Abstract: eMouseAtlas (www.emouseatlas.org) is a non-profit freely available online resource that allows researchers to visualise mouse development and to investigate gene expression. In developing an anatomical atlas of mouse development we have developed the IIP3D web tool that allows a user to view arbitrary sections of 3D embryo reconstructions using a web browser. This feature provides interactive access to very high-volume 3D images via a tiled pan-and-zoom style interface. eMouseAtlas additionally includes EMAGE (www.emouseatlas.org/emage), a curated online database of in situ gene expression patterns where gene expression domains extracted from raw data images are spatially mapped into atlas embryo models. We are currently extending this resource to include 3D maps of transcriptome data captured using Optical Projection Tomography and Transcriptome Tomography. Towards this end, eMouseAtlas have been developing novel spatial mapping techniques that can cope with the pose variability of embryos and will allow 3D mapping of mouse embryo data onto standard atlas models. Here I report on the application of the constrained distance transform (CDT) algorithm and the WlzWarp interface to overcome the distinct challenges of mapping 3D mouse embryo data. I additionally report on the application of Advanced Normalization Tools (ANTS) - derived from the Insight Segmentation and Registration Toolkit (ITK) - as a means of augmenting this process.