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To realize very high performance computing system, we have proposed a novel opto-electronic 3-D LSI in which both electrical and optical devices are integrated. For seamless optical interconnects both vertically and horizontally, through Si photonic via (TSPV) and unidirectional optical coupler (UDOC) are indispensable. We succeeded in fabrication of conventional TSVs and the TSPVs comprising Si core and SiO2 cladding simultaneously. We also developed optical interconnects embedded in the intelligent Si neural probe. Both neuronal signal recording and cell optical stimulation can be achieved with the Si neural probe having optical interconnects. Our neural probe becomes a novel tool for brain function analysis, neurophysiology, and optgenetics.