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As a special-purpose computer system to solve specific problems, the embedded system is very suited to be implemented by the FPGA. However, without fixed hardware architecture, the FPGA-based computing system is mostly a mixture of hardware and software. This kind of system is difficult to design because hardware and software are developed using quite different models of computation. To handle this problem, a FPGA-based platform supporting Java programming language is proposed in this paper. This platform has two aspects: 1) to find the applications amenable to very large speedup using FPGA-based systems, such as computer vision, image processing, microarray analysis and so on. 2) To provide a three level solution making the hardware transparent to application programmers. This platform is expected to provide an effective way to accelerate FPGA-based custom computing to be used in embedded systems.