Under the electron microscope, the scales of most species appear as flat plates. The base of the plate may be unornamented, or ornamented with thickened strips (cross-striate) or thin spots (punctate). In species with nearly linear scales, the scales may be solid or nearly-solid rods. In most species, scales are constant in shape and size, but in a few, variations are encountered even in the scales from a single cell. Each scale is produced separately in a specialized membrane sac, the "silica deposition vesicle" (SDV). The numerous SDVs lie just beneath the cell membrane, and are scattered around the periphery of the cell.

The centroplast consists of a trilaminate disc sandwiched between two electron-dense caps. Surrounding the centroplast is an extensive exclusion zone from which most cell organelles are absent. The axopodial axonemes (groups of microtubules that form the structural core of the axopodia) emanate from electron-dense material immediately surrounding the centroplast. It is presumed that the centroplast is the organizing center for these microtubules.

The axopodial axonemes consist of an array of numerous (ca. 20-100) cross-linked microtubules, arranged in an intricate repeating pattern of triangles and hexagons.

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