Cellular processes are orchestrated by many biomolecules in a spatially and temporally coordinated manner within a tiny volume. To uncover the underlying organizational principles and their functional relevance, we take microscopy visualization as the primary approach to systematically map their spatial localization, temporal dynamics, and activity profiles. By combining small tags engineered from split fluorescence proteins and CRISPR/Cas9-mediated gene editing, we have enabled the creation of the OpenCell library: > 1300 human cell lines with endogenously tagged proteins for both microscopy visualization and biochemical analysis. We have further developed the deep-learning framework to connect cellular images of proteins to their amino acid sequences.