- Author:
- Mabelle Lin <mlin865@aucklanduni.ac.nz>
- Date:
- 2020-11-27 15:05:02+13:00
- Desc:
- Update README
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/613/rawfile/9e2fb6a5edbaf95a5f276bdc9d7be6cabbf600a1/README.rst
In this workspace we have the `Scaffold Maker <https://github.com/ABI-Software/scaffoldmaker>`_ workflow and configuration files needed to produce the generic pig colon scaffold for the `SPARC <https://commonfund.nih.gov/sparc>`_ project.
.. image:: thumbnail.png
:width: 50%
:alt: 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).
Please see the `SPARC Portal <https://sparc.science>`_ for more details about the SPARC project.
