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Generic rat lung scaffold

Arti Sukasem
,
Zohreh Ekhlasi
,
Peter Hunter
,
Richard Christie

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

Updated on September 21, 2022 (Version 3)

Corresponding Contributor:

Zohreh Ekhlasi
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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 Collection: 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: The primary folder contains a provenance.json file containing all the software versions to generate this dataset. The derivative folder contains the JSON files used to generate a visualization of the scaffold on the web portal, and its annotations.

Code Availability: https://github.com/ABI-Software/scaffoldmaker (ABI-Software/scaffoldmaker Anatomical scaffold generator using OpenCMISS), https://models.physiomeproject.org/e/687 (scaffold source files)

PMR Exposure link: https://models.physiomeproject.org/e/8ee

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About this dataset

Publishing history

June 2, 2021
Originally Published
September 21, 2022 (Version 3)
Last Updated

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