P>Direct measurements of cells from photo micrographs are becoming increasingly used when investigating the position and/or distribution of chromosomal loci in bacteria. In general, these measurements have been done manually, and without clear definition of how they are made. Here we present a procedure for standardizing the measurement of cell properties from phase contrast images. Furthermore, we present a program using these standardized methods that can measure the intracellular positions of fluorescent foci in bacterial cells faster and with more precision than manual measurement.