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The microarray technique, which can provide parallel detection with high throughput in biomedical research, has generated considerable interest since the end of the 20th century. A number of instruments have been reported for microarray detection. In this paper, we have developed a quasi-confocal, multichannel parallel scan hyperspectral fluorescence imaging system for multicolor microarray research. Hyperspectral imaging records the entire emission spectrum for every voxel within the imaged area in contrast to recording only fluorescence intensities of filter-based scanners. When coupled with data analysis, the recorded spectral information allows for quantitative identification of the contributions of multiple, spectrally overlapping fluorescent dyes and elimination of unwanted artifacts. This system is improved with a specifically designed, high performance spectrometer which can offer a spectral resolution of 0.2 nm and operates with spatial resolutions ranging from 2 to 30 μm. We demonstrate the application of the system by reading out arrays for identification of bacteria. [ABSTRACT FROM AUTHOR]