A unique hybrid photo-cathode S-band gun accelerator is in operation at Ariel University. The accelerator produces an ultra-fast relativistic electron beam with beam characteristics of 6 MeV kinetic energy, 30 pC charge, and 150 fs pulse duration. In this paper, we present a compact transverse emittance measurement system using the multi-slit mask technique. The system is calibrated using a fully automatic calibration routine, and the results are obtained instantaneously. To find the optimal parameters required to obtain the lowest transverse emittance value, we scan the currents in the focusing coils surrounding the gun including a bucking coil current scan to minimize the magnetic field upon the photo-cathode. In the last step, we verify the relation between transverse emittance and electron beam charge in RF guns emitted from a photo-cathode. The verification is done by a beam charge scan.