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 3D Viewer provides volumetric visualization, orthogonal slicing, spectral/spatial section views, opacity control, and 3D K-means segmentation of hyperspectral datacubes.
A hyperspectral cube is treated as a three-dimensional array:
X - spatial horizontal dimension Y - spatial vertical dimension Generate 3D renders the complete hyperspectral datacube using MATLAB volumetric visualization.
Before rendering, IDCubePro normalizes the cube using robust intensity limits to reduce the influence of extreme values.
Displays the complete intensity distribution throughout the 3D cube.
Voxel visibility is controlled by the selected opacity profile.
Displays a surface corresponding to a selected normalized intensity level.
The Iso Value slider controls the intensity threshold used to construct the surface.
The Iso Value control is active only when Isosurface mode is selected.
The colormap determines how normalized intensity values are converted to colors.
Available maps include gray, parula, turbo, jet, hot, cool, spring, summer, winter, hsv, bone, and copper.
Custom LUT opens the IDCubePro LUT editor.
A custom LUT allows a user-defined N x 3 RGB color mapping to be applied to the visualization.
Opacity determines which voxels are visible during Volume Render mode.
Linear - opacity increases approximately with normalized intensity.
Profile 1 - emphasizes higher-intensity voxels.
Profile 2 - gives relatively greater visibility to lower intensities.
Profiles 3 and 4 suppress lower-intensity ranges using progressively stronger thresholds.
Custom opens the interactive opacity-curve editor.
The custom editor allows opacity to be shaped interactively as a function of normalized intensity.
This is useful when important structures occupy a narrow intensity range or when low-intensity background obscures higher-intensity structures.
X, Y, and Z scale controls change the displayed geometry of the volume.
These controls do not change the underlying data.
They are useful when physical voxel dimensions are anisotropic or when the spectral dimension needs to be visually compressed or expanded.
For hyperspectral data, Z normally represents spectral bands rather than a physical depth dimension. Therefore, 3D shape along Z should not automatically be interpreted as physical sample geometry.
3D Slice displays intersecting X, Y, and Z slice planes inside a common 3D coordinate system.
Use the X, Y, and Z sliders to move the slice positions through the cube.
This mode is useful for examining how spatial and spectral structures intersect within the datacube.
Orthogonal Slice 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 and cube dimensions.
X selects the horizontal spatial position.
Y selects the vertical spatial position.
Z selects the spectral-band position.
The slicer controls become active when 3D Slice or Orthogonal Slice mode is selected.
Segmentation applies K-means clustering directly to the normalized three-dimensional datacube.
- Maximum number of iterations
IDCubePro then generates a 3D label volume.
After 3D K-means segmentation, IDCubePro provides:
- Individual cluster display
- Cluster-in-3D visualization
The segmented slice viewer allows navigation through Z slices of the label volume.
A specific cluster can be selected and displayed independently within the current slice.
Cluster in 3D displays only the selected cluster as a volumetric object.
- Percentage of the complete cube occupied by that cluster
Brightness and cluster colormap can also be adjusted.
K-means identifies groups according to numerical similarity in the datacube.
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, controls, and independent validation.
Back to Original leaves the active volumetric or slice view and displays the original cube at approximately the middle spectral band.
The Export menu can copy or save the current 3D Viewer interface as an image.
Copy Interface View copies the current interface rendering to the Windows clipboard.
Save Interface View As saves the current interface as PNG, JPEG, or TIFF.
Reset View restores the initial 3D Viewer display.
Theme Refresh updates the viewer status after an IDCubePro theme change.
1. Load a hyperspectral dataset.
4. Choose Volume Render or Isosurface.
5. Select an appropriate colormap.
6. Adjust opacity or Iso Value.
7. Adjust X/Y/Z scale if necessary.
8. Use 3D Slice to examine intersecting sections.
9. Use Orthogonal Slice for separate XY, YZ, and XZ views.
10. Use Segmentation if 3D cluster analysis is needed.
11. Inspect individual clusters before biological or material interpretation.
12. Export the visualization when needed.
Large hyperspectral cubes may require substantial memory and GPU/CPU resources.
Volume rendering and 3D segmentation may take longer for large datasets.
The viewer internally converts and normalizes data before volumetric rendering.
The third array dimension of a hyperspectral cube normally represents wavelength or spectral band, not physical depth.
Therefore, a rendered hyperspectral cube should generally be interpreted as a spectral-spatial data visualization rather than a literal three-dimensional physical object.
This distinction is especially important when displaying XZ and YZ sections or changing the Z-axis scale.
Close the 3D Viewer help window.