Microscope system with transillumination-based autofocusing for photoluminescence imaging

Microscope system for, and methods of, imaging a sample including biological cells. In an exemplary method, light transmitted through the sample may be detected for a first set of focal positions to collect a first stack of images. Values of a focus metric may be calculated for the first stack of images. A candidate focal position may be determined based on the values. Photoluminescence may be detected from the sample for a second set of focal positions to collect a second stack of images. The second set of focal positions may define a smaller range than the first set of focal positions. At least one focal position of the second set of focal positions may be based on the candidate focal position. In other words, the candidate focal position may serve as a guide for finding a suitable photoluminescence focal position.