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Hyperspectral imaging instruments produce large amounts of raw data. These raw data in A/D converter counts have a number of errors that can be corrected by calibration. The use of multiple Spectralon calibration standards is shown to correct for both spectral and spatial variations. Optimal results are achieved using a two-step calibration and correction process. A series of full field of view or external calibration standards is used to transform raw data counts to reflectance values. A grayscale series of internal standards embedded within each hyperspectral image is used to compensate for instrument instability. Second-order regression models based on these multiple standards provide maximum accuracy. The external standards allow for standardization within a hyperspectral image. The internal standards permit instrument standardization or calibration transfer between hyperspectral images.

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A hyperspectral image in the near infrared contains thousands of position-referenced spectra. After imaging reference materials of known composition it is possible to build Partial Least Squares (PLS) regression models for predicting unknown compositions from new images or spectra. In this paper a comparison is made between spectra from a hyperspectral image and spectra from two spectrometers: a scanning grating instrument with rotating sample holders and an FT-NIR instrument utilizing a fiber-optic probe. The raw spectra and the quality of the PLS calibration models and predictions are compared. Two sample datasets consist of a set of 13 designed artificial mixtures of pure constituents and a selection of 13 sampled cheeses. The prediction error from the hyperspectral image spectra is between that of the two spectrometers. For a typical food sample, the average bias [and replicate standard deviation] was -0.6% [0.5%] for protein and -0.2% [1.3%] for fat. Comparable values for the best spectrometer were -0.2% bias for protein and -0.5% for fat. Some of the advantages of working with hyperspectral images are highlighted: the simultaneous exploration of representations of both spectral and spatial data, and the analysis of concentration profiles and concentration maps all contribute to better characterization of organic and biological materials.

When known reference values such as concentrations are available, the spectra from near infrared (NIR) hyperspectral images can be used for building regression models. The sets of spectra must be corrected for errors, transformed to reflectance or absorbance values, and trimmed of bad pixel outliers in order to build robust models and minimize prediction errors. Calibration models can be computed from small (<100) sets of spectra, where each spectrum summarizes an individual image or spatial region of interest (ROI), and used to predict large (>20 000) test sets of spectra. When the distributions of these large populations of predicted values are viewed as histograms they provide mean sample concentrations (peak centers) as well as uniformity (peak widths) and purity (peak shape) information. The same predicted values can also be viewed as concentration maps or images adding spatial information to the uniformity or purity presentations. Estimates of large population statistics enable a new metric for determining the optimal number of model components, based on a combination of global bias and pooled standard deviation values computed from multiple test images or ROIs. Two example datasets are presented: an artificial mixture design of three chemicals with distinct NIR spectra and samples of different cheeses. In some cases it was found that baseline correction by taking first derivatives gave more useful prediction results by reducing optical problems. Other data pretreatments resulted in negligible changes in prediction errors, overshadowed by the variance associated with sample preparation or presentation and other physical phenomena.