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An AOTF based microscopic hyperpsectral imaging system which can capture both spectral and spatial information of tissue sections is developed and used in histopathological rat skin analysis. This new type of imaging system has the advantage of having no moving parts and the spectra can be scanned at very high speed. This makes the structure of the new system more compact and more suitable for coupling with a microscope. To evaluate the performance of the new system, scenes of molecular hyperpsectral images of rat skin sections are captured by the new system. Preliminary experiment results show a great deal of potential of this system for histopathological analysis of tissue sections.