Fig. 5.

3D spatial mapping using WlzWarp. a 3D volume data are warped onto target reference models via a mesh that envelopes the target and excludes background and luminal areas. b The mesh is read into the WlzWarp interface, alongside the reference and source objects. WlzWarp allows user-defined pairwise landmarks to be placed on source and target and subsequently allows warping via the CDT algorithm. c 3D mapped data from multiple embryos can be viewed as a volumetric reconstruction or can be visualized on an arbitrary section by using a novel 3D search interface based on the IIP3D viewer. d Volumetric data can be queried in web browsers using a painted domain as the basis of a spatial query. e It is possible to refine 3D spatial mapping using advanced neuroimaging tools (ANTs) (Avants et al. 2011). These additional steps are performed after initial registration using WlzWarp. In this example, both cross-correlation (CC) and mutual information (MI)—two similarity metrics used to enhance 3D image registration—are used to refine the WlzWarp transformation of an OPT gene expression pattern. The target is the EMAP TS17 reference model, shown from its dorsal view (top left) with corresponding approximate section planes shown. The source embryo to be warped (top right) is an OPT gene expression pattern of Wnt6 expression at the equivalent Theiler stage. ANTs can use various algorithms to perform automated nonrigid image registration. In the examples shown, CC and MI methods were tested subsequent to a manual 3D warping step using WlzWarp. The results are presented as a colour overlay of warped source (see key) onto a grey-scale section plane of the target. ANTs improves the overall registration of the source (compare CC6SyN0 vs. WlzWarp and MISyN0 vs. WlzWarp)