- Author:
- keeran97 <85910337+keeran97@users.noreply.github.com>
- Date:
- 2021-08-24 12:56:01+12:00
- Desc:
- add Y4Q4 version of mouse bladder scaffold
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/6e7/rawfile/77bc51a2ffd26d3768f1c17b690b1364eaa427ee/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 bladder scaffold for the `SPARC <https://commonfund.nih.gov/sparc>`_ project.
.. image:: thumbnail.png
:width: 50%
:alt: Rendering of the generic mouse bladder scaffold.
As with the other organ systems, the lower urinary tract (LUT) contains different sub-scaffolds consisting of the bladder, its ureters, and the urethra. The bladder scaffold consists of different tissue layers to represent the smooth muscles as well as the epithelial region. The smooth muscle layer transitions gradually into skeletal muscles as we move down the neck of the bladder into the urethra. The neck of the bladder is represented in the scaffold as a narrowing of the body at the region where ureters penetrate the surface into the lumen of the bladder. The parameters include the diameters for different axes, wall thickness, neck angle (for bladder only), etc., which are all defined for the bladder and urethra separately. Importantly, the entire scaffold is generated based on a central path defined by the user, which facilitates the initialization of the shape as well as annotation. The scaffold can now be used to register and map various data including neurons, or to define time-varying fields such as pressure or volume measured experimentally.
Please see the `SPARC Portal <https://sparc.science>`_ for more details about the SPARC project.
