Generic rat stomach scaffold

Kumar Mithraratne
,
Mabelle Lin
,
Richard Christie
,
Peter Hunter

Annotated rat stomach scaffold available for registration of segmented neural anatomical-functional mapping of enteric neural circuits.

Updated on February 4, 2021 (Version 1)

Corresponding Contributor:

Mabelle Lin
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Dataset Overview

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: A statistically representative and anatomically-based 3D scaffold of the rat stomach is created to map nerve ending pathways. Micro-CT image data of 11 animals are used to construct this 3D scaffold. Imaging and data segmentation is performed at the Powley laboratory using Neurolucida (MBF Bioscience). An approximate surface is generated for each case using gross morphometric measurements of the organ. These surfaces are then fitted to the segmented data. The surfaces from the fitted scaffolds are combined to form an average stomach surface of representative thickness to generate the 3D scaffold, which includes anatomically-distinct layers of serosa, longitudinal muscle, myenteric nerve plexus, circular muscle, submucosa and mucosa.

Primary Conclusion: None stated


Curator’s Notes

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 colon 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 which contains parameter settings to reproduce the scaffold in ScaffoldMaker. The derivative folder contains json files which 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/627 (scaffold source files)

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About this dataset

Publishing history

February 4, 2021
Originally Published
February 4, 2021 (Version 1)
Last Updated

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