This microarray scanner acquires data at user-selectable resolutions between 2.5 and 100 μm per pixel, allowing the optimization of image resolution and file size for each experiment. The system is capable of automatically choosing photomultiplier gain value, for fast and easy optimization of signal intensity and channel balance. Configurations include 2.5 μm per-pixel maximum scanning resolution, choices of up to four lasers for excitation, and sixteen emission-wavelength filters. These options allow the systems to detect a wide variety of fluorophores. Coupled with Axon GenePix Pro microarray image analysis software and Axon Acuity® microarray informatics software, the Axon GenePix systems provide powerful, flexible, and easy-to-use solutions for the acquisition and analysis of data from all types of arrays, including nucleic acids, proteins, tissues, and cells.