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Besides the etymologic explanation that @aandreev gave, in cell culture this term is commonly used to describe the density of adherent cells and it is used as a measure of their proliferation. It is usually combined with an estimated (or counted) percentage, so 10% confluency means that 10% of the surface the dish or flask used is covered with cells, 100% ...
con- (com-) is prefix that usually means "togetherness", joining. Root fluency/fluent comes from latin fluere, to flow. Source: Google's definitions for con- and fluency. Google, probably, takes information from Merriam-Webster dictionary.
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