1. A method of generating in-focus images of measurement locations of a sample holder in a microscopy imaging system, the method comprising: (a) positioning a camera array at a first distance from the sample holder; (b) acquiring a first image of a measurement location using an imaging device disposed on the camera array; (c) developing a candidate output image associated with the imaging device in accordance with the first image; (d) positioning the camera array at a second distance from the sample holder; (e) acquiring a second image of the measurement location using the imaging device; (f) updating a portion of the candidate output image with a portion of the second image in accordance with a selection criterion; and (g) transmitting the updated candidate output image.