The main window (shown below) provides easy access to the capabilities of the program. On the right side of the window are the tools and view panel which allow you to switch modes of operation or switch the viewing direction by clicking the appropriate button. This can also be accomplished by using the main menu.

The status bar at the bottom of the window displays information such as cursor coordinates, zoom factor, measurement output, etc.

Buttons

The zoom tool is used to zoom in or out of the 2D display.

TIP: If your mouse has a scroll wheel it may be used to quickly zoom in and out of the display, regardless of which tool is active.

The move tool is used to translate the display for the current view. It is also used to translate and rotate selected parts of the model.

The seed tool is used to select starting locations for automatic tracing.

The measurement tool is used to sample the image data to determine such information as diameter(width) and length. It is also used to select measurements and manually create new sections of the model.

The spine tool is used to manually add new spines and to select spines for editing.

The neurite tool is used to create new sections of the model by semi-manual tracing. It is also used to select vertices of the model for editing.

The R.O.I. tool is used to adjust the region of interest for the current dataset, allowing for faster visualization of the data contained within it, since data outside of the region is ignored. In addition, it is used to limit analysis to a specified cuboid section of the data for some operations.

The magnet tool is used to quickly select vertices of the model for editing and translation. It can also be used to translate the display for the current view.

Sets the 2D display to the forward view. The line of sight is parallel to the Z (optical) axis.

Sets the 2D display to the side view. The line of sight is parallel to the X axis.

Sets the 2D display to the bottom view. The line of sight is parallel to the Y axis.

Menus

() indicates an option that can be toggled on or off. () indicates a sub-menu.

Edit
Delete Neurites   X+N	Delete the dendrites.
Delete Spines   X+S	Delete all spines.
Delete Measurements   X+M	Delete all measurements.
Delete All   X+A	Delete model, spines, and measurements.
Delete Selected   Delete	Delete the selected elements depending on the current mode.
Join / Unjoin 2-Selected   J	Add or remove an edge between 2 selected vertices. Neurite tool must be active and only 2 vertices selected.
Set 1-Selected as Origin	Set the selected vertex as an origin. Only 1 vertex must be selected.
Select All Connected	Select all vertices in the same connected component of any selected vertices.
Select Sub-Trees	All vertices within the same sub-tree as a selected vertex also become selected.
Select by Type / Function ()	A sub-menu for selecting objects by type or function.
Select Spine Stems	Select spines that may be created due to inadequate resolution of spine necks.
Select Spines on Selected Neurites	Selects spines that are attached to any currently selected neurites.
Select Spines with Invalid S.A.	Selects those spines with an attachment area that is greater than their surface area.
Create Neurite Selection Paths	Selects all vertices along paths between any currently selected vertices.
Set Order of Selected Neurites	Opens a dialog box for manually setting the branch order of any selected neurites.
Add Selected Spines to Classifier	Adds any selected spines to the current neural network classifier.
Transpose Children of Selected Vertices	Reverses the layout in memory of edges for selected vertices. Useful for rearranging section labeling.
Hide Selected	Hides any selected vertices.
Unhide All	Unhides any vertices that were previously hidden.
Select All   Ctrl+A	Selects all elements depending on which tool is active.
Deselect All   Esc	Deselects any selected elements.
Convert Measurements   C	Converts measurements into a section of the model.
Mode ()	A sub-menu for setting the current mode (tool).

Run
Settings...	Open the settings dialog.
Spine Classifier...	Open the spine classifier dialog.
Build Neurites   N	Start the automatic tracing procedure.
Build Spines   S	Start the spine detection and analysis procedure.
Recompute Spine Attachments	Recompute the points where the spines attach to the model.
Recompute Manual Spines	Recompute various spine attributes for manual spines only.
Visualize R.O.I.   F9	Accepts the current region of interest. The projections and volume rendering (if active) are automatically regenerated.
Image Filter ()	A sub-menu for various image processing routines.
Projections ()	A sub-menu for various options for generating projections.
Edge Labeling ()	A sub-menu for various ways of labeling edges.
Sholl Analysis	Runs and saves a sholl analysis on the current model.
Number of CPU's ()	Specify the number of CPU's for your machine.

View
Image ()	Toggle display of the image.
Palette ()	Set the current palette for the 2D and 3D displays.
Line/Point Size ()	Set the line and point size (in pixels) for various rendered elements.
Colors...	Open the colors window to set the colors of various elements of the display.
3D Viewer...	Open the 3D view window.
XY Slice Viewer ()	Start the slice viewer display.
XY Projection (Axial) ()	Set the 2D display to the forward view.
ZY Projection (Side) ()	Set the 2D display to the side view.
XZ Projection (Side) ()	Set the 2D display to the bottom view.
Fit Image   F	Adjust the zoom factor so that the image fits completely within the 2D display window.
Actual Pixels   A	Set the zoom factor to 100% (no magnification).
Center & Limit Image ()	Toggle activation of centering and limiting the image display.
Seed Always Visible ()	Toggle whether to display the current seed no matter which mode is active.
R.O.I. Always Visible ()	Toggle whether to display the current region of interest no matter which mode is active.
Spine Axes ()	Toggle whether or not to show the attachment axis of the spines.
Spine ID's (2D Only) ()	Toggle the display of the spine ID numbers in the 2D window.
Edge Order Numbers (2D Only) ()	Toggle the display of the edge order numbers in the 2D window.
Edge Section Numbers (2D Only) ()	Toggle the display of the edge section numbers in the 2D window.
Sholl Spheres (2D Only) ()	Toggles the display of the sholl analysis spheres in the 2D window.
Projection Axes ()	Togglw whether or not to show the current axes of the projection in the 2D window.
Flash Model   F4	Temporarily displays only the dataset.
Flash Hidden   F3	Temporarily displays any hidden objects.

Render
Neurite Vertex Shape ()	A sub-menu for various ways of displaying the vertices of the model.
Neurite Vertex Color ()	A sub-menu for various ways of coloring the vertices of the model.
Neurite Edge Shape ()	A sub-menu for various ways of displaying the edges of the model.
Neurite Edge Color ()	A sub-menu for various ways of coloring the edges of the model.
Spine Shape ()	A sub-menu for various ways of displaying spines.
Spine Color ()	A sub-menu for various ways of coloring spines.
Model Shape (Neurite, Edge, Spine) ()	A sub-menu for various ways of setting the shapes of the neurites, edges, and spines with a single click.
Flicker Free (Slower) ()	Toggle synchronized drawing of the 2D and 3D windows.