Generic mouse stomach scaffold

In this workspace we have the mapping tool provenance data file needed to produce the generic mouse stomach scaffold for the SPARC project. The mapping tool will be accessible from the release download page on the SPARC Portal.

An anatomically-based 3D scaffold of the mouse stomach is created to map nerve ending pathways. The stomach scaffold is generated with a configurable central path defined from the fundus apex to the duodenum. A user can annotate the fundus, body, antrum, pylorus, and duodenum along the central path and use that to define the respective regions of the stomach. The cross axes of the central path provide control of the major and minor radii of the stomach in different sections.

Four wall layers (mucosa, submucosa, circular muscle, and longitudinal muscle) are added to the mouse stomach scaffold. The outer surface of the scaffold is annotated as the serosa.

The scaffold has a geometric coordinates field which gives an approximate, idealized representation of the stomach shape for the species, which is intended to be fitted to actual data for a specimen. It also has a coordinate field called split coordinates which follows the geometric field but provides disconnected and duplicated derivatives for nodes on the margin between the dorsal and ventral stomach (the boundary where stomach specimens are usually dissected into halves for imaging purposes). This field is intended for fitting data obtained from the dorsal or ventral stomach. Apart from that, the scaffold also has a material coordinates field which defines a highly idealized coordinate system to give permanent locations for embedding structures in the stomach. It is defined by a capsule-shaped structure with an inlet cylindrical tube representing the esophagus and another outlet tube representing the duodenum.

Please see the SPARC Portal for more details about the SPARC project.