Edit Trees Panel (3D)

See Editing trees (3D) for detailed instructions

You can edit entire trees or individual points on a tree.

To view more options in the panel, select trees first (click the Select All button or click a tree model).

Selecting and Show/Hide Controls

Select All

Click the Select All button to select all the traced trees.

Hide/Show Selection

  • Select a tree and click the Hide selection button to hide it.
  • You can show the tree again later by clicking the Show selection, or the Show all hidden button if you've hidden multiple trees.

Tree-editing buttons

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

Points

  • Click the button to view the trees displayed as a series of points.

  • The Points mode enables Detach at a specific point, Connect and Directionality.

  • You can move and delete points, and adjust a point's thickness.

Detach

  • Click the button to enable the Detach mode. If you also click Points, you'll be able to detach with more precision.

  • Click a tree to detach.

    • If you click somewhere on a single branch, the tree is split in two.
    • If you click the site of a bifurcation, the tree is split in three

  • When you're done detaching, make sure you click Detach again to disable it.

Connect

  • Click the button to display trees as series of points and enable the Connect mode.

  • Click and drag an end point toward the desired connection area. The end point briefly turns green and a green line appears. Release the mouse button to connect the branches.

Cleanup

(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.

  • Branch fragment found: Singlepoint branches attached to trees -- Fix will detach those branches and then delete them.
  • Tree fragment found: Twopoint trees not attached to anything -- Fix will delete these trees.
  • Root fragment found: Twopoint 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: Singlebranch trees (i.e., with at least three points) not connected to anything -- There is no automatic Fix; you need to connect manually.

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.

  • To delete all the fragments marked by in the list, use the Clean All button.
  • To inspect a specific issue, click the issue; you'll be redirected to the corresponding area in the tracing.
  • To resolve a specific issue, click in the Fix column.

Classify

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

  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.

Remove

Click the Remove button to delete selected trees/branches.

Type

Use to assign tree types, which may be useful for later analysis in Neurolucida Explorer.

  • Select a tree then select a type from the Type drop-down menu.

Tree color

To change the color, select a tree then click the arrow near the colored square to access the Color menu.

Transparency

Select a tree then drag the Transparency slider.

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

Smooth

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

  • Select a tree, check the box, and drag the slider to obtain a less jagged tracing.

Thickness

You may change the thickness of an entire tree or the thickness at a single point (or a group of points).

For a single point, click the Points button, click a point in the model to select it, then drag the slider.