We developed an implantable one-chip biofluoroimaging device (termed biomedical photonic LSI; BpLSI) which enabled real-time molecular imaging with conventional electrophysiology in vivo in deep brain areas. The multimodal LSI enabled long-term sequential imaging of the fluorescence emitted by proteolysis-linked fluorogenic substrate. Using the BpLSI, we observed a process of stimulation-dependent modulation at synapse with multi-site (16 x 19 pixel) in widespread area and a high-speed video rate, and found that the gradual up-regulated proteolytic activity in a wide range of hippocampal CA1 area and the steep activity in local area, indicating that the proteolysis system is a basis for the fixation of long-term potentiation in post-excited synapses in the hippocampus. Mathematical data analysis confirmed the direct involvement of functional proteolysis for neural plasticity.