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The complex detection algorithm can be implemented in a real-time embedded system using Field Programmable Gate Array (FPGA). This paper presents the development of real-time moving target detection System-on-Chip (SoC) using FPGA for deployment on a UAV. The detection algorithm utilizes area-based image registration technique which includes motion estimation and object segmentation processes. The moving target detection system has been prototyped on a low-cost Terasic DE2-115 board mounted with TRDB-D5M camera. 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