The design of photoinjectors for modern free electron laser linac relies heavily on particular beam behavior in the few meters after the gun. To experimentally characterize it a movable emittance meter was proposed and built [L. Catani et al., Rev. Sci. Instrum. 77, 093301 (2006)] based on the beam slicing technique. This paper addresses all the aspects of analysis of the data acquired with the emittance meter and common to any slit based emittance measurement for low energy beams.