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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.

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.

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

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
  • Drag to move that face inward or outward
  • The opposite face remains fixed

Moving​

  • Some configurations allow dragging the entire 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

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 position is preserved when re-enabling
  4. Use this to quickly compare the full dataset with the isolated 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