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It really depends on the application. If the goal is to make lots of 3D structures to extract for protein analysis or a homogenous end point assay embedded protocols might be a good option as they are quick and straightforward. If imaging is required embedded protocols are not ideal as the 3D objects are mixed throughout which can cause long scan times from having to focus on so many different planes. Sandwich protocols involve laying a bed of polymerized Matrigel down before adding cells. This allows cells to settle in a more narrow focal plane making for easier and faster imaging.