The fluorescence intensity of each spot on the array, where each spot represents a DNA, RNA or protein probe. The result is a massively parallel measurement of thousands of interactions on a single support.

It depends on the density of the array: current commercial formats require resolutions of a few microns per pixel. A scanner with insufficient resolution mixes signals from neighboring spots and invalidates the analysis.

Yes, in targeted applications: genotyping, expression of defined panels, cytogenetics and protein arrays, where they offer a lower cost per sample, a simple workflow and mature analysis. Sequencing dominates discovery; the array, targeted routine work.

Both: the array defines the content, but the scanner provides the dynamic range, sensitivity and excitation uniformity that make experiments comparable to each other and over time.