Answer to Question 1
Element substitutions. Examples: purple quartz contains iron substituting for silicon, pink quartz contains titanium substituting for silicon, dark blue, green, or brown calcite contain iron substituting for calcium, pale purple to deep red calcite contains manganese substituting for calcium.
Impurities without element substitution. Examples: milky quartz has water droplet impurities.
Radiation damage: black smoky quartz.
Answer to Question 2
Most of the size of an atom consists of the cloud of electrons that orbit the nucleus. If there are many electrons in a small area around the nucleus, then there is a good chance that electrons fired in the TEM will collide with an orbiting electron and bounce off elsewhere in the microscope rather than continuing through to the detector. If, however, the electrons are widely spaced around a nucleus, then the fired electrons may pass through the atom without hitting any obstacles. This means that the shadows in the TEM image may not represent all of the types of atoms in a mineral, but rather only the atoms with closely clustered electrons.
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