1. A computer implemented method, comprising: obtaining a digital image of at least a portion of a scan region containing a sample using a digital image capture device operably coupled to an optical microscope, the sample having a perimeter and occupying a sample region that is smaller than the scan region; electronically dividing the digital image of the scanned region into segments; analyzing the digital image with a computer implemented algorithm to determine the presence or absence of segments containing a first desired feature of the sample; analyzing each segment for the presence of the first desired feature and identifying each segment that contains the first desired feature including segments that intersect the perimeter of the sample and contain the first desired feature as well as non-sample portions; logically separating the segments identified as containing the first desired feature from the segments that do not contain the first desired feature; and electronically dividing only those segments of the image identified as containing the first desired feature into a plurality of substantially contiguous subimage segments at the same magnification, the substantially contiguous subimage segments together defining a contiguous area that corresponds to the sample region; determining the presence or absence of a second desired feature in each subimage segment; and logically separating the subimage segments identified as containing the second desired feature from the subimage segments that do not contain the second desired feature.