AFM, SEM and TEM are complementary

In the case of biomolecules, the transmission electron microscope (TEM) is where most researchers start thanks to the abundance negative staining and cryoTEM data. If available, negative staining is an excellent option for early optimization for later cryoTEM studies. This approach mainly works for purified systems and for macromolecules <500 nm. The downsides are that for negative staining contrast formation relies on the use of toxic heavy metal stains (typically uranium or lead compounds), and that cryo-electron microscopes are even more expensive (>> $1M) and difficult to access.

The scanning electron microscope (SEM) is a good choice to analyze larger macromolecular complexes and can also be used for cryo-samples. The problem here is the more limited resolution and contrast, and the significant beam damage that occurs on cryo-samples. The cost and complexity of SEMs required for macromolecular resolution and cryo-samples is substantial as well (> $800k).

The AFM outperforms both TEM and SEM in cost and simplicity as a screening method, but mainly in its ability to scan and measure forces on biomolecules in a liquid environment. The downside here is that the molecules need to be tightly bound to the substrate to generate high-quality images. Compared to SEM/TEM, our AFM systems used here deliver this data at a >10x lower purchasing cost without the need for costly maintenance contracts, and without the use of toxic heavy metal stains.