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Generic rat stomach scaffold

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 September 21, 2022 (Version 5)

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 Collection: 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


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 stomach of subjects used in other studies.

Primary vs derivative data: The primary folder contains the mapping tool provenance data file needed to produce the generic rat stomach scaffold. The mapping tool will be accessible from the release download page on the SPARC Portal. The derivative folder contains json files which are used to generate a visualization of the scaffold on the web portal.

Code Availability: https://github.com/ABI-Software/scaffoldmaker (ABI-Software/scaffoldmaker Anatomical scaffold generator using OpenCMISS), https://models.physiomeproject.org/e/8f3 (scaffold source files)

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About this dataset

Publishing history

February 4, 2021
Originally Published
September 21, 2022 (Version 5)
Last Updated

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