Editing trees (3D)

• To select a single tree, click the tree.
• To select all the trees, click the Select All button.
• 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 to exit points-editing.

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

1. Select a tree and click Points.
2. Drag the Adjust point display slider to change the size of the selected points.

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

1. Click the Points button.
2. Click the desired origin point on the tree.
3. Click the button Set point as Origin.
4. Click the Points button to exit points-editing.

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 the Detach button again to exit.

1. Click the Connect button. 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 the Connect button again to exit.

1. Click a tree to select it.
2. Drag the slider in the Thickness subpanel at the bottom of the Edit Trees panel.

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

1. Click the CLASSIFY button to enable classification of tree segments.
2. Click to select a tree segment or select several segments by holding the Ctrl key and clicking the segments of interest. Selected segments are indicated by three white squares that represent the beginning, middle, and end of the segment.
3. Select a name from the drop-down menu.
4. To customize the names in the list, click the COLOR SETS button, 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.

1. Click a tree 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!

1. Click a tree to select it or click the Select All button.
2. Click the arrow near the colored square to access the color picker.
3. Select a new color by clicking on it or click Custom Color… for more options.

1. Click a tree to select it or click the Select All button.
2. Click the Hide selection button

To show hidden trees, click the Show all hidden button

1. Click a tree to select it.
2. Drag the Transparency slider.

If you want a tree to be entirely invisible, use the Hide selection button. If you set transparency to its maximum value, you won't be able to select that tree again later.

Use this option to obtain a less jagged tracing.

This feature is for visualization purposes only (e.g., snapshots for publications); it doesn't affect your data.

1. Select a tree.
2. Check the Smooth box.
3. Drag the slider to the right for more smoothing or to the left for less smoothing.

(Available with Neurolucida 360 Studio only)

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

• To view a list of issues, click the Cleanup button.
• To delete all the fragments that can be automatically deleted ( in the list), use the Clean All button.
• 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 window, turn off line thickness. Nodes are displayed as solid circles.
2. Click Trace>Edit>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.