We propose a FPGA based real-time calcium trace extraction solution for the calcium imaging miniaturized microscope. We introduce a tracing accelerator and a corresponding cell mapping algorithm that can extract traces from a large number of cells in short latency. In addition, we come up with a few latency optimization techniques to further reduce the trace extraction latency with minimal overhead. Our implementation can extract calcium trace values from 1024 cells in a 512x512 calcium image with sub-ms latency, which marks comparable timing resolution of cell firings and existing optogenetic intervention