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A wood stain consists of a colorant suspended or dissolved in an agent or solvent. The suspension agent can be water, alcohol, petroleum distillate, or the actual finishing agent (shellac, lacquer, varnish, polyurethane, etc.). Colored or 'stained' finishes, like polyurethane, do not penetrate the pores of the wood to any significant degree and will disappear when the finish itself deteriorates or is removed intentionally.
Pigments and dyes are largely used as colorants. The difference between the two is in the size of the particles. Dyes are microscopic crystals that dissolve in the vehicle and pigments are suspended in the vehicle and are much larger. Dyes will color very fine grained wood, like cherry or maple, which pigments will not. Those fine-grained woods have pores too small for pigments to attach themselves to. Pigments contain a binder to help attach themselves to the wood.
The type of stain will either accentuate or obscure the wood grain. Most commercial stains contain both dye and pigment and the degree to which they stain the appropriate wood is mostly dependent on the length of time they are left on the wood. Pigments, regardless of the suspension agent, will not give much color to very dense woods but will deeply color woods with large pores (e.g. pine). Dyes are translucent and pigments are opaque.