Abstract: A system and method of implementing a two-stage scanning technique with a high-speed microscope. The microscope is operable to provide spectrally resolved, multi-dimensional images from a single scan of a sample. The microscope may include one of a multi-beam point scanning microscope, a single beam line scanning microscope, and a multi-beam line scanning microscope. The sample is first tagged such that, if the sample has a particular makeup, it emits energy at particular wavelengths upon receiving excitation beams. The microscope is used to perform a first, wide area scan. If the sample is determined to have emitted energy having particular characteristics, the microscope performs a second, focused scan of the area that emitted the energy having the particular characteristics. The two-stage scanning technique is automated and may be used to quickly identify rare cells, microbes, viruses, and other components within one or more samples.