A system and method is provided for rapidly collecting high quality images of a specimen through controlling a re-focusable beam of an electron microscope. An intelligent acquisition system instructs the electron microscope to perform an initial low-resolution scan of a sample. A low-resolution image of the sample is received by the intelligent acquisition system as scanned image information from the electron microscope. The intelligent acquisition system then determines regions of interest within the low-resolution image and instructs the electron microscope to perform a high-resolution scan of the sample, only in areas of the sample corresponding to the determined regions of interest or portions of the determined regions of interest, so that other regions within the sample are not scanned at high-resolution. The intelligent acquisition system then reconstructs an image using the collected high-resolution scan pixels and pixels in the received low-resolution image.