Any source used for imaging a sample can only resolve an object that is bigger than half of the respective wavelength. When we look at the range of visible light we see that the resolution is limited to 200nm (based on the wavelength range from 380nm - 700nm (Ultraviolet to infrared). If we want to go smaller in size we can exchange the imaging source used. Electrons used in EM have a typical wavelength of around 2pm - 4pm (0.002nm - 0.004nm), thus the wavelength is significantly smaller, which allows us to image drastically smaller objects.
In our lab we use transmission electron microscopy. This means we detect electrons that interacted and pass through the sample. This is only possible if the sample is thin (max 150nm) enough for the electron to penetrate.
Like with every method there are some disadvantages. One of the main constraints comes from the sample source which is used in our research. Biological samples mainly consist of Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus and Sulfur. All of these elements have a relatively small mass which makes interaction between electrons and sample less likely. The result are noisy images that need to be processed after image acquisition.
Another constraint comes from the high potential energy of individual electrons. This will eventually cause radiation damage and drift that limits the quality of the micrographs.