Raphidiophrys cells usually are encountered as rounded, axopodial amoebae, either suspended in the water column or loosely adhering to substrate. In most species, the cells are solitary, but in a few the cells may form loose, unorganized colonial aggregates.

The trophic cells range from 10 to 150 micrometers in length; individual species have characteristic size ranges within these limits. No flagella are present. The cells appear coarsely "furry" due to a covering of flattened silica scales. The scales may adhere to each other, to the cell body (which may have a gelatinous coat around it), and to the axopodia radiating from the cell body; but they do not project at right angles to the cell surface. Depending on the species, the scales may be circular, ellipsoidal or nearly linear.

Axopodia, unlile the scales, radiate from the cell body at right angles to the cell surface. They are longer and much more slender than the scales and may bear prominent beads ("kinetocysts", a structurally distinct type of extrusome). Axopodia are used to capture prey and to move cells along a substrate. Disturbed cells may retract the axopodia.
The axopodia radiate from a prominent body, the centroplast, located in the geometric center of the cell. Both the centroplast and the axopodial microtubules radiating from it are strongly birefringent, easily visible in plane-polarized light and optical systems (such as differential interference contrast = Nomarski optics) based on plane-polarized light.

The single nucleus is eccentrically located. Most other organelles are located in the peripheral cytoplasm; these organelles typically include one or more contractile vacuoles. In several species, the peripheral cytoplasm may harbor endosymbiotic coccoidal green algae ("zoochlorellae"); the species illustrated here was named pallida ("pale", "pallid") precisely because zoochlorellae are absent, and this lack was considered unusual at the time the species was described.

The centrally-located, birefringent centroplast separates centrohelid heliozoa from other radially-symmetrical, axopodial amoebae. The absence of "spine" scales projecting at right angles from the cell surface separates Raphidiophrys from other centrohelids.

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