An infrared imaging microscope uses spatial encoding to divide an sample being examined into a plurality of pixel regions. The spatial encoding is provided by a digitally controlled mask, which is preferably a multiple mirror array, and which masks the imaging radiation directed from a radiation source to the sample. The signal reflected or transmitted from the sample is detected using a single-element detector. As the mask pattern provided by the mask changes, the output signal of the detector is monitored, and the spectroscopic composition of each of the pixel regions is resolved using a spatial decoding method, such as a Hadamard transform. The digital control of the mask allows fast, easily-implemented changes to the masking pattern, and provides a low processing load relative to imaging devices that use multiple-element detectors. The invention may be implemented in a stand-alone microscope, or as a probe in which most of the elements of the device are located in a main housing, while the mask is located in a remote probe housing connected to the main housing by fiber optic cables. This allows reflective-mode scanning of free-standing objects. In one alternative embodiment, a multiple-element detector is used with the digitally-controlled mask. In this embodiment, visible light is spatially encoded by the mask along with the imaging radiation. By masking the visible light in this manner, visual examination of the sample allows correlation between the area of the sample being examined and the output of the appropriate element of the detector.