Generic human brainstem scaffold

Arti Sukasem
,
Richard Christie, Ph.D.
,
Valerie Chopovda
,
Peter Hunter

Annotated human brainstem scaffold available for registration of segmented neural anatomical-functional mapping of neural circuits.

Updated on September 5, 2024 (Version 4)

Corresponding Contributor:

Valerie Chopovda
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Dataset Overview

Study Purpose: The goal of this work is to create an annotated generic human brainstem scaffold for the registration of segmented data obtained by experimental groups.

Data Collection: The generic scaffold is initially created based on the general description of the human brainstem from literature (BodyParts3D V4.3i; DOI: 10.1093/nar/gkn613).

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 not subject/sample specific but represents a generic human brainstem.

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

Files

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About this dataset

Publishing history

June 29, 2021
Originally Published
September 5, 2024 (Version 4)
Last Updated

Cite this dataset

Sukasem, A., Christie, R., Chopovda, V., & Hunter, P. (2024). Generic human brainstem scaffold (Version 4) [Dataset]. SPARC Portal. https://doi.org/10.26275/OFGG-9X6J

References

Is Source of

Mitsuhashi, N., Fujieda, K., Tamura, T., Kawamoto, S., Takagi, T., & Okubo, K. (2009). BodyParts3D: 3D structure database for anatomical concepts. Nucleic Acids Research, 37(Database), D782–D785. https://doi.org/10.1093/nar/gkn613

Is Supplemented by

Lin, M., & Sorby, H. (2024). Publishing Generic Organ Scaffold as a SPARC Dataset v2. https://doi.org/10.17504/protocols.io.6qpvr8q72lmk/v3