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Volumetric Analysis

3D Viewer

The 3D Viewer provides volumetric visualization, orthogonal slicing, spectral/spatial section views, opacity control, and 3D K-means segmentation of hyperspectral datacubes.

Overview

The IDCubePro 2026 3D Viewer is an interactive visualization environment designed to explore the spatial and spectral structure of hyperspectral datasets.

A hyperspectral datacube is represented as a three-dimensional array:

  • X: Horizontal spatial dimension.
  • Y: Vertical spatial dimension.
  • Z: Spectral dimension (wavelength bands).

The viewer provides volume rendering, isosurface visualization, three-dimensional slicing, orthogonal sections, and unsupervised clustering.

Before rendering, IDCubePro normalizes the datacube using robust intensity limits to reduce the influence of extreme values.

1. Volume Rendering and Isosurface

Volume Render

Volume Render displays the complete intensity distribution throughout the three-dimensional hyperspectral datacube.

Voxel visibility is controlled by the selected opacity profile, allowing structures within different intensity ranges to be emphasized.

Isosurface

Isosurface mode displays a surface corresponding to a selected normalized intensity level.

  • The Iso Value slider determines the intensity threshold used to construct the surface.
  • The Iso Value control becomes active only when Isosurface mode is selected.

2. Colormap Selection

The colormap determines how normalized intensity values are converted into display colors.

Available colormaps include:

  • Gray
  • Parula
  • Turbo
  • Jet
  • Hot
  • Cool
  • Spring
  • Summer
  • Winter
  • HSV
  • Bone
  • Copper

Custom LUT

Selecting Custom LUT opens the IDCubePro Lookup Table editor.

A custom LUT allows users to define an N × 3 RGB color mapping for the visualization.

3. Opacity Controls

Opacity determines the visibility of individual voxels during Volume Render mode.

Available opacity profiles include:

  • Linear: Opacity increases approximately with normalized intensity.
  • Profile 1: Emphasizes higher-intensity voxels.
  • Profile 2: Provides relatively greater visibility to lower-intensity voxels.
  • Profile 3: Suppresses lower-intensity ranges.
  • Profile 4: Applies stronger suppression of lower-intensity ranges.
  • Custom: Opens the interactive opacity-curve editor.

Custom Opacity Editor

The custom opacity editor allows the user to interactively shape the opacity response as a function of normalized intensity.

This is particularly useful when important structures occupy a narrow intensity range or when low-intensity background obscures higher-intensity features.

4. X, Y, and Z Scaling

The X, Y, and Z scale controls modify the displayed geometry of the volume without changing the original data values.

Scaling is useful for:

  • Adjusting the appearance of anisotropic datasets.
  • Compressing or expanding the spectral dimension.
  • Improving the visibility of volumetric structures.
  • Optimizing visualization proportions.

Important: For a hyperspectral datacube, Z normally represents spectral bands rather than physical depth. Therefore, the three-dimensional rendered shape should not automatically be interpreted as physical sample geometry.

5. 3D Slice Visualization

The 3D Slice mode displays intersecting X, Y, and Z planes within a common three-dimensional coordinate system.

The X, Y, and Z sliders allow users to move each slice position interactively through the datacube.

This mode is useful for examining how spatial and spectral features intersect within the dataset.

6. Orthogonal Slice Visualization

The Orthogonal Slice mode displays separate two-dimensional sections through the cube.

  • XY: Spatial image at the selected spectral band (Z).
  • YZ: Vertical spatial/spectral section at the selected X position.
  • XZ: Horizontal spatial/spectral section at the selected Y position.

The information panel reports the current X, Y, and Z coordinates along with the datacube dimensions.

Slice Navigation

  • X slider: Horizontal spatial position.
  • Y slider: Vertical spatial position.
  • Z slider: Spectral-band position.

Slice navigation controls become active when either 3D Slice or Orthogonal Slice mode is selected.

7. 3D K-means Segmentation

The Segmentation function applies K-means clustering to the normalized three-dimensional datacube.

K-means groups voxels according to numerical similarity in the data representation used by the viewer.

Segmentation Settings

Configure the available clustering parameters, including the number of clusters and maximum number of iterations.

IDCubePro then generates a three-dimensional label volume containing the cluster assignments.

Segmentation Results

After segmentation, IDCubePro provides:

  • Segmented slice visualization.
  • Individual cluster selection and display.
  • Cluster-in-3D visualization.
  • Cluster occupancy statistics.
  • Brightness adjustment.
  • Cluster colormap selection.

Segmented Slice Viewer

The segmented slice viewer allows users to navigate through Z slices of the label volume.

Individual clusters can be selected and displayed independently within the current slice.

Cluster in 3D

The Cluster in 3D function displays only the selected cluster as a volumetric object.

The viewer also reports the percentage of the complete datacube occupied by the selected cluster.

Interpreting Segmentation Results

Important: K-means identifies groups based on numerical similarity. A cluster does not automatically correspond to a validated tissue type, material, chemical species, or biological structure.

Interpretation should be supported by spectral analysis, spatial context, appropriate controls, and independent validation.

8. Viewer Controls

Back to Original

The Back to Original function leaves the active volumetric or slice visualization and displays the original datacube at approximately the middle spectral band.

Reset View

Restores the initial 3D Viewer display.

Theme Refresh

Updates the viewer status after an IDCubePro theme change.

9. Exporting Visualizations

The Export menu allows users to copy or save the current 3D Viewer interface.

  • Copy Interface View: Copies the current rendering to the Windows clipboard.
  • Save Interface View As: Saves the interface as PNG, JPEG, or TIFF.

10. Step-by-Step Workflow

The following workflow demonstrates a typical 3D Viewer analysis.

  1. Load a hyperspectral dataset in IDCubePro.
  2. Open the 3D Viewer from the volumetric analysis tools.
  3. Generate the 3D representation of the datacube.
  4. Select Volume Render or Isosurface mode.
  5. Choose an appropriate colormap.
  6. Adjust opacity or Iso Value as necessary.
  7. Adjust X, Y, and Z scaling if required.
  8. Use 3D Slice to examine intersecting sections.
  9. Use Orthogonal Slice for separate XY, YZ, and XZ views.
  10. Apply K-means segmentation if cluster analysis is needed.
  11. Inspect individual clusters and occupancy statistics.
  12. Export the resulting visualization.

11. Performance Considerations

Large hyperspectral datasets may require substantial system memory and CPU/GPU resources.

  • Volume rendering may be slower for large datacubes.
  • Three-dimensional segmentation can require additional processing time and memory.
  • The viewer internally converts and normalizes data before volumetric rendering.

12. Important Interpretation Notes

The third array dimension of a hyperspectral datacube normally represents wavelength or spectral band, not physical depth.

Therefore, the rendered hyperspectral datacube should generally be interpreted as a spectral-spatial data visualization, rather than a literal three-dimensional physical object.

This distinction is particularly important when examining XZ and YZ sections or changing the Z-axis scale.

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