We provide a unique dataset of 3D mapped gene expression patterns that operate within a vital signalling system for normal development, openly available to the scientific community for further analysis. The associated published manuscript provides novel insight to the function of the Wnt pathway genes and demonstrates how the data can be used to build testable hypotheses. This dataset includes the spatial expression patterns of the whole Wnt and Fzd families of genes plus selected additional pathways genes mapped onto standard spatial reference embryos at three stages of mouse embryo development. These were selected as of the most critical times for organ development and are E9.5 (Theiler stage 15), E10.5 (Theiler stage 17) and E11.5 (theiler stage 19). The patterns have been converted to a “point-cloud” representation to allow the 3D visualisation of individual and combined patterns in a standard web-browser such as Chrome, Firefox or Safari. Any webGL enabled browser should work.See README.txt