We present a Fourier transform (Fr) spectrometer that is suitable for real-time spectral analysis in fluorescence imaging and flow cytometry. The instrument consists of (i) a novel type of interferometer that can be modulated at frequencies of up to 100 kHz and has a high light throughput; and (ii) a dedicated, parallel array processor for the realtime computation of spectral parameters. The data acquisition array processor can be programmed by a host computer to perform any desired linear transform on the interferogram and can thus separate contributions from multiple fluorochromes with overlapping emission spectra. We describe optics configurations for use in both flow cytometry and fluorescence microscopy. The integration of a flow cytometer and a spectral imaging fluorescence microscope is discussed, and the concepts of direct and reversed "virtual sorting" are introduced.© (1990) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.