A system and method for automatically observing and counting cells without using a stain or a fluorescent material. The system includes an optical microscope having a sensor that provides an electrical signal representative of a field of view. The microscope is motorized so as to allow automatic change of focus. A sample containing cells to be analyzed is provided. No stain or fluorescent substance is used. When the microscope is operated in a deliberately out-of-focus condition, cells appear to have either a bright or a dark spot that can be used to report the number of cells in the sample. The intensity variation detected in images acquired in different focal planes is used to identify cell shapes using image analysis software such as CellProfiler. A result is reported in any convenient format, such as a false color image.