Generic rat lung scaffold

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 the mapping tool provenance data file describing the software environment in place when this dataset was created. The primary folder also contains the settings files which in conjunction with the software information in the provenance file, will reproduce the output files stored in the derivative folder. The derivative folder contains JSON files that are used to generate a webGL visualization of the scaffold on the SPARC portal, as well as the VTK and STL formats of the scaffold.

Code Availability: Scaffold Mapping Tools