This is a simplified procedure. Consult protocols of greater or lesser complexity from different laboratories preparing cleared diatoms for light and electron microscopy on a routine basis.

1. Place sample containing diatoms in a centrifuge tube.
2. Allow cells to sediment by gravity, or spin briefly (a few seconds) to obtain pellet (try not to compact cells)
3. Draw off supernatant, leaving pellet in the tube.
4. Resuspend pellet in household chlorine bleach or 30% hydrogen peroxide. Hold at least 1 hr at room temperature (no maximum).
5. Repeat 2.
6. Wash at least 2x in distilled water.
7. Inspect an aliquot with the light microscope. Frustules should be clear, without associated cytoplasm.
8. If necessary, resuspend sample in clearing agent (if you originally used bleach, try peroxide, and vice versa; another option is concentrated HCl or nitric acid). Hold at least 1 hr at room temperature (no maximum).
9. Repeat 5-7. If some diatoms are not cleared, see the instructors.
10. Water mounting. Mount some diatoms in distilled water; examine with bright-field, phase contrast and/or differential interference contrast microscopy. Compare with live images of the same species.
11. SEM mounting. Place a drop of aqueous diatom suspension on the flat surface of an SEM stub and allow to dry. Hold stub in labelled box for sputter coating and SEM observation. Sometimes a glass coverslip is affixed to the stub with double-sided sticky tape before the diatom sample is applied.
12. Immersion oil and resin mounting. Place a drop of aqueous diatom suspension on a coverslip and allow to dry. [Drying may be hastened in either of two ways. (a) Place the coverslip on a warm (60 C) surface. (b) Pellet the cells, draw off the water and replace with ethanol; resuspend and placedrop on slide.] Place a drop of mountant on a clean slide. [Mountants are immersion oil, index of refraction 1.515; Histoclad, 1.545; Diatex, 1.70.] Place the coverslip, diatom side down, on the mountant. Tap down on the coverslip with e.g. a pencil eraser to flatten the preparation and squeeze out excess resin; avoid air bubbles. Immersion oil slides: blot away excess oil with absorbent paper (paper towel) and ring with nail polish; they can be viewed immediately. Resin slides: allow to dry at least overnight without blotting excess resin; when ready, the excess will be hard and can be scraped away with a razor blade.