Generic rat lung scaffold

Arti Sukasem
Peter Hunter
Richard Christie

Annotated lung scaffold for rat available for registration of segmented neural anatomical-functional mapping of pulmonary neural circuits.

Updated on June 2, 2021 (Version 1)

Corresponding Contributor:

Arti Sukasem
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Dataset Overview

Study Purpose: The goal of this work is to create an annotated generic rat lung scaffold for the registration of segmented data obtained by experimental groups.

Data Collected: An anatomically-based 3D scaffold of the lungs is created to visualise various data (such as neural network, blood vessel and ventilation) on a 3D structure of the lungs. The lung scaffold was independently designed for the human, mouse and rat based on their anatomical structures of the lungs in each species. For instance, a rodent has one lobe in the left lung and an accessory lobe in the right lung, while a human has two lobes (upper and lower lobes) in the left lung and no accessory lobe. Thereby, the lung scaffolds are able to represent and annotate the anatomical structure of the lungs in each species accurately. The lung scaffold is parameterised with the data from the segmentation of CT images (NeuroRat V4.0; DOI: 10.13099/VIP91106-04-0)

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 subject/sample specific (NeuroRat V4.0; DOI: 10.13099/VIP91106-04-0).

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: (ABI-Software/scaffoldmaker Anatomical scaffold generator using OpenCMISS), (scaffold source files)


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Publishing history

June 2, 2021
Originally Published
June 2, 2021 (Version 1)
Last Updated

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