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3D Visualization Techniques

Effective visualization communicates the content and structure of your data. This tutorial covers advanced rendering techniques, including volume rendering, surface shading, clipping operations, and camera controls for creating publication-quality images.

Estimated time: 30 minutes

Prerequisites:

  • Completed basic tutorials
  • A project with volumes, masks, and/or surfaces

Volume Rendering Concepts​

Volume rendering displays 3D data by calculating how light interacts with the entire dataset—not just surfaces. Each voxel contributes to the final image based on its intensity and assigned visual properties.

Key concepts:

  • Transfer Function — Maps intensity values to color and opacity
  • Opacity — How transparent each intensity appears
  • Sampling — How many rays pass through the volume
  • Shading — Lighting calculations for depth perception

An opacity transfer function with a colour bar, and one ray through twelve voxels showing the opacity each voxel gets, the opacity accumulated front to back along the ray and the resulting pixel colour

Configuring Volume Display​

Window/Level Adjustment​

The fundamental visualization control:

  1. Navigate to View → Slice Views → Window/Level.
  2. Adjust:
    • Level — Center intensity (brightness)
    • Window — Intensity range (contrast)

Interactive adjustment:

  • Hold Left mouse button and drag in slice views
  • Horizontal: Window | Vertical: Level

The mapping from gray value to display value for level 40 and window 350: black below the window, a linear ramp inside it, white above; and the ramps of a narrow CT-Brain window and a wide CT-Lung window

Lookup Tables (LUTs)​

Apply color mapping to intensity values:

  1. In the Window/Level panel, select a Lookup Table.
  2. Available options include:
    • Grayscale — Standard medical imaging
    • HotMetal — Fire-like warm colors
    • Spectrum — Full spectrum
    • Jet — Blue-cyan-yellow-red

LUTs enhance visualization of:

  • Intensity gradients
  • Analysis results
  • Presentation graphics

Mask 3D Preview​

Use one of the two mask preview modes depending on whether you need a calculated surface or immediate 3D updates:

  1. Navigate to View → 3D View.
  2. For a surface preview, use Mask 3D Preview (Mesh) and select a quality level:
QualityDescriptionUse Case
LowFast, coarseQuick exploration
MediumBalancedGeneral review
HighEnhanced detailSpecial applications
OptimalFull resolutionMeasurements, export

The outline of a mask at full resolution, and the outline after the mask is downsampled first, which lies in a different place

  1. Click Mask 3D Preview (Mesh) to generate.

For immediate 3D feedback while editing, enable Mask 3D Preview (Direct) instead. Direct mode renders mask voxels as a volume, does not create a surface mesh, and is turned off automatically when you generate a mesh preview.

Quality for Measurements

Use Optimal quality when performing measurements on mask previews. Lower quality settings use downsampled data that may introduce geometric error.

Managing Previews​

  • Remove All Previews — Clear generated previews to free memory
  • Existing mesh previews can regenerate automatically after edits if enabled in Preferences
  • Direct preview updates immediately from the mask volume and does not regenerate a mesh

Surface Representation Modes​

Control how surfaces appear in the 3D view:

ModeKeyDescription
SolidSFilled, shaded surfaces
Solid EdgesEFilled with visible triangle edges
WireframeWTriangle edges only
PointsQVertices only

Access from View → 3D View → Surface Representation or use keyboard shortcuts.

Shading Algorithms​

Configure lighting calculations:

AlgorithmAppearance
NoneFlat, unlit
FlatPer-face shading
GouraudSmooth vertex interpolation
PhongPer-pixel highlights
PBRPhysically based rendering

The same six-facet cylinder shaded with None, Flat, Gouraud and Phong interpolation, from unlit and faceted to smooth

Access from View → 3D View → Surface Shading.

Phong provides good quality for most applications. Use PBR for realistic material appearance in presentations.

Lighting Configuration​

Proper lighting enhances depth perception and surface detail.

Light Studio​

  1. Navigate to View → Camera → Light Studio.
  2. Orbit to the viewpoint you want to light.
  3. Choose Presets → Three-Point Studio for a balanced starting point.
  4. Select the key, fill, or back light to adjust it. The preset enables Cast shadows only on the key light so the scene has one coherent shadow direction.

Light Properties​

For each light:

PropertyEffect
IntensityBrightness level
Diffuse, specular, and ambient colorSurface illumination, highlights, and ambient tint
PositionLocation relative to scene
TypeScene light, camera light, or headlight
Positional lightChanges a directional light to a positioned spotlight or point light
Cast shadowsAllows the selected scene or camera light to produce mapped shadows

A directional light with parallel rays, a spotlight with its cone angle aimed at an object, and a point light shining in every direction, with the floor shadows the first two can cast

Lighting for Detail

For examining surface detail, use a strong key light from a side angle. For softer presentation images, reduce the fill light rather than enabling shadow casting on every light. See the complete Light Studio guide for manipulators, presets, floor shadows, and reusable JSON setups.

3D Clipping​

Reveal internal structures by removing portions of the display.

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 Clipping​

  1. Navigate to View → 3D Clipping → Enable.
  2. The clipping box activates.
  3. Content outside the box is hidden.

Adjust the Clipping Box​

  1. Click Show Box to display interactive handles.
  2. Drag face handles to resize along each axis.
  3. Drag edges or corners for multi-axis adjustment.

