Study Purpose: The goal of this work is to create an annotated generic mouse brainstem scaffold for the registration of segmented data obtained by experimental groups.
Data Collected: The generic scaffold is initially created based on the general description of mouse brainstem from magnetic resonance images (Mouse Imaging Centre in Toronto, Canada).
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 generic scaffold is not subject/sample specific but represents a generic mouse brainstem.
Primary vs. derivative data: In the primary folder, nodal information and elements 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 JSON file contains the parameter settings to reproduce the scaffold in the ScaffoldMaker software. 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.
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