The generated body scaffold was fitted to data and the organ fiducial markers were embedded in the rat whole-body. The landmarks were obtained from image data and also were defined in the body scaffold.
Study Purpose: The goal of this work is to create an annotated rat whole-body scaffold with embedded organs.
Data Collected: The generic scaffold is created based on the generic body coordinates that fit data for the rat whole-body. The generated organ scaffolds were embedded by embedding the fiducial markers.
Primary Conclusion: None stated
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 body scaffold is not subject/sample-specific, but the morphed scaffold was fitted to the given data.
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.
Code availability: https://github.com/ABI-Software/scaffoldmaker (ABI-Software/scaffoldmaker Anatomical scaffold generator using OpenCMISS), https://models.physiomeproject.org/workspace/655 (scaffold source files)
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