A system for automated focus tracking of a sample is disclosed. The system comprises an illumination source, a set of illumination optics in an illumination path, a set of collection optics in a collection path, a first slit device in the illumination path, a second slit device in the collection path, at least one detector configured to generate an image of the sample, and a controller configured to receive through-focus information from the image, and provide corrective motion to a stage holding the sample to maintain a position of the sample at a selected focus. A method for automated focus tracking of a sample is also disclosed.