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3D Clipping

The 3D Clipping section of the View tab provides tools to define a region of interest in the 3D view. Geometry outside (or inside, if inverted) the clipping region is hidden, allowing you to focus on specific structures.

A slice plane shown in the 3D view can cut the scene the same way, on its own or together with the box. See Slice Plane Clipping.

Overview​

The clipping box is an axis-aligned bounding region that controls what geometry is visible in the 3D view. It affects:

  • Volume rendering
  • Surface models
  • Mask 3D previews
  • Volume meshes

Clipping is a visualization tool—it does not modify or delete underlying data.

The clipping box, where only what is inside the box is drawn or only what is outside with Invert, and slice plane clipping, where the scene is cut open along a slice plane and one half is kept

Enable​

Click Enable to activate clipping. When enabled:

  • The clipping box is applied to all visible objects in the 3D view
  • Geometry outside the box is not rendered
  • The box initializes to the bounds of visible objects

Click Enable again to deactivate clipping and restore full visibility.

note

Clipping affects the 3D view only. Slice views display the complete data regardless of clipping settings.

Show Box​

Toggle the visibility of the clipping box outline and interactive handles.

When Visible​

  • The box appears as a wireframe cube in the 3D view
  • Handles on each face allow resizing by dragging
  • Edge and corner handles may be available for multi-axis adjustments
  • The box outline helps visualize the clipped region boundaries

When Hidden​

  • Clipping remains active (if enabled) but the box is not drawn
  • Use for cleaner visualization once the region is set
  • Re-enable to adjust the region

Box Appearance​

The clipping box uses configurable colors for:

  • Outline edges
  • Face handles

Colors can be adjusted in File > Preferences > 3D View.

Invert​

Reverse which region is clipped:

StateVisible Region
NormalGeometry inside the box
InvertedGeometry outside the box

Invert applies to the clipping box only. A slice plane that cuts carries the side it keeps in its own setting.

note

Invert is unavailable while a shown slice plane is actively cutting, and is switched off if one starts to. This combination is not supported. Turn the plane clipping off, or hide the plane, to use Invert again.

Invert is also unavailable while a visible volume with clipping enabled uses CPU rendering. Use GPU rendering if the volume supports it, hide the volume, or turn off clipping for that volume to use Invert.

Use Cases​

  • Normal: Isolate a specific structure by defining a box around it
  • Inverted: Remove an occluding structure by defining a box around it
tip

Use Invert to "cut away" parts of the scene that block your view of internal structures, such as removing outer anatomy to reveal interior features.

Reset​

Click Reset to restore the clipping box to the bounding box of all visible objects. This is useful when:

  • The box has been moved or resized away from the data
  • You want to start over with a fresh clipping region
  • Objects have been added or removed and the bounds have changed

Reset does not disable clipping—it only repositions the box.

Adjusting the Clipping Box​

When the box is visible, you can interactively adjust its position and size:

Resizing​

  • Hover over a face handle until the cursor changes
  • Left-drag to move that face inward or outward
  • The opposite face remains fixed
  • Ctrl+right-drag to resize the whole box

Moving​

  • Ctrl+left-drag to translate the whole box
  • Alternatively, resize opposing faces equally

Precision Adjustments​

For precise control, consider using the slice views:

  • The clipping box corresponds to physical coordinates
  • Adjust based on known anatomical landmarks or measurements

Slice Plane Clipping​

A slice plane shown in the 3D view can cut the scene open instead of, or in addition to, the clipping box. Everything on one side of the plane is hidden, so the objects are drawn as if they had been cut along the current slice.

Turning It On​

The quickest way is from the slice view itself:

  1. Right-click the slice view whose plane should cut
  2. Choose 3D Slice Plane > Use as Clip Plane > Keep Front or Keep Back

This also shows the plane, because a plane only cuts while it is shown.

The same entries are in the Slice Planes menu of the View tab, under the submenu for the plane.

