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However, when amplifying fibrils from patient\u2010derived samples in multiwell plates, it is currently highly challenging to accurately quantify the aggregates. It is therefore desirable to transfer such assays into a digital format in microemulsion droplets to enable direct quantification of aggregate numbers. To achieve transfer from conventional plate\u2010based to the microfluidic digital format, effective seed amplification needs to be achieved inside the microdroplets. Therefore, we establish a new set of assay conditions that enable highly efficient seed amplification in plates without any shaking. However, the same set of conditions displayed a very different behavior upon transfer to a microfluidic platform where no amplification was observed. We demonstrate that this is caused by the suppression of all secondary processes that could amplify the seeds in the complete absence of mechanical perturbations inside the microdroplets. We further show that the amplification inside droplets can be achieved by subjecting the microemulsions to high\u2010frequency vibrations using a piezo device. 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