Figure 1. EMAP section browser: one of the browser interfaces for the mouse atlas framework. The left-hand window depicts a diagram of the selected embryo stage (in this case Theiler 13), to provide feedback for the selected section view (center panel). The section view provides live feedback of the underlying anatomy, which can be selected and highlighted (blue region). When selected, the corresponding component in the anatomical nomenclature hierarchy is shown in red (right-hand panel).

Figure 2. Mapping gene expression from an experimental specimen to a reference model in the EMAP by warping. The specimen containing raw data is matched to a model of the corresponding stage in the atlas framework. A section plane in the model (left panel) is selected that best corresponds to the specimen (middle panel). Corresponding positions (shown as green dots, see magnified region) are identified in the two images and used to derive an image transformation that enables all positions in the specimen to be approximately mapped to the atlas model (right panel: green, model; lilac, transformed specimen image). The result can be edited to ensure that the mapped data corresponds as closely as required to the original raw data.

Figure 3. Screen-shot of the MAPaint program (left-hand group) used for viewing arbitrary sections through the framework models. The planes of section are shown in shaded yellow within the 3D navigator window, which also shows the outlines of selected anatomical structures. Each of the section windows has independent controls for adjusting the section location and orientation (center window). The right-hand window shows patterns returned from a database query: two mapped patterns compared. The comparison is between Msx2 (red) and Msx1 (homeobox Msh-like 1; green).