Study Purpose: The goal of this work is to create an annotated generic rat stomach scaffold for the registration of segmented data obtained by experimental groups.
Data Collected: An anatomically-based 3D scaffold of the rat stomach is created to map nerve ending pathways. The stomach scaffold is generated with a configurable central path defined from the fundus apex to the duodenum. A user can annotate the fundus, body, antrum, pylorus, and duodenum along the central path and use that to define the respective regions of the stomach. The cross axes of the central path provide control of the major and minor radii of the stomach in different sections. The rat stomach scaffold is parameterized with average data from segmentation of Micro-CT image data of 11 animals performed at the Powley laboratory using Neurolucida (MBF Bioscience).
Primary Conclusion: None stated
Experimental design: Not applicable.
Completeness: The study is ongoing and potentially will link to other datasets where the data is used for mapping onto the scaffold.
Subjects & Samples: The generic scaffold is not subject/sample specific but represents an average stomach of subjects used in other studies.
Primary vs. derivative data: In the primary folder, nodal information and element connectivity of the scaffold are formatted as an exf file. Using the commands in the cmgui file, the scaffold can be visualized using open source software CMGUI. The primary folder also contains a json file that contains parameter settings to reproduce the scaffold in ScaffoldMaker. The derivative folder contains json files that are used to generate a visualization of the scaffold on the web portal, as well as a vtk file for mesh visualization.
Code availability: https://github.com/ABI-Software/scaffoldmaker (ABI-Software/scaffoldmaker Anatomical scaffold generator using OpenCMISS), https://models.physiomeproject.org/e/664 (scaffold source files)
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