- Strongly diffracting regions of crystals can appear darker because there are fewer electrons transmitted along the primary beam. These crystals may be sitting on the grid holder at a tilted angle so that a lattice of the crystal lines up parallel to the beam.
- Thicker regions can also appear darker due to greater scattering. This can be seen in the image here, where some crystals lie on top of one another.
As the sample is tilted it will change in appearance to darker or lighter contrast depending on how the beam is interacting with the internal lattice. When strong diffraction conditions are achieved, the image will appear darker as more electrons are scattered outside of the objective aperture.