Generic rat heart scaffold

Study Purpose: The goal of this work is to create annotated generic rat heart scaffolds for registration of segmented data obtained by experimental groups.

Data Collected: The generic scaffold is initially created based on the general description and average dimensions of rat hearts as measured by experimental groups. The scaffold was later calibrated and improved based on segmented image data from the experimental group who provided their data for registration of neural data.

Primary Conclusion: None stated

Curator’s Notes

Experimental design: Not applicable.

Completeness: The dataset is complete, but will be used to link to other datasets.

Subjects & Samples: The generic scaffold is not subject/sample specific but represents a generic rat heart.

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, RRID: SCR_019271. The JSON file contains the parameter settings to reproduce the scaffold in the ScaffoldMaker software, RRID:SCR_019003. The derivative folder contains the legacy VTK format file which can be used to visualize the scaffold in many different visualization software e.g. ParaView. The Scaffold folder in the derivative folder contains the json files used to generate a visualization of the scaffold on the web portal.

Code availability: https://github.com/ABI-Software/scaffoldmaker.