Hyperspectral imaging was used to identify and to visualize the coffee bean varieties. Spectral preprocessing of pixel-wise spectra was conducted by different methods, including moving average smoothing (MA), wavelet transform (WT) and empirical mode decomposition (EMD). Meanwhile, spatial preprocessing of the gray-scale image at each wavelength was conducted by median filter (MF).Support vector machine (SVM) models using full sample average spectra and pixel-wise spectra, and the selected optimal wavelengths by second derivative spectra all achieved classification accuracy over 80%. Primarily, the SVM models using pixel-wise spectra were used to predict the sample average spectra, and these models obtained over 80% of the classification accuracy. Secondly, the SVM models using sample average spectra were used to predict pixel-wise spectra, but achieved with lower than 50% of classification accuracy. The results indicated that WT and EMD were suitable for pixel-wise spectra preprocessing. The use of pixel-wise spectra could extend the calibration set, and resulted in the good prediction results for pixel-wise spectra and sample average spectra. The overall results indicated the effectiveness of using spectral preprocessing and the adoption of pixel-wise spectra. The results provided an alternative way of data processing for applications of hyperspectral imaging in food industry.Coffee is one of the most popular beverage in the world. Coffee variety is among the key factors influencing the coffee quality and price. According to International Coffee Organization (ICO), the estimated average number of global coffee consumption in the past 4 years was higher than 8 × 10 6 tons 1 . Identification of coffee beans has been studied by traditional reagent-based laboratory chemical methods 2,3 , spectroscopy techniques 4,5 and digital imaging techniques 6,7 . Reagent-based chemical methods are time consuming, reagent dependent and complex to operate. Spectroscopy and imaging techniques have been widely adopted as rapid, non-destructive and accurate techniques. Hyperspectral imaging (HSI), a technique integrating both spectroscopy and imaging techniques, has drawn raising attentions from researchers of different fields. HSI acquires spectral and spatial information simultaneously. The hyperspectral image is a three-dimensional (3D) data cube (x, y, λ) with the two-dimensional spatial information (x, y) and the third dimension of spectral information (λ). Each pixel has a spectrum in the hyperspectral image together with a gray-scale image at each wavelength. Hyperspectral imaging has been reported to detect coffee quality [8][9][10][11][12][13] , and the use of pixel-wise spectra have not been discussed in coffee quality determination.One of the main advantages of hyperspectral imaging is to form and visualize the distribution maps of the samples. It reveals not only the physical attributes but also the chemical compositions within or between samples. Theoretically, visualization of the physical attributes and the chemical...