It is a little foggy, but to most biochemists, a 'cell-based' assay would be in vivo (although to a macrobiologist this might be considered in vitro. Essentially (again, to a biochemist), in vitro (literally "In glass") assays are those that take place removed from the actual living system. Usually you will have a fractionated part of a cell, or even just an enzyme or two, as your assay. In contrast, while most cell-based assays are nowadays done 'in glass', by which I mean in a tube of some sort, since the cell is still alive it would generally be considered in vivo.
And having survived many in vivo and in vitro experiments and publications, I can tell you that it is awfully difficult to get most cell biologists to accept work done entirely in vitro. That is, while in vitro is great for dissecting a system into its component parts, you then have to work back up to the in vivo system to prove that your in vitro work is reflected in a real living organism.
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