One embodiment disclosed is a method of detecting defects in objects. A selected surface area of an object is inspected with a multi-pixel electron microscope, and first set of data is generated having signal values representing image content of each pixel thereof. Further selected surface area of the object is inspected with said multi-pixel electron microscope, and second set of data is generated having signal values representing image content of each pixel thereof. Corresponding portions of first and second sets of data are stored in memory. Misalignment between stored portions of the first and second sets of data is detected with resolution of a fraction of a pixel, and the stored portions of first and second sets of data are aligned using subpixel interpolation to correct the detected misalignment therebetween. Finally, corresponding subportions of the aligned portions of first and second sets of data are compared to detect differences therebetween.