Generic pig colon scaffold

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

Rendering of the generic pig colon scaffold.

The colon scaffold is designed topologically as a tube defined by a central line which follows the path of a colon traced from an image, which could be obtained from photography, CT or MRI. The scaffold captures the haustral sacs appearance due to presence of two tenia coli. The colon scaffold's haustra are currently very regular, and are representative rather than matching any individual. The ability to control dimensions such as colon diameter, wall thickness, and tenia coli properties, as well as variations of these properties throughout the entire length of the colon allows the scaffold to be configurable for different center paths and sizes to support different species and individuals.

The pig colon scaffold is generated from images and measurements provided by Million Mulugeta, Muriel Larauche and Yvette Tache (UCLA).

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

The colon scaffold defines the geometric, flat and material coordinates. The geometric coordinates field gives an approximate, idealized representation of the colon shape for the species, which is intended to be fitted to actual data for a specimen. The flat coordinates represents the geometric field when the colon scaffold is cut along its length and laid flat. This field is intended for fitting data obtained from a flat colon preparation. The material coordinates field (colon coordinates) is defined by a cylindrical tube and provides a highly idealized coordinate system to give permanent locations for embedding structures in the colon.

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

Derived from workspace Generic pig colon scaffold at changeset 11939c1ee6ce.
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