- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2020-11-26 23:45:44+13:00
- Desc:
- update README to remove title as PMR will render the workspace title
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/612/rawfile/3941cca419fa10dff6edd3df4d661a05e9f21edc/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 mouse colon scaffold for the `SPARC <https://commonfund.nih.gov/sparc>`_ project.
.. image:: thumbnail.png
:width: 50%
:alt: Rendering of the generic mouse 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 is capable of representing the characteristics observed in the cross-sectional profiles of colons from different species. For instance, mouse colon presents a tubular structure due to the absence of tenia coli whereas both human and pigs have more of a haustral sacs appearance due to presence of 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 central path used to generate the current mouse colon scaffold is obtained from tracing a central path from a dissection image obtained from literature. Lengths and diameter data are provided by Lixin Wang (UCLA) and Yvette Tache (UCLA) and Marthe Howard (University of Toledo).
Please see the `SPARC Portal <https://sparc.science>`_ for more details about the SPARC project.