The setting is also available in the Render Properties tool, which is the place to use when the plane belongs to a volume other than the active one:

  1. Open Render Properties from the Image tab
  2. Go to the Widgets page and enable Show slice planes
  3. Select the plane in the plane selection combo box
  4. Set Use as clip plane to Keep front or Keep back in the plane settings

Keep front and Keep back select which of the two halves stays. Which half each one keeps depends on the orientation of the image data, so if the wrong half disappears, pick the other entry.

The plane cuts as long as it is shown. Hiding the plane stops the cut, and each plane carries its own setting, so one, two, or all three planes can cut at the same time. Two parallel planes set to keep the space between them leave a slab.

tip

To keep the cut without seeing the plane itself, set the plane opacity to 0 and turn Outline visibility off rather than hiding the plane. Hiding it stops the cut.

Behavior​

  • The cut follows the slice. Scrolling through slices, dragging the plane in the 3D view, or moving the crosshair moves the cut with it
  • It applies to every visible object with clipping enabled, not only to the volume the plane belongs to. A plane can therefore cut surfaces and masks while its own volume is hidden
  • The side is a property of each plane. Invert in the 3D Clipping section belongs to the clipping box and does not change it
  • The clipping box and the slice planes can cut at the same time; only what survives both is drawn. Invert is not available in that combination
  • Invert is unavailable while a visible volume with clipping enabled uses CPU rendering
  • An object whose own Clipping option is switched off is never cut, by either source
  • Up to six planes cut at a time, or two while the clipping box is enabled. If the limit is reached, extra clip-plane settings are turned off and a message explains why
  • Slice views are not affected
tip

A single slice plane set to clip gives a cut-away view that stays aligned with what the corresponding 2D view shows, which makes it easier to relate a feature in the slice to its position in the 3D scene.

The setting is stored with the volume and is saved in the project.

Clipping and Object Types​

Different object types respond to clipping:

Object TypeClipping Behavior
Volume RenderingVoxels outside the box are not sampled
SurfacesPolygons are clipped at box boundaries
Mask PreviewsSame as surfaces
Volume MeshesElements are clipped at box boundaries
info

Whole Cell Clipping: An option in Preferences controls whether volume mesh clipping shows partial cells or keeps only whole cells inside the region.

info

For per‑object clipping, open the Render Properties of the selected object type and use the Clipping option to toggle 3D clipping on or off. This allows you to clip only the chosen object while keeping other visible objects unaffected.

Common Workflows​

Workflow: Isolating an Anatomical Region​

  1. Load the dataset and ensure relevant objects are visible in the 3D view
  2. Open the View tab in the ribbon
  3. In the 3D Clipping section, click Enable to activate clipping
  4. Click Show Box to display the clipping region handles
  5. Drag the face handles to surround the region of interest
  6. Fine-tune by dragging each face inward to exclude unwanted geometry
  7. Click Show Box again to hide the box while keeping clipping active

Workflow: Revealing Internal Structures​

  1. Enable clipping with the box encompassing all objects
  2. Click Invert to clip geometry inside the box instead of outside
  3. Resize the box to define the "cut-away" region
  4. Drag the box faces inward to remove occluding outer structures
  5. The interior anatomy is now visible

Workflow: Creating a Cross-Section View​

  1. Enable clipping and show the box
  2. Drag one face of the clipping box to the center of the structure
  3. This creates a cross-section, showing the internal structure at the clipping plane
  4. Combine with slice plane visibility in the 3D View section for reference
  5. Toggle Show Box off for a cleaner presentation view

Workflow: Comparing Clipped and Unclipped Views​

  1. Set up the clipping region as needed
  2. Toggle Enable to switch between clipped and unclipped states
  3. The box resets to the visible object bounds when re-enabled
  4. Adjust the box again if you need to restore the previous region

Preferences​

Related settings in File > Preferences > 3D View:

SettingDescription
Keep only whole cells when clippingVolume mesh clipping shows complete elements only
Outline colorColor of the clipping box edges
Handle colorColor of the interactive face handles

Limitations​

  • Slice views are not affected by 3D clipping
  • Up to six slice planes can cut at a time, or two while the clipping box is enabled
  • Invert cannot be combined with slice plane clipping
  • Invert requires GPU rendering for every visible volume that has clipping enabled