Animal bodies are composed of hundreds of cell types that differ in location, gene expression, morphology, cytoarchitecture, and physiology. Integrating information from these distinct levels has the potential to unravel developmental, physiological, and evolutionary principles. We established and explored the link between cell-type-specific gene expression and subcellular morphology for the entire body of the marine annelid Platynereis dumerilii. For this, we registered a whole-body cellular expression atlas to a high-resolution electron microscopy dataset, segmented all cell somata and nuclei and traced a subset of the neurons in the head. The neuron reconstructions as provided for download here allow for detailed analyses of morphology, projections and subcellular features of different neuron types. The reconstructions can be visualized in PyKNOSSOS (https://github.com/adwanner/PyKNOSSOS). H.M. Vergara, C. Pape, K. Meechan, V. Zinchenko, C. Genoud, A.A. Wanner, B. Titze, R. Templin, P.Y. Bertucci, O. Simakov, et al. (2020). Whole-body integration of gene expression and single-cell morphology. bioRxiv (2020), 10.1101/2020.02.26.961037 https://www.biorxiv.org/content/10.1101/2020.02.26.961037v1