Spotfinder is a multi-channel image analysis tool. This tool was designed for the rapid, reproducible, user-aided analysis of microarray images and the quantification of gene expression. Spotfinder reads paired 16-bit or 8-bit TIFF image files generated by most microarray scanners. Semi-automatic grid construction defines the areas of the slide where spots are expected. Automatic and manual grid adjustments help to ensure that each rectangular grid cell is centered on a spot. A number of segmentation methods available define the boundaries between each spot and the surrounding local background. Local background correction is available as default choice.