Identification of diatoms in water samples is usually best done by using phase contrast optics, which reveal especially well lightly silicified structures, like delicate Chaetoceros setae, and also the organic chitan threads in Thalassio-siraceae. Brightfield or differential interference contrast (DIC) may be preferable for the study of cell organelles. Ten or 25 X objectives should be sufficient to recognize common species. If the goal is to pick out single cells, an objective with a long working distance is preferable. Normally, a compound microscope with a 10 X objective is the best choice, allowing enough space for the use of a micropipette and sufficient magnification to control the isolation of the single cell. A dissecting (binocular) microscope will provide even more space for operating the pipette.

The study of the finer structures of the silica wall requires cleaned, embedded material and a 40 X dry or, preferably, a 100X oil immersion objective. Phase contrast and/or DIC are recommended for the examination of lightly silicified diatoms to increase the contrast. For extremely lightly silicified diatoms this is best done with a so-called negative phase contrast objective. For the examination of heavily silicified diatoms there is no need to increase the contrast and brightfield is a better choice. For a superficial scanning of a water or permanent mount a darkfield illumination, obtained by a 10 x objective and the phase contrast condensor in a position corresponding to a 100 X objective, is useful for showing the siliceous elements distinctly against a black background.

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