tree fragments. This function automatically identifies these issues and helps you resolve them quickly.

• Click Cleanup to view a list of issues.
• To delete all the fragments that can be automatically deleted ( in the list), click Clean All.
• To inspect a specific issue, click the description of the issue; you'll be redirected to the corresponding area in the tracing.
• To resolve a specific issue, click in the Fix column.

Types of issues

• Branch fragment found: Single-point branches attached to trees—Fix will detach those branches and then delete them.
• Tree fragment found: Two-point trees not attached to anything—Fix will delete these trees.
• Root fragment found: Two-point roots with bifurcating nodes—Fix will re-assign the origin to the node at the bifurcation and delete the fragment below the bifurcation.
• Fragment found: Single-branch trees (i.e., with at least three points) that are not connected to anything—There is no automatic Fix; you need to connect manually.

Solutions

Indicates that the fragment can be deleted automatically.

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

Indicates automatic reassignment of the origin to the node at the bifurcation and deletion of the fragment below the bifurcation.

1. In the Main (2D) window, turn off line thickness. Nodes are displayed as solid circles.
2. Go to the Trace ribbon, Edit section and click Select Objects to display the Edit Tool panel.
3. In the Edit Tool panel, check Individual Points.
4. Click the node you want to delete to select it.
5. Right-click and select Eliminate node. Note that removing a node will also delete part of the tracing. Make sure you return to the tracing.

You may want to adjust the displayed size of the points in your trees to make them easier to view and edit; see Changing point-size display below.

1. Click Points
2. Click the desired origin point on the tree.

3. Click Set point as Origin.

   Note that only end points can be set as the origin.

4. Click Points again to exit points-editing.

Use CLASSIFY to categorize tree segments for later analysis in Neurolucida Explorer.

If applicable, see separate instructions for SPARC users below.

Note: Classification color changes will not be visible in 2D software window.

1. Click to select a tree segment or select several segments by holding the Ctrl key and clicking the segments of interest.

2. Select a name from the drop-down menu.

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

It is useful to specify the types of tree-like structures in your images for later analysis in Neurolucida Explorer.

1. Click a tree to select it.
2. Select a type from the Type drop-down menu.

Use the Reduce Points slider to reduce the number of points in selected trees. This can make it easier to edit trees. Note that the resulting data file is saved with the suffix "_Reduced" so that the original data file is not overwritten.

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

1. Click a tree to select it, hold down CTRL and click several trees to select them, or click the Select All button to select all trees.
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 tree to select it, hold down CTRL and click several trees to select them, or click the Select All button to select all trees.
2. Click the arrow next to the Show as drop-down menu and choose one of the display options.

1. Click a tree to select it, hold down CTRL and click several trees to select them, or click the Select All button to select all trees.
2. Access the color picker by clicking the arrow near the colored square (next to the Type: 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 trees with a specific color channel.

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

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

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

1. Click a tree to select it, hold down CTRL and click several trees to select them, or click the Select All button to select all trees.
2. Click a tree to select it.
3. Drag the Transparency slider.

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

Use this option to obtain a less jagged tracing.

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

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

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

   • Branch Order: Colors trees according to their branch order.

   • Class: Displays trees in classification colors if branch segments have been Editing trees (3D).

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

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

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

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

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

   • Texture: Select an image with the texture you want to apply to the surface of selected trees from the Load Texture Image window that opens.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.