1. A method for analyzing cells comprising: (a) providing an array of locations which contain multiple cells wherein the cells contain one or more fluorescent reporter molecules; (b) scanning multiple cells in each of the locations containing cells to obtain fluorescent signals from the fluorescent reporter molecule in the cells; (c) converting the fluorescent signals into digital data; and (d) utilizing the digital data to determine the distribution, environment or activity of the fluorescent reporter molecules within the cells.