The 3D view in the lower-right shows the image slices from the 2D views as well as the current object's surface model, if one exists. It also shows the reference frame of the image data, with its origin in the lower-left corner of the first image slice in the data file. When the mouse cursor hovers over the 3D view, its border turns yellow indicating the window has become active.

The following interaction is possible in an active 3D view:

• 3D rotation (virtual trackball) using the left mouse button,
• panning using the middle mouse button,
• zooming using the mouse wheel or right mouse button, and
• spinning (in-window-plane rotation) using the left mouse button while pressing the Ctrl key.