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Best thing to do would be to build a frame synchroniser using external ram. You need external ram because you need to be able to store two whole fields/frames from both sources in memory. You need it double buffered so you are always reading from one while writing to the other. You may even need it triple buffered to cope with them being out of sync. This way you know you are always processing the same frames in parrallel.
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I'll be using those FIFOs as external RAMs. Actually the cameras' inputs will be written into the FIFO, not to the FPGA. I am using the FPGA to control the FIFOs reads and writes.
I was also thinking of a double-buffered solution, but the FIFOs I found do not have these features. How about "simultaneous read and write ports"? (Found it on a Cypress 18Mbit programmable FIFOs).