Spectral / Vegetation Indices
Spectral / Vegetation Indices calculates common hyperspectral and remote-sensing indices from the currently loaded IDCubePro datacube.
Overview
Spectral / Vegetation Indices calculates common hyperspectral and remote-sensing indices from the currently loaded IDCubePro datacube.
The tool provides standard indices, custom three-band formulas, threshold-based masks, RGB composites made from index images, and export of calculated results.
1. Select an Index Category.
3. Review the index description and matched wavelengths.
4. Click Display Index, or leave Auto-update enabled.
5. Adjust Min and Max if a restricted display or mask range is required.
6. Optionally enable Show threshold mask overlay.
7. Create an RGB composite from three index images if desired.
8. Export the index image, mask, or RGB composite.
All - displays all available indices.
Common - widely used vegetation indices such as NDVI, SAVI, OSAVI, and MSAVI.
Chlorophyll - indices emphasizing chlorophyll, red-edge, or photosynthetic behavior.
Water / SWIR - indices using water-sensitive, nitrogen-sensitive, cellulose, salinity, or SWIR bands.
Structure - indices related to vegetation or canopy structure.
Custom - enables a user-defined formula using w1, w2, and w3.
Standard index definitions request specific wavelengths. IDCubePro uses the nearest available measured band to each requested wavelength.
The description panel reports both the requested wavelength and the actual matched wavelength and band number.
Nearest-band matching does not create a new interpolated spectral band. The calculation uses the measured band that is closest to the requested wavelength.
An index is marked "out of range" when one or more wavelengths required by its definition fall outside the spectral range of the loaded dataset.
Out-of-range indices are not calculated because nearest-band substitution outside the measured spectral range would not represent the intended index definition.
Calculates the selected index and displays the result as a 2-D index image.
Auto-update recalculates the index whenever the standard-index selection changes.
Min and Max define the selected index-value range.
These limits are used for display scaling and for generation of the threshold mask.
Auto Contrast sets Min and Max to approximately the 2nd and 98th percentiles of the current index image. This reduces the influence of extreme outliers on display contrast.
Reset Threshold restores automatic limits and hides the mask overlay.
When Show threshold mask overlay is enabled, pixels whose index values fall between Min and Max are selected.
The selected pixels are overlaid on the index image. The mask can be exported independently.
IMPORTANT: a threshold mask is a numerical selection based on index values. It is not automatically a validated vegetation, tissue, material, or biological classification.
Custom Index allows an element-wise formula using three selected spectral bands: w1, w2, and w3.
Example normalized-difference formula:
Use element-wise MATLAB operators for image calculations: .*, ./, and .^.
Allowed functions include sqrt, log, exp, abs, min, and max.
The w1, w2, and w3 dropdowns show both band number and wavelength so the exact data used by the custom formula are visible.
The RGB composite combines three independently calculated index images into the red, green, and blue channels.
Each selected index is robustly normalized before the three channels are combined.
The composite is therefore intended primarily for visualization and exploratory contrast enhancement. RGB color should not be interpreted as a direct physical color measurement.
NDVI - Normalized Difference Vegetation Index.
NDWI - Normalized Difference Water Index.
SAVI - Soil Adjusted Vegetation Index.
OSAVI - Optimized Soil Adjusted Vegetation Index.
RDVI - Renormalized Difference Vegetation Index.
MSR - Modified Simple Ratio.
MCARI-1 / MCARI-2 - Modified Chlorophyll Absorption in Reflectance Indices.
MTVI-1 / MTVI-2 - Modified Triangular Vegetation Indices.
TCARI - Transformed Chlorophyll Absorption Ratio Index.
TVI - Triangular Vegetation Index.
PRI - Photochemical Reflectance Index.
LAIDI - Leaf Area Index Determining Index.
MSAVI - Modified Soil Adjusted Vegetation Index.
NDNI - Normalized Difference Nitrogen Index.
NDSI - Normalized Difference Salinity Index.
REIP-1 - Red Edge Inflection Point.
CAI / CAI-2 - Cellulose Absorption Indices.
SRWI - Simple Ratio Water Index.
Exports the current numerical index image together with metadata describing the index and analysis settings.
Exports the current threshold mask together with analysis metadata.
Exports the generated RGB index composite together with metadata.
Clears the current index image, threshold mask, RGB composite, and threshold limits and returns the main image display to the original preview.
Spectral indices are mathematical combinations of reflectance or intensity values at selected wavelengths.
The biological or physical meaning of an index depends on the sample, acquisition system, calibration, spectral coverage, preprocessing, and application.
An index developed for vegetation remote sensing may not have the same interpretation when applied to another material or biomedical specimen.
Preprocessing And Calibration
Index values depend directly on the input cube. Reflectance correction, dark correction, bad-pixel removal, smoothing, normalization, and other preprocessing operations can change the calculated values.
For quantitative comparisons between datasets, use a consistent acquisition and preprocessing workflow.
Spectral / Vegetation Indices Close the Spectral / Vegetation Indices help window.