What diatomists do to diatoms

My research is on the diatom communities of the Everglades. To study how the communities respond to environmental changes, I have to identify and count each of the diatom species I encounter under the microscope. To do that though, the diatoms have to be stripped clean of any organic material and other 'junk' in the sample. The diatoms go through a harsh bath of acid and heat, until all that is left of them are their empty but beautiful cell walls. This is possible because diatom cell walls are essentially glass.

Beakers of diatom samples mixed with hydrogen peroxide and nitric acid boiling away on a hot plate. Different amounts of organic matter (like peat or plants) and inorganic matter (like sand or clay) result in different colors and reactions.

In the Everglades, the limestone bedrock adds a lot of calcium carbonate into the soil and periphyton. Some components of periphyton (especially mucilage-producing filamentous algae) attract calcite crystals like a magnet. The addition of calcium carbonate, an inorganic substance, makes Everglades periphyton a bit more difficult to process all the junk away. That's because inorganic things don't really dissolve with the normal chemicals we use to get rid of organic stuff. But we don't want to try to dissolve too much of the inorganic material either, because we don't want to damage the diatom cells! Everglades samples go through an intense process including sulfuric acid, potassium permanganate, and oxalic acid. Check out this animation that shows how Everglades periphyton is transformed into a bubbly and acidic concoction, then into a white powdery layer of clean diatom cells at the bottom of the beaker:

Here are some before and after processing images of periphyton and diatoms under the microscope: