This technology uses microwell reactions to detect up to 6 miRNAs from as few as 10 cells. To quantify miRNA expression, this method first seeds raw cells from liquid suspension or a tissue slices into plates with 100-1,000 microwells that each contain up to 6 probes against miRNAs of interest. Next, the cells are lysed and miRNAs are hybridized to the probes, then, adapters are ligated onto probe-bound miRNAs. Finally, the adapter handles are used to attach a fluorescent label and the fluorescence intensity of each probe is quantified via microscopy to determine the concentration of each miRNA. This assay is faster and less labor intensive than existing miRNA analysis techniques, which require intensive sample preparation and/or PCR amplification of miRNAs prior to detection. Importantly, this technology can also be applied to previously archived tissue samples to provide a quantitative readout of miRNA expression that maintains spatial information to correlate miRNA expression with histopathological features.