Three-dimensional organization of the human genome regulates many cellular functions. The authors characterized the first high-resolution 3D structures of full-length human chromosomes using a multiplexed imaging platform to trace the contour of chromatin in single cells. In addition, they presented a high-throughput multimodal genome scale imaging strategy that allows for the visualization of thousands of genomic regions and transcriptional foci along with landmark structures in the cell nucleus. This technological advancement enables scientists to probe interesting questions related to chromatin organization in its functional context.