Abstract: A method and system performs Fourier transform infrared (FT-IR) imaging microspectroscopy on a biological sample fixed on a substrate with a supporting surface that generally reflects infrared light while generally transmitting visible light. Infrared light impinging on the biological sample is reflected by the supporting surface of the substrate. Infrared light from the sample is focused onto a focal-plane array detector with multiple pixels for detecting infrared images of the sample. The detected infrared images are processed to generate spectral images of the sample. The same biological sample is suitable for conventional pathological studies.