1. A method for acquiring image data representing an image of at least part of microscope specimen using an imaging system the method comprising: moving the specimen relative to the imaging system continuously in a scanning direction along a predetermined path; and during said step of continuously moving the specimen relative to the imaging system capturing a plurality of adjacent overlapping two dimensional images of the specimen, the overlap being in the scanning direction; and assembling a composite image from the plurality of overlapping adjacent two dimensional images by using cross correlation and removing duplicate overlapping regions from the captured adjacent overlapping two dimensional images.