This paper demonstrates a novel readout platform for ISFET-based ion imagers capable of high data-throughput acquisition and real-time monitoring of high-speed chemical reactions. The front end sensor comprises of a 128 x 128 array of integrated ISFET pH sensors fabricated in CMOS. The array operates at a frame rate of up to 3000 fps for detecting hydrogen ion diffusion, generating a data stream at a bit rate of 491.52 Mbps. A digital readout system consisting of a readout module for data buffering, an AXI master controller for accessing on-board DDR3 memory and a PCIe subsystem that is capable of transmitting data packets to the PC at a bit rate of 16 Gbps (PCIe 2.0 x 4) is implemented on an Alinx AX7103 development board to link the chip and the PC. The platforms capabilites are demonstrated with a real-time ion imaging experiment, by observing the diffusion of NaOH pills in water within 320 ms, visualized on screen with a latency of 0.15 s. Lastly, different image processing algorithms including Gaussian, Bilateral and Non-local Mean are evaluated for noise reduction and an accelerator for the optimum filter is implemented for real-time ion-imaging.