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Rat whole-body with embedded organs using automatic workflow for inserting the organs

Elias Soltani
,
David P Nickerson, Ph.D.
,
Richard Christie
,
Peter Hunter

This dataset includes lung, bladder, heart, stomach and brainstem inserted into the rat whole-body using an automated workflow.

Updated on July 13, 2022 (Version 2)

Corresponding Contributor:

Elias Soltani
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Dataset Overview

Study Purpose: The goal of this work is to automate the rat insertion of 3D organ scaffolds into the whole-body scaffolds and produce rat whole-body with embedded organs.

Data Collection: Organs datasets and whole-body dataset were obtained from datasets in Pennsieve. A MAP Client workflow was created with a new step (organinserter) in python language to automate the insertion of 3D organs into the whole-body scaffolds. The whole-body scaffold along with the organs are passed to the workflow and then it finds the common fiducial markers in the whole-body and each organ. These fiducials then are used to register the organ into the body. The embedded organs include lungs, heart, stomach, bladder, and colon.

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 automated workflow is not subject/sample-specific and the resultant output is produced for rat models.

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 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/7da (scaffold source files and workflow to reproduce the files)

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About this dataset

Publishing history

December 8, 2021
Originally Published
July 13, 2022 (Version 2)
Last Updated

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