Microscopes have a very shallow/thin/short depth of field. Because of this, I have to take anywhere from 10 to 200 images for every image you see. The series of images then have to be stacked. Stacking combines the images using the areas that are in focus on each image. The first image here is a screen shot from the stacking process.
The second image is a representation of scale. My microscope and camera capture 5mm at a time, so almost all of my micrographs will represent a section no more than 5mm in width.