Geologists most commonly use polarizing microscopes. The light passes through a polarizing filter before it passes through the specimen. That acts to select only light waves that are vibrating in a particular direction. After passing through the specimen the light passes through another polarizer. That is usually oriented at right angles to the first, and unless something in the specimen changes the directions of vibration, it blocks all of the light.
Crystals typically do change the directions, however, and thus become visible.
Polarizing scopes are invaluable for mineral identification, because they can be used to determine crystal structure and orientation, refractive index, and more. They are also widely used for examining crystalline organic chemicals. Metallurgical microscopes cannot work with transmitted light. Instead they use epi-illumination, that is, light from above, reflected from the specimen. There is no substage unit or condensor.