- Author:
- mlin865 <mlin865@aucklanduni.ac.nz>
- Date:
- 2024-08-19 17:12:34+12:00
- Desc:
- Add files for mouse small intestine
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/ba2/rawfile/43815ea53fba43f050632775972604ea37bc5e3b/README.rst
In this workspace we have the mapping tool provenance data file needed to produce the generic mouse small intestine scaffold for the `SPARC <https://commonfund.nih.gov/sparc>`_ project. The mapping tool will be accessible from the release download page on the `SPARC Portal <https://sparc.science>`_.
.. image:: smallIntestineMouse_Layout1_thumbnail.jpeg
:width: 50%
:alt: Rendering of the generic mouse small intestine scaffold.
The small intestine scaffold is generated using geometry from ellipsoid and cubic functions based on a one dimensional network layout which describes the path of the small intestine. The network layout used to generate the current mouse small intestine scaffold is obtained from tracing central path from dissection images and average dimensions obtained from the literature. The mucosa, submucosa, circular muscle, longitudinal muscle and serosa layers of the small intestine are fully represented on the scaffold.
The small intestine scaffold defines the geometric, flat and material coordinates. The geometric coordinates field gives an approximate, idealized representation of the small intestine 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 small intestine scaffold is cut along its length and laid flat. This field is intended for fitting data obtained from a flat small intestine preparation.
The material coordinates field small intestine coordinates defines a highly idealized coordinate system to give permanent locations for embedding structures in the small intestine. It is a cylindrical tube and can be viewed by visualising this field in the Display tab of Scaffold Creator.
Please see the `SPARC Portal <https://sparc.science>`_ for more details about the SPARC project.
