1. A system for capturing image data using a line scan camera, the system comprising: an objective lens positioned for viewing at least a portion of a sample during constant relative motion; a line scan camera optically coupled to the objective lens and configured to capture image data of the sample as a plurality of image stripes; and at least one processor configured to, while the line scan camera is capturing at least one of the plurality of image stripes of the sample, coarsely align two or more adjacent ones of the plurality of image stripes of the sample according to a synchronization process, and, subsequently, finely align the two or more adjacent ones of the plurality of image stripes of the sample using pattern matching.