This work was begun while Paula Murphy was a member of the Davidson Group at the MRC Human Genetics Unit and continued by the Murphy Lab at the University of Dublin (Trinity College) in collaboration with the Edinburgh Mouse Atlas Project (EMAP), funded by Science Foundation Ireland (SFI). The work created a data set of 3D gene expression patterns of Wnt signalling pathway regulatory genes (encoding Wnt ligands, Fzd receptors, transcription factors and pathway modulators) across three developmental stages. The data were generated using whole mount in situ hybridisation and OPT imaging (Summerhurst et al., 2008 DOI: 10.1016/j.gep.2008.01.007; Vendrell et al. 2009 DOI: 10.1016/j.gep.2009.03.001; Martin et al 2012 DOI: 10.1111/j.1525-142X.2012.00534.x). 3D mapping of the data was carried out using EMAP generated tools. The items in this collection include the 3D reconstructions of the original data and the mapped expression patterns in the context of the eMouseAtlas OPT model embryos. The mapped data is provided as a single item to allow convenient download for viewing and further bioinformatics analysis.