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Display Interior Labels by Clipping Volume Planes

Open Live Script

This example shows how to interactively clip a quadrant of a volumetric image to expose a surface within the volume.

Display Volumetric Image in Scene

Load a volumetric image and corresponding labels.

dataDir = fullfile(toolboxdir("images"),"imdata","BrainMRILabeled");
load(fullfile(dataDir,"images","vol_001.mat"));
load(fullfile(dataDir,"labels","label_001.mat"));

Create a 3-D scene with a white background color. Display the volume in the scene.

viewer = viewer3d(BackgroundColor="white",BackgroundGradient="off");
hVolume = volshow(vol,Parent=viewer);

Display Quadrant of Volume

To interactively add a clipping plane, click the clipping plane button in the axes toolbar. The Viewer3d object adds the clipping plane in a default location and orientation in the center of the scene.

You can manipulate the location of the plane using the context menu of the plane, or by interacting directly with the plane on the screen.

  • Translate the plane along the normal vector by clicking and dragging the plane.

  • Rotate the plane by clicking and dragging on the push pin on the plane. While rotating, you can hold down Shift to snap to 45 degree angles.

  • Interactively remove a clipping plane by clicking "Remove Plane" in the context menu.

All interactive controls can be restricted using the ClippingInteractions property. You can turn off clipping interactions entirely using the Interactions property.

Add another clipping plane by clicking the clipping plane button in the axes toolbar again. The colors of the planes indicate that the planes are aligned with a particular axis. Oblique planes are black and white. You can add up to six planes in the scene.

Remove Quadrant of Volume

By default, the Viewer3d object hides all regions that are clipped by any clipping plane. The two perpendicular clipping planes cause the scene to display only a quadrant of the volume.

To hide only regions that are clipped by all clipping planes, set the ClipIntersection property of the Viewer3d object to false. For these two perpendicular clipping planes, the scene removes the quadrant of the volume that intersects both planes.

viewer.ClipIntersection = "on";

Add Surface Representing Labeled Object

Create a binary mask for the class with numeric label 3.

label3 = label==3;

Create a Surface object encompassing the binary mask and display the surface in the scene. The scene applies the clipping planes to the surface. 

surf = images.ui.graphics3d.Surface(viewer,Data=label3,Alpha=1);

Remove Clipping Planes from Surface

By default, the Viewer3d object applies clipping planes to all objects that are children of the object. To apply different clipping planes to different children, set the GlobalClipping property of the viewer to "off". The volume and the surface no longer appear clipped because their ClippingPlanes property is empty.

viewer.GlobalClipping = "off";

The ClippingPlanes property of the viewer stores the position and orientation of the global clipping planes. Copy these values to the ClippingPlanes property of the volume. The volume is clipped, but the surface object remains intact.

hVolume.ClippingPlanes = viewer.ClippingPlanes;

Refine Volume Clipping Planes

Notice that the two interactive planes are no longer visible. When GlobalClipping is turned off, you can interactively manipulate the clipping planes for only one object at a time. The active object for interactive clipping planes is the object specified by the CurrentObject property of the viewer. By default, the current object is the most recent object added to the scene, which in this case is the surface.

To continue modifying the clipping planes of the volume interactively, set the CurrentObject property of the viewer as the volume. Interacting with the clipping planes impacts the volume and not the surface.

viewer.CurrentObject = hVolume;

See Also

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