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Strong cycle-to-cycle variations of fuel spray are observed due to the highly transient in-cylinder airflow in spark-ignition direct-injection (SIDI) engine. The spray structure comparison based on ensemble-averaged image may be misleading sometimes because the spray images for the same engine running condition could be different from cycle to cycle. Also, the visual comparison of spray images from many cycles is only qualitative and very time-consuming. Therefore, the present paper provides a novel approach to make quantitative comparison of spray structures from different engine conditions, or comparison between experiment and simulation (such as large eddy simulation, LES). The methodology is based on the proper orthogonal decomposition (POD), which has been utilized for in-cylinder turbulent flow research for over a decade.