Schematic of whole-body template generation and gene expression registration in Platynereis. We generated each template from 40 scanned larvae stained with a reference marker (DAPI or acetylated tubulin) by iterative alignment and averaging. The templates were used to register gene expression patterns. We scanned several in situ hybridization samples (five to ten) for each gene, co-stained with the reference marker. We first rotated the images rigidly and registered them non-rigidly to the templates using the reference signal. We averaged the registered expression patterns for each gene to obtain a representative average expression pattern. These average gene expression patterns were integrated into the atlas. DAPI, 4’,6-diamidino-2-phenylindole.