Clipping Options​

OptionEffect
EnableToggle clipping on/off
Show BoxDisplay/hide interactive handles
InvertShow outside instead of inside
ResetReturn to full scene bounds

Clipping Workflow Example​

To create a cross-section view:

  1. Enable clipping.
  2. Show the box.
  3. Drag one face to cut through your structure.
  4. Hide the box for clean presentation.
  5. Rotate the view to examine the cross-section.

Camera Controls​

Standard Orientations​

Quick camera positioning using keyboard shortcuts:

KeyView
XRight (+X)
Shift+XLeft (-X)
YFront (+Y)
Shift+YBack (-Y)
ZTop (+Z)
Shift+ZBottom (-Z)
IIsometric

Or access from View → Camera → Standard Views.

Projection Modes​

ModeCharacteristics
PerspectiveObjects appear smaller with distance (realistic)
ParallelObjects maintain size regardless of distance (technical)

Press V to toggle between modes.

Camera Settings​

  1. Navigate to View → Camera → Camera Settings → 3D View.
  2. Configure:
    • View angle — Field of view (perspective mode)
    • Clipping range — Near/far rendering limits
    • Focal point — Center of rotation

Center of Rotation​

Set a custom rotation center:

  1. Position mouse over the point of interest.
  2. Press C to set it as the center of rotation and center that point in the 3D view.
  3. Subsequent rotations orbit this point.

Object Visibility and Widgets​

Scene Tree Controls​

For each object in the Scene Tree:

  • Visibility icon — shows or hides the object in the views
  • Click the name — selects the object and makes it the active object of its type, shown in bold. Tools that work on "the active mask" or "the active volume" use it
  • Double-click the name — renames the object in place
  • Right-click — opens the operations for that object type, including visibility, isolate, duplicate, export, rename, delete, and render properties

Object Widgets and Scene Helpers​

The 3D View section of the View tab holds these scene helpers:

ControlDescription
Additional → Object Widgets → Toggle OutlineBounding box around visible objects, per object type
Additional → Object Widgets → Toggle Corner OutlineCorner markers instead of a full box, per object type
Slice PlanesShows the slice planes of the active volume in the 3D view, and can use one as a clip plane
Axes PlanesReference planes along the principal axes

Object Widgets carries a submenu for Volume, Surface, and Volume Mesh, so each object type can be outlined on its own. Additional also holds Colors, which draws surface objects with their own color data.

Capturing Images​

Screenshots​

Capture static images of the current view:

  1. Navigate to File → Save Screenshot.
  2. Select target:
    • Application — Entire window
    • 3D View — 3D viewport only
    • Specific View — Individual view panel
  3. Choose destination (file or clipboard).
  4. Configure:
    • Format — PNG, JPEG, BMP
  5. Click Capture.

Video Recording​

Create animations with the Video Recorder panel:

  1. Navigate to File → Media → Record Video to open the Video Recorder at the bottom of the window.
  2. Configure:
    • Target view — Which view to record
    • Animation — Interactive (live), turntable rotation, rock, camera path (keyframes), slice sweep, or a timeline of multiple tracks (camera, opacity, clipping, slices, background)
    • Duration and frame rate — Length and smoothness of the animation
    • Quality, format, and folder — Output resolution, MP4/AVI format, and save location
  3. Click Preview to check the animation in the view without recording.
  4. Click Record. Animated recordings are rendered frame by frame and saved automatically when they complete. For Interactive (live), click Stop when finished.

Creating Presentation Views​

Multi-Structure Visualization​

When displaying multiple structures:

  1. Assign distinct colors to each surface/mask.
  2. Consider opacity:
    • Outer structures: Lower opacity (0.3-0.5)
    • Inner structures: Higher opacity (0.7-1.0)
  3. Use clipping to reveal internal relationships.

Publication-Quality Images​

For journal figures or presentations:

  1. Maximize 3D view — Use 3D Only layout.
  2. Set high resolution — Configure screenshot for publication DPI.
  3. Use white/transparent background — Works better in documents.
  4. Apply consistent lighting — Phong or PBR shading.
  5. Remove distracting elements — Hide widgets, use clean representation.

Practical Exercise: Create a Visualization​

Part 1: Configure Display​

  1. Load a project with a bone mask and soft tissue.
  2. Generate 3D preview for both masks.
  3. Set bone color to white/ivory.
  4. Set soft tissue color to pink with 50% opacity.
  5. Apply Phong shading.

Part 2: Create Views​

  1. Use clipping to create a cross-section.
  2. Capture a screenshot.
  3. Switch to isometric view (I key).
  4. Capture another screenshot.
  5. Create a 360° rotation video.

Part 3: Optimize for Export​

  1. Maximize the 3D view.
  2. Hide the clipping box.
  3. Set white background.
  4. Capture high-resolution image.

Best Practices​

Visualization Goals​

PurposeApproach
ExplorationStandard lighting, quick preview
MeasurementOptimal quality, no distortion
PresentationPolished lighting, clean background
PublicationHigh resolution, consistent style

Performance​

  • Use lower quality previews during exploration
  • Reduce triangle count for faster rendering
  • Disable widgets when not needed
  • Close unused views to allocate resources

Consistency​

  • Document your visualization settings
  • Create presets for repeated workflows
  • Use consistent coloring across related projects

Troubleshooting​

Display appears black​

  • Check Window/Level settings
  • Verify object visibility in the Scene Tree
  • Reset the view (press R)

Slow rendering​

  • Reduce preview quality
  • Decimate surfaces
  • Hide unnecessary objects

Colors appear wrong​

  • Check lookup table selection
  • Verify Window/Level range
  • Review light colors and enabled lights in Light Studio

Next Steps​

Continue learning with:

See Also​